Protecting the microbiome in times of strict hygiene measures

International research team including Kiel University’s Professor Thomas Bosch fears that microbiome-associated environmental diseases could increase further in the wake of the Corona pandemic

The Corona pandemic, as a global health crisis, is causing infection and casualty rates not seen in more than 100 years. On an unprecedented scale, it has disrupted global human coexistence and economies. Its full dimensions, duration and outcome can hardly be foreseen today. In recent months, the international scientific community has focused sharply on researching the novel pathogen and has developed promising approaches to combat the virus at an unprecedented pace. A group of highly respected scientists from the Canadian Institute for Advanced Research’s (CIFAR) “Humans & the Microbiome” research program, with the participation of Professor Thomas Bosch of Kiel University, is now broadening the scientific perspective to include a prognosis of longer-term indirect consequences beyond SARS-CoV-2 infections. In a perspective paper, the international researchers predict even more far-reaching health consequences: they fear a sharp increase in so-called environmental diseases such as diabetes, obesity or chronic inflammation. These and many other diseases are based on a loss of microbial diversity in the human body.

For decades, the depletion of the microbiome, the totality of microorganisms in and on a body, has been progressing in the wake of a modern, globalized lifestyle. This loss of microorganisms might be critically accelerated by the increased hygiene and isolation measures needed to contain infection, the researchers write. A disrupted microbiome may at the same time be linked to severe or even fatal COVID-19 courses, according to new scientific findings. Nevertheless, the CIFAR research group explicitly endorses the hygiene and isolation measures introduced to combat the pandemic as absolutely essential at this time. In addition, however, it advocates a balance of infection control and long-term health risks: The researchers recommend that pandemic control should also take into account a healthy microbiome and allow contact with health-promoting microorganisms as much as possible. This aspect, they said, is important for economic and social recovery after the pandemic and for public health in the long term. The international researchers recently published their work in the scientific journal Proceedings of the National Academy of Sciences of the United States of America (PNAS).

How the microbiome and coronavirus influence each other
The novel SARS-CoV-2 and the COVID-19 disease it causes have not been studied in sufficient detail yet to demonstrate causal links between the microbiome and the course and severity of the disease. However, recent studies suggest that microbiome composition may influence how susceptible the organism is to SARS-CoV-2 infection. “It is striking that individuals suffering from a severe COVID-19 course often have pre-existing conditions related to gut microbiome dysfunction,” emphasized CIFAR Fellow Bosch, head of the Collaborative Research Center (CRC) 1182 “Origin and Function of Metaorganisms” at Kiel University. “Recent studies in COVID-19 sufferers indicate a severe imbalance of the gut microbiome, characterized by the accumulation of characteristic bacterial species, fungal pathogens and the loss of beneficial microbes,” Bosch adds.

Thus, on the one hand, the risk of becoming severely ill with COVID-19 may be closely related to pre-existing diseases that are correlated with disruption of the composition and diversity of the microbiome. On the other hand, the measures introduced to combat the pandemic inversely affect the human microbiome. In particular, the drastic reduction of social interactions in the course of isolation, physical distancing, and the extensive restriction of mobility, together with intensive hygiene, which currently have no alternative, appear to have a significant impact on its composition – namely, by interrupting the transmission of microorganisms from person to person. Under normal circumstances, this transmission takes place in a variety of ways, such as through touch or the sharing of objects or even premises.

Preventing infections and protecting the microbiome
How the individual hygiene and isolation measures affect the microbiome still needs to be clarified in detail by research. However, it is already clear that there is a trade-off between infection control and preventing environmental diseases. “To put it bluntly, the top priority at present must be to slow down the spread of SARS-CoV-2 and prevent it as far as possible – and to do this, hygiene measures and contact restrictions are unavoidable,” Bosch emphasizes. “However, we have learned in recent years – also through the work in the Kiel Collaborative Research Center 1182 – how important a diverse gut microbiome is for maintaining health and how much our modern lifestyle threatens this diversity. The protection against infection now required in the pandemic therefore currently overlaps dramatically with the loss of microbial diversity that has been progressing for decades. This trend must also be counteracted in pandemic times in order to prevent a drastic increase in environmental diseases in the near future,” Bosch continued.

To meet this challenge, it is important to continue to allow contact with health-promoting microorganisms as far as possible, according to the international research team. To do so, it recommends measures that are useful for maintaining a healthy microbiome even under normal circumstances. These include regularly spending time outdoors in environments close to nature, promoting a healthy diet that is friendly to the microbiome, and avoiding unnecessary use of antibiotics. These and other approaches may allow for the preservation and transmission of health-promoting microorganisms even under conditions of infection control.

Scientists also see the current situation as a significant opportunity to study the interactions of a highly contagious pathogen with the microbiome and its effect as a key regulator of health. In the future, the knowledge that is currently emerging will help to mitigate the course of the Corona crisis and bring it to an end more quickly overall. Potentially more serious future pandemics could also be better controlled or even prevented with the knowledge derived and measures based on it, the CIFAR researchers hope.

Original publication:
B. Brett Finlay, Katherine R. Amato, Meghan Azad, Martin J. Blaser, Thomas C.G. Bosch, Huitung Chu, Maria Gloria Dominguez-Bello, Stanislav Dusko Ehrlich , Eran Elinav Naama Geva-Zatorsky, Philippe Gros, Karen Guillemin, Frédéric Keck, Tal Korem, Margaret J. McFall-Ngai, Melissa K. Melby, Mark Nichter, Sven Pettersson, Hendrik Poinar, Tobias Rees, Carolina Tropini, Liping Zhao, Tamara Giles-Vernick (2021): The hygiene hypothesis during a pandemic: consequences for the human microbiome. PNAS First Published on 20. January 2021
DOI: 10.1073/pnas.2010217118

About the Canadian Institute for Advanced Research (CIFAR):
Since its founding in 1982, CIFAR’s mission has been to create interdisciplinary research teams, involving leading scientists from around the world, to address scientific topics of particular relevance to society. At present, more than 400 researchers from around 130 institutions worldwide are working on 13 interdisciplinary research projects with, for example, life science, social or technical issues. The CIFAR research teams have a total annual budget of around 28 million euros at their disposal. In its research program “Humans & the Microbiome”, CIFAR brings anthropologists, biologists and other scholars together to provide biocultural context to host-microbiome interactions. They’re asking new questions about what aspects of individual and societal behaviour are critical to understanding the role of the microbiome in human health and development.

About CRC 1182:
The Collaborative Research Centre “Origin and Function of Metaorganisms” is an interdisciplinary network involving about 80 researchers that investigates the interactions of specific microbial communities with multicellular host organisms. It is supported by the German Research Foundation (DFG) and deals with the question of how plants and animals, including humans, form functional units (metaorganisms) together with highly specific communities of microbes. The aim of SFB 1182 is to understand why and how microbial communities form these long-term connections with their host organisms and what functional consequences these interactions have. The SFB 1182 brings together scientists from five faculties of Kiel University, the GEOMAR Helmholtz Centre for Ocean Research Kiel, the Max Planck Institute for Evolutionary Biology Plön, the Heinrich-Heine-Universität Düsseldorf, the Leibniz Institute for Science and Mathematics Education and the Muthesius University of Fine Arts and Design.

Prof. Thomas Bosch
Spokesperson CRC 1182
“Origin and Function of Metaorganisms“, Kiel University
Phone: +49 (0) 431-880-4170

More information:
Research program „Humans & the Microbiome“,
Canadian Institute for Advanced Research (CIFAR):

AG Bosch, Kiel University:

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