One Scientist's Race To Help Microbes Help You

The rate of recent discoveries about the human microbiome has been dizzying. And Rob Knight wants to crank up the pace.

One of the top scientists in a field that's discovering possible bacterial influences on everything from diabetes to depression, Knight was also co-founder of a massive citizen science experiment called the American Gut Project. He recently moved from the University of Colorado, Boulder and took the gut project with him — to the medical school at the University of California, San Diego.

The project lets anybody, for a $99 fee, have the microbes of the gut, mouth, skin or other orifices inventoried. And it's not just for people, but pets, too. Last year I roped my husband, mom and dog into having their gut microbes analyzed along with mine in hopes of discovering what microscopic stories we share. (You can read more about the results here.)

I caught up with Knight by phone on Friday to talk about what's next. Below is an edited version of our chat.

What is the current state of microbiome research?

Right now a lot of microbiome research is about pattern discovery. We're finding connections between microbes and all kinds of conditions we never knew they were involved with — ranging from obesity to colon cancer to rheumatoid arthritis and (in mouse models) even things like autism, depression and multiple sclerosis.

In the future it's going to move beyond the correlations to actually finding out which of those conditions microbes cause — and which of those conditions we can either predict or modify with improved knowledge about the microbial world.

What are some of the current challenges in microbiome research?

In microbiome studies, some of the effects are so obvious that you can see them with just a handful of people. But other effects you might need to get a population of fives of thousands or tens of thousands to be able to understand what's going on.

That becomes especially true if you start to look at combinations of variables. So, maybe exercise has a particular effect on your microbiome if you're on a special diet, or if you're taking a particular drug. Once you start to look at those combinations of factors (talking about, say, racial or ethnic background, or medication or lifestyle effects, such as diet and exercise) in combination and trying to make predictions, you could see how you would need relatively large numbers of people to even begin to get anywhere.

Another challenge is in computation. The ability to generate the data has greatly outstripped a lot of people's ability to analyze the data.

Then there's the user interface. Especially if we want to get this into the hands of clinicians, which we do, and to people who want to interpret their own microbiome results, you really don't want a huge table of numbers. So we are trying to make this easy for users to understand — the same way that GPS went from being just inscrutable numbers to being a map where you can see, turn by turn, where you're supposed to go. That's what we mean to do for the microbiome — to make it easy to use.

With your move from CU Boulder to UCSD, where do you hope to take microbiome research next?

There are several things that are exciting about this move. One is that San Diego is one of the world's premier biotechnology hubs. So being able to collaborate with companies on technology and being able to help companies discover, for example, if a particular probiotic, prebiotic or diet will affect your microbiome. Being able to work with these companies directly to figure out whether their product has an effect — and whether that effect is beneficial or harmful — is really exciting.

Another factor is getting the resources at the [UCSD] medical school — and at the Rady Children's Hospital. The bio bank here is collecting 300,000 biological specimens a month, so we will be able to add a microbiome dimension to the study of diseases — including diseases where there is no hint yet that the microbiome is involved. When you consider the number of diseases where, just over the last five years, it went from being crazy to think the microbes were involved to now being crazy to think the microbes aren't involved, it's amazing how rapidly the evidence has been accumulating. There's a lot of potential there.

What's happening with the American Gut Project?

We have our equipment up and running in San Diego, so we're able to do DNA extractions, PCRs, sequencing and so forth. And samples that have been sent to Boulder are being redirected to San Diego, so no one needs to worry about their sample being lost!

What's next?

We're hoping to scale it up and decrease costs.

We want to reach out to people who share the same factors — whether it's people who live in the same area, do the same sport, have the same diet, are taking the same medication or have the same medical condition. Finding out what matters and what doesn't matter in your microbiome — and which of these factors in which you resemble another person also cause your microbiome to be similar — is going to be really fascinating.

I can't say anything too explicit yet, but we're also looking to partner with companies where we might be able to do things like integrated human genome and microbiome sampling.

We already launched the British Gut Project and the Australian Gut Project, and expanding those kinds of spinoffs to more countries is going to be exciting.

It's going to take a while, but the potential is just tremendous, especially given the disparities between countries — even those that share a border — in a lot of conditions that we now know are linked to the microbiome. So understanding what factors affect those health issues across different geographic regions is going to be very exciting.

We are also hoping to create an open platform where any scientist, physician, educator, student or anyone at a company can very rapidly look at the dataset to get an idea about what the effect on the microbiome a treatment or product might have — and then use that as a basis for designing more carefully controlled studies.

And we think there's a tremendous amount of potential for medical education about probiotics, prebiotics, antibiotics and the microbiome.

I think the possibility of not just discovering patterns but turning those patterns into things that actually affect and benefit people's lives is tremendous.

Katherine Harmon Courage is a freelance health and science journalist based in Colorado. She is the author of Octopus! The Most Mysterious Creature In the Sea, now available in paperback.