International Human Microbe Program Looks Ahead

Friend or foe? Researchers are studying the role that the billions of bacteria that live in our bodies, such as the gut bacterium Enterococcus faecalis (pictured), play in making us sick and keeping us healthy.

U.S. Department of Agriculture

PARIS—We are not alone. Every human being is teeming with billions of microbes, which inhabit our guts, our skin, our mouths and noses, and our reproductive tracts. Scientists call this the microbiome, and over the past several years the International Human Microbiome Consortium has mounted an intense research effort to understand its crucial role in disease and health.

But two key programs that helped jump-start this field are coming to an end, and follow-up efforts have yet to be put in place. It's also unclear whether industry, government regulators, or the public are ready to take microbiome insights into the clinic. That was the news this week in Paris as 650 researchers gathered for the third annual meeting sponsored by the International Human Microbiome Consortium, whose members include the U.S. National Institutes of Health (NIH), European Commission (EC), and major health and science agencies from France, Japan, Canada, and several other countries. Both the NIH and EC microbiome programs, which have provided $140 million and $27 million respectively over the past 5 years, are in their sunset phases right now, and the community is awaiting news about future funding from both sides of the Atlantic.

If the scientific progress made so far is any guide, then there is plenty of justification for such extended funding, according to S. Dusko Ehrlich, a molecular biologist at the French research agency INRA and coordinator of MetaHIT, the EC-funded microbiome program. "We are now in a position to not just look at the data but start interpreting them," Ehrlich told ScienceInsider. "We are finding promising avenues for the future," including exploring the findings that a higher degree of biodiversity of microbes in the human body is positively correlated with good health, whereas low diversity is often correlated with poor health.

Lita Proctor, coordinator of the NIH-funded Human Microbiome Project (HMP), adds that the field is now mature enough to start having debates about the data, including whether the controversial claim that humans can be classified into three different "enterotypes" depending on their microbial profiles is valid. "At first we were just focused on methodology," Proctor told ScienceInsider, "but now we are having debates about different ideas and perspectives."

As for continued NIH funding, Proctor says that the agency is currently having intense discussions with the microbiome research community as well as internal debates over whether to launch an "HMP2" beginning next year. Proctor says that decision will probably be made sometime this summer. And during the ending panel discussion at the meeting, Proctor outlined what the renewed program would be likely to concentrate on: bioinformatics and computational tools to handle sequencing of microbiomes; large-scale, high throughput assays to analyze the makeup of the human microbiome; and possibly animal models, which some researchers have already begun employing to see the effects on health of experimentally altering the microbiome makeup.

On the European side, Ehrlich says he is hopeful that MetaHIT, which will come to an end in 3 months, will be continued in some form. "The scientific community expects the EC to put out a call for new proposals in July," Ehrlich says. "Everybody would be very surprised if there were no microbiome research funded, from the signs we are getting."

Indeed, the positive atmosphere for continued microbiome research in Europe has helped attract industry to the research effort, as evidenced by the presence on the final panel of top officials from three French companies: the food conglomerate Danone, the pharmaceutical company Institut Merieux, and a new microbiome start-up called Enterome.

Pierre Belichard, Enterome's CEO, told the meeting attendees that his company is particularly interested in harnessing microbiome research to create "biomarkers" for different diseases. And Christian Bréchot, vice president for medical and scientific affairs at Merieux (and former director of the biomedical research agency INSERM, France's version of NIH), stressed the importance of academic researchers patenting their findings if microbiome research is to achieve its full commercial potential.

In the United States, however, industry has been slower to get involved, according to Proctor, although companies like the global health care company Abbott Laboratories and the baby food producer Gerber Products Co. are now showing an interest.

But some serious obstacles to translating basic microbiome research into clinical trials could come from the U.S. Food and Drug Administration (FDA), warned Richard Sharp, director of bioethics research at the Cleveland Clinic in Ohio, one of the world's largest private medical centers. "The FDA has adopted a largely conservative stance towards such clinical trials," Sharp said during his panel presentation. "They will come with enormous levels of regulatory burden in many cases, and it could become a major roadblock."

Indeed, Sharp said at the meeting, patients who come to Cleveland Clinic for treatment of inflammatory bowel disease express their own concerns about such approaches, which could include the use of probiotics, the consumption of live microorganisms, to treat intestinal and other maladies. "Many patients are worried about manipulating their gut microbiota," Sharp said, adding that "they see these kinds of studies through the lens of genetically modified foods. They worry that tampering with the gut microbiome could lead to irreversible effects."

Sharp also urged the microbiome research community, along with funding agencies, to start doing more public outreach to counter the often "grossly misleading" statements made by companies that sell probiotic products, including claims that probiotics can cure cancers and treat autism spectrum disorders. "Most of what people know about this area of research comes from these retailers," Sharp said. "We should not be relying on these companies to put out the first messages about this area of research."