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Founding director of the Center for Microbiome Innovation and professor of pediatrics and computer science & engineering at UC San Diego, Rob Knight, discusses several aspects of his past and ongoing contributions to the field of microbiome research.

He also discusses his recent focus on the COVID-19 pandemic. On this episode, you’ll learn the following:

  • Why COVID-19 is causing a very time-sensitive need for serology tests to detect antibodies
  • What dietary factors affect the microbiome in certain viral and bacterial diseases (e.g. salmonella, influenza)
  • Why planting eucalyptus trees outside Australia was a terrible idea, and how this relates to pathogenic bacteria and microbial communities in the human gut

Rob Knight helped develop the technology that enabled the field of microbiome research to get where it is today. For example, Knight’s lab has developed software for microbiome analysis, lab protocols for looking at thousands of microbiomes simultaneously, and the American Gut Project, which analyzed hundreds of thousands of microbiome samples from humans to plants to soil and oceanic environments.

He explains that while the human genome is fixed, the microbiome is constantly changing. The idea is that if it can be understood what causes or leads to changes in the microbiome, then it may be possible to control the microbiome in ways that confer health advantages.

When COVID-19 began spreading globally, Knight was working on a project that aimed to determine the relationship between diet and the microbiome, and how it might make people more or less susceptible to disease. He’s now carrying out this research with an eye towards the current pandemic, and hoping to identify whether there are dietary or supplemental interventions that can help people combat the virus, or prevent symptoms of the virus altogether.

Knight is currently trying to develop technology that will allow for a broader, simultaneous view of the entire metabolome and microbiome, and the influence of diet upon them both. “In many ways, COVID-19 is providing a stress test of what we can do right now, which is going to be very useful for pointing the way towards what we need to develop over the next few years,” says Knight.

He continues by explaining the importance and challenge of being able to detect antibodies to COVID-19, as this would indicate whether someone has been exposed to the virus and is therefore likely to have immunity against it. Armed with this knowledge, people could re-enter work spaces where the risk of COVID-19 exposure is high, and do so knowing that they are unlikely to contract and fall ill from the virus. He also explains the protocol he’s developing to this end, which includes COVID-19 surveillance of individuals who are at risk but currently unaffected by the virus, testing of individuals who are showing symptoms, and testing of people who have recovered from the virus.

Knight dives deep into the fascinating details of this work and the continuously evolving field of microbiome research. He offers listeners with an impressive amount of information on microorganisms, the latest research on virus-host microbiome mechanisms based on animal models, how bacterial and viral infections respond to certain dietary interventions, how microbiome analysis can be predictive for the development of certain diseases, and more.

To learn more, check out the following resources:

https://cmi.ucsd.edu/

http://americangut.org/

https://microsetta.ucsd.edu/

https://scholar.google.com/citations?hl=en&user=_e3QL94AAAAJ

https://knightlab.ucsd.edu/wordpress/

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