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Humans are hosts to a diverse microbiome, including these organisms. Clockwise from top left are Streptococcus (Credit: Tom Schmidt); a microbial biofilm of mixed species, from human body (Credit: A. Earl, Broad Institute/MIT); Bacillus (Credit: Tom Schmidt); and Malassezia lopophilis (Credit: J.H. Carr, CDC). Image credit: Jonathan Bailey / NHGRI.

The White House today unveiled more than half a billion dollars’ worth of public and private programs aimed at unraveling the mysteries of microbes – and Seattle’s Bill and Melinda Gates Foundation will be contributing more than $100 million to that National Microbiome Initiative over the next four years.

The initiative will take advantage of the key role that microbial communities, also known as microbiomes, play in our gut as well as in agriculture and global ecosystems. Research into the workings on microbiomes could lead to new treatments for diseases, better crops and a healthier environment. Microbial transplants are already being used to treat conditions such as C. difficile, a debilitating bowel disease.

“Clearly, applications are critical. Ultimately the promise of the microbiome has to be realized,” microbiologist Jo Handelsman, associate director for science at the White House Office of Science and Technology Policy, said at today’s White House kickoff briefing.

U.S. Rep. Louise Slaughter, a New York Democrat who is also a trained microbiologist, said the scientific payoff “is going to be like splitting the atom, I think, when you get all this done.”

Handelsman noted that the federal government spent more than $900 million on microbiome research in the 2012-2014 time period. The new initiative calls for another $121 million in spending by a wide range of agencies, including the Department of Agriculture, the National Institutes of Health, NASA, the Department of Energy and the National Institute of Standards and Technology.

Some of the Energy Department money will go to the Pacific Northwest National Laboratory for research into the role of microbiomes in ecosystem sustainabiliity and human health. For example, one project is looking at how climate change could affect the mix of soil bacteria, and what that would mean for agriculture.

“I had been working on microbiomes before it was cool,” joked Janet Jansson, PNNL’s director of biological sciences.

The initiative will also draw on more than $400 million in commitments from groups outside the government. The biggest single commitment is the Gates Foundation’s $100 million plan for research into human nutrition and crop protection.

In a briefing paper, the White House said the Gates Foundation’s money will support clinical studies assessing the effects of the human microbiome on childhood malnutrition and stunting, along with trials aimed at treating microbiome-related maladies that contribute to malnutrition.

“This will have profound implications for solving the problem of childhood malnutrition, and helping children survive and thrive everywhere in the world,” said Anita Zaidi, director of the enteric and diarrheal diseases program at the Gates Foundation. She pointed to foundation-funded studies in Malawi that suggest adjustments in the microbiome could head off malnutrition and stunting.

Another focus of the research funded by the Gates Foundation will be to fight pests and diseases that affect crops grown in sub-Saharan Africa.

The Gordon and Betty Moore Foundation will provide $31 milllion over the next four years to support ocean microbiome research, including a new microbe classification project called UniEuk, in cooperation with the University of British Columbia and other institutions. Other programs will study human bacterial communities and their potential for treating conditions ranging from cancer and diabetes to brain diseases, the potential of probiotics, and the microbiomes found in soil, crops, forests and at industrial sites.

J. Craig Venter, who helped pioneer the sequencing of the human genome in 1999 as well as the development of the first synthetic genome in 2010, said “this is a great day of celebration for people working in this field.”

Someday, Venter said, voyagers to Mars may well be given synthetic microbiomes. “Instead of sending up a lot of people, with each of their billions of different microbes to contaminate another planet, we should make a synthetic microbiome so they at least carry known species up there,” Venter said.

White House science adviser John Holdren said it will take years of work to understand Earth’s microbial communities, let alone any on Mars.

“Great and widespread applications will not happen overnight,” he said. “But they will ultimately happen, as a result of the work that has been going on in the microbiome space, and the work that this initiative will foment.”

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