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April 24, 2020

Calling citizen scientists: contribute to research on COVID-19 and the microbiome

Daniel McDonald, PhD, and Rob Knight, PhD, explain how the Microsetta Initiative will use its infrastructure to better understand SARS-CoV-2, the virus causing COVID-19.
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By Daniel McDonald, PhD, UC San Diego School of Medicine, and Rob Knight, PhD, UC San Diego School of Medicine and Member, AGA Center for Gut Microbiome Research and Education Scientific Advisory Board

The Microsetta Initiative, the global microbiome citizen science extension of UC San Diego School of Medicine’s American Gut Project, has pivoted toward COVID-19 research. It is applying its infrastructure and resources to help better understand the distribution of SARS-CoV-2, and whether the microbiome predicts SARS-CoV-2 infection or COVID-19 susceptibility. To invest in the research, the initiative has taken a few essential steps:

Daniel McDonald
Rob Knight, PhD
  1. 1. We are working closely with the broader San Diego Coronavirus Response efforts which include sharing of instrumentation, supplies, data and the development of research-grade screening of SARS-CoV-2 using reagents that do not compete with the CDC testing protocol.
  2. 2. We have performed experiments to suggest that the 95% ethanol-based collection devices we now use are suitable for de-activating SARS-CoV-2, while preserving RNA to enable RT-qPCR detection and viral genome sequencing.
  3. 3. Thanks to generous support from Becton Dickinson, we have included skin prick devices in our collection kits to collect blood for antibody testing.
  4. 4. We have obtained Institutional Review Board approval for the use of the skin prick devices, and are in the process of finalizing and approving a coronavirus specific questionnaire.
  5. 5. Our kits pass all the necessary domestic and international shipping regulations.

We are now in the process of partnering with principal investigators who have established cohorts, who would like to utilize these collection kits (either under our IRB or their own), and would be further be interested in adding a microbiome component (fecal/oral/skin) to their existing studies. Our April production run will be in excess of 20,000 kits, and we are eager to collaborate and help get these into the field. 

If you are an investigator with an established COVID-19 cohort that is interested in partnering with The Microsetta Initiative, please contact

If you are interested in contributing to the Microsetta Initiative as a citizen scientist, please visit for more information.

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