Gut Reaction

What if your health isn’t solely dependent on what you eat and your genes? Associate professor Rob Knight’s research reveals that bacteria in your body could play a more vital role than previously thought.

When a colleague first approached Rob Knight about writing a grant for the Bill and Melinda Gates Foundation to address childhood malnutrition in the developing world, the CU-Boulder biochemistry associate professor thought he had the wrong guy.

“I was extremely skeptical,” says Knight who specializes in bioinformatics, which is the merging of computer science and biology. “I said, ‘Shouldn’t the Gates Foundation be spending its money on food, rather than DNA sequencing?’ Fascinatingly, the answer is no. It’s not that simple.”

In reality mounting research has shown that the vast array of microorganisms inhabiting the human gut play a critical role in helping the body break down carbohydrates, fats and proteins efficiently. If that microbial community is damaged by malnutrition or other factors, food alone won’t solve the problem, explains Knight.

“You can feed these kids as much corn or vegetable porridge as you like and it won’t reverse,” he says.

Armed with an $8.3 million Gates Foundation grant, lightning-fast computational tools developed in Knight’s lab and an army of rats and pigs colonized with gut bacteria from youth in Bangladesh and Malawi, an international team of researchers will collaborate over the next two years to answer two essential questions: What prompts one child’s gut bacteria to develop in a healthy way while another’s does not? And what can be given to a malnourished child, along with food, to repair a damaged microbial community and restore nutritional health?

“The microbiota [microscopic living organisms] does not develop in isolation,” explains Jeffrey I. Gordon, a doctor and director of Washington University’s Center for Genome Sciences, and the team leader for the Gates Foundation Breast Milk, Gut Microbiome and Immunity Project (BMMI).

“There are many factors that shape its structure and function, including breast milk and the first foods a child eats. Ultimately, we hope to identify next-generation foods and probiotics that can be given to these children to prevent or ease malnutrition.”

The BMMI project is the latest in a series of research endeavors that have propelled Knight, at the young age of 35, to star status in the nascent field of human microbiome research. The field hinges upon the recent realization that the hundred trillion or so bacteria inhabiting our bodies play a critical role in everything from our susceptibility to disease to our appetite to the way we respond to medications.

Until recently, the few scientists interested in better understanding those microorganisms were stifled by high costs and long waits for gene sequencing. They also were hindered by the inability to compare the microbial community of one group of people with that of another.

Enter Knight and his team of 30 students and researchers at the CU Biofrontiers Institute who have largely solved those problems. Whereas it once cost $8 to analyze one gene sequence, it now costs $30,000 to analyze 1 billion gene sequences using the team’s new rapid-fire “error-correcting bar-coded sequencing” techniques developed with members of distinguished professor Norm Pace and professor Larry Gold’s molecular, cellular and developmental labs at CU.

And thanks to new UniFrac software they developed, it’s now possible to compare what lives in the gut of youth in rural Malawi with what occupies that of kids in, say, Boulder. In fact this group performed many of the earliest large-scale human micorbiome studies using this technology with associate professor Noah Fierer of ecology and evolutionary biology.

“[Knight’s] lab work has propelled the field forward tremendously,” says Gordon of Washington University in St. Louis, a pioneer in microbiome research.

As a precocious outdoor-lover growing up in the coastal burg of Dunedin, New Zealand, Knight gained an affinity for microbiology early on. But ironically, one professor during his undergrad years in the 1990s tried to steer him away from the field.

“There was an impression that microbiology was over,” he recalls, speaking in a thick accent and dizzyingly fast pace that seems to match the speed at which his field is progressing. “We had antibiotics, so why study it? The concept of the human microbiome didn’t have any currency at the time.”

He followed his interest nonetheless, earning a doctorate in evolutionary biology from Princeton University and schooling himself in the computational techniques he needed to better understand the microscopic world. When the computer program he needed didn’t exist, he wrote it. After a few years of splitting his time between lab experiments and writing code, he landed at CU-Boulder as an assistant professor of chemistry and biochemistry in 2004.

His first entrée into microbiome research came in 2005 when he teamed up with Gordon to study the potential relationship between microorganisms and obesity. Their joint paper showed that lean and obese mice differed in their gut microbiota. Later Gordon’s lab showed that when the gut bacteria of an obese mouse was transplanted into a lean, germ-free one, the recipient plumped up.

“Somehow, the altered microbial community made them want to eat more,” Knight says.

Seven years later — having published dozens of papers involving the human microbiome and advancing the computational tools exponentially — he’s teaming up with Gordon again and researchers from the University of California Davis and Ohio State University, among others, to explore the flip side of the equation — the malnutrition-microbiota link.

To do so, scientists in Bangladesh, Malawi and other countries will collect monthly fecal samples from 600 babies beginning at birth and ship the frozen specimens to the United States. Those specimens will be used to colonize “germ-free” mice and pigs (with no resident bacteria whatsoever), essentially creating miniature clones of the microbial communities of their human counterparts overseas.

“You can essentially take one person, take their gut microbiota, put it into a whole bunch of different mice or pigs and then do experiments on those mice or pigs to see what interventions they respond to — what works and what doesn’t work,” Knight explains.

His lab will be responsible for collecting the gene sequences and metabolite data and running the data analysis center. He also has traveled to Bangladesh to teach scientists there how to use cloud computing, an exciting emerging technology that will allow them to do data analyses without their own super computer.

Ultimately, he says, the project could allow a child to be tested for certain gut microorganisms and then given a safe, custom probiotic to replenish what bugs they’re missing or eradicate those doing harm. Ideally the hope is to isolate probiotics from the same individual or family to increase the chance they are safe and reduce potential ethical issues with transferring microbes across populations without understanding the side effects.

But the power of the microbiome revolution doesn’t end there, Knight stresses.

“It’s just spectacularly exciting,” he says. “There are so many questions that can be answered that could not be answered five years ago and so many ways this can all be applied.”

In June the Human Microbiome Project Consortium — a federally funded group of 200 scientists, including Knight — mapped the entire microbial makeup of a healthy human for the first time, using 4,788 specimens from 242 healthy adults.

Knight and colleagues also published data comparing the gut bacteria from residents of Venezuela, rural Malawi and the United States and found “pronounced differences” between the U.S. samples and those in developing countries. U.S. samples possessed very different species of gut bacteria than those in developing countries where the diet is less processed, suggesting that the Western diet has altered the microbial landscape of the American gut.

While both papers raised more questions than answers, the take-home message, thus far, is this, says Knight: The microorganisms we carry in our bodies set us apart far more than our genes do. As a result, they may make for a “more logical starting point for personalized medicine.”

“If you look at our host genome, we are all 99.9 percent the same,” Knight says. “But if you look at our gut microbiota, it can be 80 to 90 percent different between two people. We are beginning to think that for an expanding array of conditions, the gut microbiome may actually be a better diagnostic tool than the human genome.”

Plus, he adds, it’s a lot easier to change what’s growing in your gut than it is to change your genes.

Interested in contributing to Knight’s research? A critical need is funding for high-performance computing equipment. E-mail Jessica Wright at the CU Foundation at jessica.wright@cufund.org to learn more.