The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome
- aMichael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
- bHumans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada;
- cDepartment of Anthropology, Northwestern University, Evanston, IL 60208;
- dManitoba Interdisciplinary Lactation Centre, Children’s Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada;
- eCenter for Advanced Biotechnology and Medicine at Rutgers Biomedical and Health Sciences, Rutgers University, Piscataway, NJ 08854-8021;
- fZoologisches Institut, University of Kiel, 24118 Kiel, Germany;
- gDepartment of Pathology, University of California San Diego, La Jolla, CA 92093;
- hDepartment of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901;
- iMetagenopolis Unit, French National Institute for Agricultural Research, 78350 Jouy-en-Josas, France;
- jDepartment of Immunology, Weizmann Institute of Science, Rehovot 761000, Israel;
- kCancer-Microbiome Division, Deutsches Krebsforschungszentrum, 69120 Heidelberg, Germany;
- lTechnion Integrated Cancer Center, Department of Cell Biology and Cancer Science, Technion−Israel Institute of Technology, Haifa 3525433, Israel;
- mDepartment of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada;
- nInstitute of Molecular Biology, University of Oregon, Eugene, OR 97403;
- oCentre National de la Recherche Scientifique, 75016 Paris, France;
- pLaboratoire d’Anthropologie Sociale, Collège de France, 75005 Paris, France;
- qDepartment of Systems Biology, Irving Cancer Research Center, Columbia University, New York, NY 10032;
- rDepartment of Obstetrics and Gynecology, Irving Cancer Research Center, Columbia University, New York, NY 10032;
- sPacific Biosciences Research Center, University of Hawai’i at Manoa, Honolulu, HI 96822;
- tDepartment of Anthropology, University of Delaware, Newark, DE 19711;
- uDepartment of Anthropology, University of Arizona, Tucson, AZ 85721;
- vLee Kong Chian School of Medicine, Nanyang Technological University, 637715 Singapore;
- wDepartment of Anthropology, McMaster University, Hamilton, ON L8S 4M4, Canada;
- xTransformations of the Human Program, Berggruen Institute, Los Angeles, CA 90013;
- ySchool of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada;
- zDepartment of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada;
- aaAnthropology & Ecology of Disease Emergence, Institut Pasteur, 75015 Paris, France
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Edited by Lora V. Hooper, University of Texas Southwestern Medical Center, Dallas, TX, and approved December 14, 2020 (received for review August 3, 2020)

Abstract
The COVID-19 pandemic has the potential to affect the human microbiome in infected and uninfected individuals, having a substantial impact on human health over the long term. This pandemic intersects with a decades-long decline in microbial diversity and ancestral microbes due to hygiene, antibiotics, and urban living (the hygiene hypothesis). High-risk groups succumbing to COVID-19 include those with preexisting conditions, such as diabetes and obesity, which are also associated with microbiome abnormalities. Current pandemic control measures and practices will have broad, uneven, and potentially long-term effects for the human microbiome across the planet, given the implementation of physical separation, extensive hygiene, travel barriers, and other measures that influence overall microbial loss and inability for reinoculation. Although much remains uncertain or unknown about the virus and its consequences, implementing pandemic control practices could significantly affect the microbiome. In this Perspective, we explore many facets of COVID-19−induced societal changes and their possible effects on the microbiome, and discuss current and future challenges regarding the interplay between this pandemic and the microbiome. Recent recognition of the microbiome’s influence on human health makes it critical to consider both how the microbiome, shaped by biosocial processes, affects susceptibility to the coronavirus and, conversely, how COVID-19 disease and prevention measures may affect the microbiome. This knowledge may prove key in prevention and treatment, and long-term biological and social outcomes of this pandemic.
Footnotes
- ↵1To whom correspondence may be addressed. Email: bfinlay{at}msl.ubc.ca or tamara.giles-vernick{at}pasteur.fr.
Author contributions: B.B.F., K.R.A., M.A., M.J.B., T.C.G.B., H.C., M.G.D.-B., S.D.E., E.E., N.G.-Z., P.G., K.G., F.K., T.K., M.J.M.-N., M.K.M., M.N., S.P., H.P., T.R., C.T., L.Z., and T.G.-V. wrote the paper.
The authors declare no competing interest.
This article is a PNAS Direct Submission.
Data Availability.
All study data are included in the article.
Change History
March 8, 2021: Reference 77 has been updated; please see accompanying Correction for details.
Published under the PNAS license.
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- Hygienic Measures during a Pandemic and Their Effects on Microbiome Acquisition, Loss, and Reinoculation
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