These microbes live more than 2 kilometers below the sea floor off the coast of Japan.

These microbes live more than 2 kilometers below the sea floor off the coast of Japan.

Hiroyuki Imachi/JAMSTEC

Earth’s microbes get their own White House initiative

With its second term wrapping up, President Obama’s administration wants to fit at least one more high-profile “initiative” into its scientific legacy. Having launched efforts to map the human brain, fight drug-resistant bacteria, advance precision medicine, and cure cancer, the White House has now set its sights on the untold number of enigmatic microbes that define our environment and fill our bodies.

The National Microbiome Initiative, rolled out in an event today by the White House Office of Science and Technology Policy (OSTP), aims to fund cross-disciplinary projects that would help understand the function of individual microbes and map how they interact in communities—from those that may fend off disease in the human intestines, to those that help plants pull nutrients from soil, to those that capture and release carbon dioxide in the ocean.

The initiative would allocate $121 million in federal money—from funding already appropriated and included in the president’s 2017 budget request—to microbiome-focused research grants at NASA, the Department of Energy, the National Science Foundation, the National Institutes of Health, and the U.S. Department of Agriculture. Private foundations, companies, and academic institutions have pledged another $400 million, including $100 million from the Bill & Melinda Gates Foundation to study the effects of the microbiome on malnutrition and ways to manipulate soil microbes to improve crops in sub-Saharan Africa.

The initiative’s underlying goal, says microbiologist Jeff Miller at University of California, Los Angeles, should be to enable experiments testing cause and effect—not just showing inconclusive associations that have so far been typical of microbiome research. “We have incredibly interesting correlations between a certain type of bacterial community and obesity, or type 2 diabetes, or whether a plant is going to grow fast or not,” says Miller, among 17 researchers who helped inform OSTP by laying out their vision for a “Unified Microbiome Initiative” last year in Science. “We’re generating hypotheses, but we’ve kind of lacked the tools to rigorously test them.”

That word—“tools”—appears 17 times in the White House fact sheet released today. What might this new set of tools look like? One, Miller says, might be a precise way to eliminate a single microbial species while leaving its neighbors untouched—perhaps with a targeted nanoparticle or the precise editing of a key gene. Although it’s now possible to quickly sequence the DNA from a mixed sample of microbes, the role of individual genes—and the way species influence one another in their natural environments—are largely unknown.

Another priority: nanoscale imaging methods for observing groups of microbes without disrupting them. “We take a complex community and we grind it up and we sequence the parts,” Miller says. “If you look outside the window right now and imagine what would happen if you took that in a blender and then tried to study it, you wouldn’t really be getting much more than just what the components are, and we know that these communities are highly structured.”

A tool at the top of the wish list for microbial ecologist Janet Jansson at the Pacific Northwest National Laboratory in Richland, Washington, would be higher-throughput mass spectrometry—a technology that allows researchers to sort through the proteins in a microbial sample. Genetic sequencing “only gets you so far,” she explains. “If you want to understand more about the functions that are carried out in the communities, then it’s desirable to know about the proteins that they are producing, and also the metabolites.”

The burst of White House enthusiasm may do little more than formalize and collate investments that were likely already brewing at research centers, disease foundations, and private companies. The diabetes research foundation JDRF, for example, intends to spend $10 million over the next 5 years on microbial changes influencing type 1 diabetes. Others link up collaborators under a new title, such as the $1.3 million new microbiome center, run jointly by the University of Chicago in Illinois; the Marine Biological Laboratory in Woods Hole, Massachusetts; and the U.S. Department of Energy’s Argonne National Laboratory in Lemont, Illinois. But the initiative aims to send the same message researchers are getting from the microbes they study: that the combined community is more productive than its isolated parts.