by Dr. Lisa Bäumer

Social distancing and hygiene in times of pandemic: a double-edged sword for human health

Physical distance
What impact does the current physical distance have on the human microbiome? (Picture: © MT-R -

In this article we would like to present a publication by Domingues et al. which appeared in the journal mSphere in October 2020 (1). It described the effects of social distancing on microbial diversity in the human body and its influence on human health.

Definition of terms:

Genome: Sum of all genes in an organism.

Pangenome: Sum of all genomes within a species.

Metagenome: The entirety of the genomic information of the microorganisms of a certain community or a biotope. These can be genomes of animals, plants, humans, and microorganisms in a biotope (2). The so-called metagenomics comprise a research area in life sciences in which genetic material (DNA or RNA) is isolated directly from environmental samples and subsequently sequenced. This is followed by the bioinformatic analysis, whereby the sequences can be assigned to the corresponding genes and organisms.

Social distancing and the impact on the microbiome

We all know it - and the greatest of us have been sticking to it for one year now: some of the most important decisions in controlling the COVID-19 pandemic include avoiding interpersonal contact, disinfecting hands after touching skills and following forces rules of breathing etiquette (mask, distance, coughing in the crook of your arm, etc.). The effects are aimed at directing the spread of virus particles and aerosols. Quarantining people with the merit of the COVID-19 infection also serves as a protection to prevent virus transmission.

At the same time we notice that we are increasingly lacking social contacts. Video conferencing with friends cannot replace a pub night, not entirely. In addition to food intake and psycho-hygiene, an evening at our favorite Italian restaurant also has health effects on us: Social connections between people also lead, among other things, to the spread of the microorganisms that have developed together with humans and that are very important for maintaining human health (3). Or to put it another way: if there is no personal relationship, our microbiome becomes impoverished.

The human microbiome has symbiotic relationships with the human body. This means checking the genome of the body's full microbiome information to find many complementary functions that the human genome lacks. For example, they help break down nutrients and stimulate the immune system (4). Changes in the balance of the gut microbiome (dysbiosis) are linked to a greater susceptibility to disease and opportunistic infections, as the decrease in protective microbial colonization by symbiotic bacteria can lead to dysregulation of the immune system and autoimmune diseases (5). Research showed that such changes in the microbiome correlate with the COVID-19 prognosis (6, 7). However, so far no data were available on the impact of human contact behavior on the gut microbiome during the COVID-19 pandemic.

So, what impact does the current physical distance have on the human microbiome?

Microorganisms belonging to the oral, intestinal and nasopharyngeal microbiomes can be transmitted from person to person in a physical, social setting. People who live in the same household are more likely to have similar profiles of the bacterial species in their microbiomes, regardless of their genetic relationships to one another (8) (Fig. 1A). Coexistence was therefore seen as one of the most important factors that facilitate the asymptomatic transmission typical of SARS-CoV-2 (9). According to the National Health Service (Portugal), this was the case for 45% of 793 new cases in Portugal between 13-21 March 2020 (10). Other forms of social contact, such as in companies (19%) and nursing homes (11%), were also relevant.

It is known that bacterial colonization begins shortly after birth in babies (11). Vaginal childbirth and breastfeeding provide early exposure to maternal microorganisms and help establish gut and respiratory microbiomes, although they are not the main source of microbial diversity in adulthood (12-14).

Also of interest: What role does the microbiome actually play in human development?

Skin-to-skin or secretion contacts that occur when kissing and hugging are thus something like mini-vaccinations with human microorganisms in early life and are therefore particularly important for children (15). Contact with contaminated surfaces can also play another important role as an indirect source of colonization by microorganisms from one human microbiome to another. Babies and toddlers use their tongues to explore toys or other objects, which can ingest a variety of new microorganisms, some of which may enrich the microbiome (16). Systematic disinfection of surfaces and hands can disrupt this indirect source of human microbial inoculation.

Read more about disinfecting: What's the matter with this ongoing disinfecting of everything?

Figure 1: Social distancing
Figure 1: Social distancing

Figure 1 clearly shows how the current COVID-19 hygiene rules also reduce the likelihood of the spread of other microorganisms of the “good” human microbiome. This can reduce the diversity of functional genes in our gut microbiome (17), which can make people more susceptible to disease in the medium term.

Dysbiosis, an imbalance of different bacteria

As early as 1969, Johanson and colleagues observed differences in the oropharyngeal bacterial microbiota in people with severe pneumonia. However, these changes have not been associated with antibiotic administration, inhalation therapy, or length of hospital stay (18). The healthy microbiome is closely related to the functioning of the immune system. Changes in the health of the human host can have drastic effects on the health of the microbiome and vice versa (19, 20). Dysbiosis in the intestine is associated with many immune diseases such as Crohn's disease, ulcerative colitis, type 1 diabetes, celiac disease, allergy, and multiple sclerosis, as well as metabolic diseases such as obesity or type 2 diabetes, colon cancer or autism (21).

