Mining the microbiome with Scott Peterson

By Heather Buschman, Ph.D.
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Scott Peterson, Ph.D. is a little different than most biomedical researchers. He doesn’t just want to know what goes wrong when we get sick—he’d rather know what makes us healthy. More specifically, he wants to know how the trillions of microbes—bacteria, mostly—that live on our skin, in our mouths, and in our guts help keep us that way.

“In my view, we don’t always have to think about treating disease with drugs. We should also be mining the human microbiome for therapeutic compounds—things akin to vitamins and herbs—that can keep us from getting sick in the first place,” says Peterson, who joined Sanford-Burnham’s faculty in August 2012, as a professor in our Infectious and Inflammatory Disease Center.

The human body is made up of roughly 100 trillion cells. But only a fraction of those cells are actually human—the rest are bacteria and other microorganisms. This diverse group of microbes along for the ride is known collectively as our microbiome. We and our microbiomes co-evolved to live like this, in a mutually beneficial balance. We provide our microbes with a home and food while they help protect us from other, more menacing, bacteria, viruses, and parasites.

Thinking that our microbial makeup might impact our health in many other ways, scientists have taken great interest in sequencing the human microbiome in recent years, using genetic clues to identify which bacteria live where on whom. Interesting information has come out of these microbiome sequencing projects, telling us that, in terms of bacterial species, different people have different microbiomes and that a person’s unique microbiome can fluctuate with health, disease, and time.

But Peterson notes that we’re now moving into a new phase of microbiome research. And for that reason, he also feels it’s time for the next phase of his career.

Coming to Sanford-Burnham

“The characterization phase of the microbiome—where we sequenced and cataloged bacterial species to put order to complexity—is coming to end. We now know for the most part which species are where. The next phase will have more to do with how they interact and communicate with one another and with us, what goes wrong when disease develops, and what’s needed to maintain health,” he says. In other words, the new phase of research will be less about form and more about function.

That’s what brings Peterson to Sanford-Burnham. He comes from the J. Craig Venter Institute, which is well-known for its sophisticated genome sequencing techniques and innovative genomics projects. Now, to move his microbiome work into the second phase, Peterson needs the people and the resources that can help him do it—and he finds all that at Sanford-Burnham.

“I’m a microbiologist, so I look at things from the bacteria’s point of view. But we also need to understand that in the context of what’s going on in the host. There are many immunologists, cancer biologists, and obesity experts here at Sanford-Burnham who are studying the host perspective. I’ll be teaming up with many of them to complement what I do. In fact, I’ve only been here for two weeks and I’ve been immediately embraced by people with common interests. In this case, being ‘thrown into the fire’ has been a good thing,” Peterson says.

Projects already underway

The new research plans Peterson is making with his Sanford-Burnham colleagues are especially admirable considering that he already has three big projects in the works, each in partnership with a medical clinic. The first, a collaboration with researchers at New York University (NYU), looks at dental cavities in a large group of twins. Despite having the same underlying genetics, the twins’ teeth host vastly differing sets of microorganisms.

In another collaboration with NYU, Peterson and others have taken advantage of an old agriculture trick: if you feed livestock antibiotics, they gain more weight and you get a higher price. By giving mice small amounts of antibiotics, the NYU team created a mouse model of obesity. This low dose of antibiotics is not enough to fight infection, but it does affect the normal gut microbiome and increases the mice’s body weight by about 25 percent. Peterson and his colleagues are comparing the microbiomes of these lean and obese mice and studying the differences in weight gain that they’ve observed between males and females.

In a third project, Peterson is collaborating with colleagues at Johns Hopkins University to look at the microbiome associated with colon tumors. As they’re taking biopsies from colorectal cancer patients participating in this study, clinicians also obtain biopsies of the healthy tissue flanking the tumor. Then Peterson and his team compare the bacteria associated with the healthy tissue to the bacteria found in the tumor tissue.

“What’s especially intriguing in this project is that we don’t yet know what to make of what we’re seeing—do the differences in bacteria contribute to tumor formation or are they just a symptom? Either way is win-win because it either means we’ve found an underlying cause of colorectal cancer or we’re finding biomarkers that could help us diagnose the disease earlier,” Peterson says.

The human microbiome and our relationship with it is complex and scientists are only just beginning to understand and take advantage of it. Peterson’s work is likely to impact our understanding of a number of human conditions, including body weight, heart health, and cancer. For updates on Peterson’s research as he settles in at Sanford-Burnham, subscribe to this blog, follow us on Twitter, or like us on Facebook.

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Heather Buschman, Ph.D.

Heather was a Sanford-Burnham Communications staff member.

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1 Comment

  1. Barbara Henson on

    Could the antibiotics given to livestock be contributing to obesity? What diet prevents colon cancer? Best wishes for success in all your endeavors. Just remember, it is the question that U ask that creates the path to the answer…and that there is no such thing as a stupid question

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