50 Voices of the Future: Rob Knight examines our microbiomes


In honor of UC San Diego Extension's first 50 years, 50 Voices of the Future asks thought leaders about the trends, breakthroughs and social advances they foresee over the next 50 years.

If you stretched out the San Diego Zoo and multiplied its exhibits until they covered the entire planet, it would contain only a fraction of the organisms living on and inside each human’s body. Our microbiome comprises an intensely varied assortment of tens of trillions of microbes — bacteria, archaea, fungi, viruses and other “germs” — throughout each person’s skin, mouth, gastrointestinal tract and elsewhere. Though most microbes are harmless or beneficial, there’s still much we don’t understand about their links to human health and the environment.

Professor Rob Knight aims to change that. Tying together advanced studies in everything from computer science to pediatrics and biochemistry, Knight has author credit on more than 330 microbial research studies, as well as being principal investigator on the Earth Microbiome Project. As part of his campaign to democratize and decentralize science, Knight developed and runs the American Gut Project — the largest crowdfunded and crowdsourced research study of its kind. In 2015, the native New Zealander’s academic journey brought him to UC San Diego, where among other roles he directs the Center for Microbiome Innovation, doing interdisciplinary research powered by the Comet supercomputer.

(1) Why is the work you do important?

For directly health-relevant traits, knowing every gene in your genome is far less important than studying the three pounds of microbes you carry around in your gut. I can tell whether you’re lean or obese with 90 percent accuracy based on your microbial DNA, but only 58 percent accuracy from your human DNA. The same is true for a whole variety of other conditions linked to the microbiome, including many chronic diseases that have skyrocketed in frequency: diabetes, multiple sclerosis, cardiovascular disease, rheumatoid arthritis, colon cancer, Crohn’s disease, mental-health disorders, the list goes on and on.


During the past century, humans developed vaccinations and safe, simple nutritional interventions at the population level that eliminated many chronic diseases such as tuberculosis, rickets, beriberi and scurvy. By simply iodizing salt we completely eliminated goiter and cretinism, which sickened and decreased the quality of life for millions. What are today’s equivalents? We believe that by modifying the microbiome, we not only can reduce the risk of many modern diseases but perhaps even cure them.

(2) What are the exciting developments in your field, and why?

We’re finding ways to visualize how a person’s microbes are arranged in space and time — and what functions they perform. Previously we might characterize someone’s skin microbiome by taking a single swab, but now we can take 500 swabs and build an amazingly detailed spatial map that shows exactly how the microbes change over the body’s surface.

Another thing that’s really exciting is predictive modeling. Right now we can tell a lot about your current physiological state from your microbes. But what we want to do is to predict what your health will look like 10 or 15 or 20 years from now based on your microbes today — both if you do nothing differently, and if you completely change your lifestyle based on what we tell you.

(3) What’s the next big thing?

The next big thing will be a smart toilet that, instead of flushing information about your health away, will do a molecular analysis of your stool and plug it into a microbial health map. You’ll see if you’re headed in a good or bad direction, and you’ll get GPS-like, step-by-step instructions for reaching a better place on that map.

What’s coming next is more detail about when you change your microbiome, and how those changes are different for different people. For example, a recent Israeli study showed that for some people eating ice cream is actually better for their blood glucose than eating a bowl of white rice. We’re re-evaluating what we tell people about specific microbial relationships to their health.

(4) How big of an impact will your field play in shaping the future of the San Diego region and beyond?

We have a mandate from Chancellor Pradeep Khosla, through the Chancellor’s Initiative in the Microbiome and Microbial Sciences, to wire the whole campus for microbiome research. In the same way that the Chancellor’s Integrated Digital Infrastructure Initiative is wiring the whole campus for high-speed Internet, we’re building microbiome components into a vast range of campus projects involving biological or chemical data.

This is because microbiome research has major, far-reaching implications beyond health care and agriculture. In energy it affects everything from biofuels to bio-remediation, where we can to track and fix pollution by way of microbial metabolism. So really the implications we’re talking about are global in scale.


(5) Hop into your time machine…what does the future look like for this field in 50 years?  How can individuals/companies prepare?

For DNA sequencing, in the next 10 years we’re going to see the scaled equivalent of what separates the Cray-2 supercomputer from your smartphone — and it will be a million times cheaper than it is today, which is not an exaggeration. To prepare we need smart, creative students working across disciplines. Biology, medicine and computer science students need to interact not just with each other, but with people at Calit2 working on virtual design, and people in the Rady School of Management finding ways our research can reach the community.

Learn more about the Science programs and courses that UC San Diego Extension offers including a range of certificate programs in areas such as Algae Biotechnology Science, Biofuels Processes, Biostatistics and more.

Photo credit: David Ahntholz

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