Read more: Impacts of a damage to the microbiome

This is particularly important in older people with a less diverse gut microbiome (6, 22). It is therefore discussed whether there is a possible interaction between the lungs and the intestinal microbiome that could influence the course of COVID-19 (6).

Read more: What happens when a virus infects your lung - and which circumstances lead to a mild curse?

It is already known that dysbiosis of the gut microbiome can also increase susceptibility to influenza virus infections (6, 23). So, the authors wondered whether the recommended social distancing measures to prevent SARS-CoV-2 transmission could lead to an increase in the number of other serious instabilities. Breaking the path of infection reduces the transmission of microorganisms between people, thereby promoting dysbiosis, which in turn can result in a poor prognosis for the disease (1).

An important aspect: the transmission of antibiotic resistance

Studies by Escudeiro et al. showed that there is a positive correlation between the diversity of antibiotic resistance genes and the diversity of bacterial virulence genes in human metagenomes (24). Based on this data, Domingues et al. (1) were able to use computer simulations to confirm that bacterial transmission from one person to another is the main reason that explains this correlation. In other words, simply because people contaminate each other, we end up with the paradoxical and undesirable situation in which people with a higher diversity of bacterial virulence genes are expected to have a higher diversity of resistance genes in their metagenomes (25). In many cases, however, antibiotic resistance is linked to the current metabolic stress. Put simply, this means that after antibiotic treatment has ended, resistance will decrease because the corresponding gene is no longer needed, and the bacteria lose this gene again (26). In a metagenome study it was also observed that the diversity of antibiotic resistance genes and thus the resistance in human intestinal microbiomes increases with age up to a limited level (27). In this context, the current social restrictions could, in addition to containing COVID-19, have a further positive effect by reducing the spread of antibiotic-resistant germs during antimicrobial therapy. However, this hypothesis needs to be tested experimentally and, if confirmed, could support new recommendations for the use of antibiotics.

How should we behave

The authors of the presented article see two main consequences of the current measures:

  1. Biodiversity loss, if not effectively restored, could be perennial and persistent from one generation to the next, potentially leading to disease and causing a poorer prognosis for COVID-19.
  2. Social isolation and imposed hygiene rules lead to a decrease in the transmission of microorganisms and their genes, which in turn can have a short-term positive effect with regard to the transmission of antibiotic resistance (24, 25).

Social distancing after the outbreak of the SARS-CoV-2 pandemic is therefore a double-edged sword. It could have both negative and positive effects on the genomic dynamics of the human microbiome, and the public health effects are well worth investigating.

Now the personal discretion under the current regulations is rather limited. Nevertheless, we would like to derive a few specific recommendations for action from the study:

  1. Don't overdo it with disinfection! Surface disinfection in private households is absolutely superfluous and rather counterproductive. When you get home, wash your hands with soap rather than disinfect them.
  2. Don't forget to return to normal! The vaccination campaigns have already started, and the situation is expected to normalize over the next few months. Then we must not forget to get back to normality and social contacts without a guilty conscience.


Dr. Lisa Bäumer

The microbiologist with a PhD is fascinated by the wonderful world of microbes and has many years of experience working with pathogenic bacteria. She loves mountains, forests and rocks and enjoys having lots of friends around.

Sources / References:

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  2. Handelsmann J., Rondon M. R., Brady S. F., Clardy J. and Goodman R. M. 1998. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol. 5: R245-R249.
  3. Derovs A., Laivacuma S. and Krumina A.. 2019. Targeting microbiota: what do we know about it at present? Medicina (Kaunas). 55: 459.
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  5. Keeney K. M., Yurist-Doutsch S., Arrieta M.-C. and Finlay B. B. 2014. Effects of antibiotics on human microbiota and subsequent disease. Annu Rev Microbiol. 68: 217–235.
  6. Dhar D. and Mohanty A. 2020. Gut microbiota and Covid-19 - possible link and implications. Virus Res. 285: 198018.
  7. Gou W., Fu Y., Yue L., Chen G.-D., Cai X. et al. 2020. Gut microbiota may underlie the predisposition of healthy individuals to COVID-19. medRxiv (pre-print server).
  8. Brito I. L., Gurry T., Zhao S., Huang K., Young S. K., Shea T. P., Naisilisili W., Jenkins A. P., Jupiter S. D., Gevers D. and Alm E. J. 2019. Transmission of humanassociated microbiota along family and social networks. Nat Microbiol. 4: 964 –971.
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  10. Direção-Geral da Saúde. 2020. 45% das novas infeções contraídas dentro de casa—COVID-19.
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