Scientists Urge National Initiative on Microbiomes

Scores of leading scientists on Wednesday urged the creation of a major initiative to better understand the microbial communities critical to both human health and every ecosystem.

In two papers published simultaneously in the journals Science and Nature, the scientists called for a government-led effort akin to the Brain Initiative, a monumental multiyear project intended to develop new technologies to understand the human brain.

“This is the beginning of the shot to the moon,” said Jeffery F. Miller, the director of the California NanoSystems Institute at the University of California, Los Angeles, and a co-author of the Science paper. “There is so much to learn, and so many benefits of learning it.”

The White House is already considering increasing its support of research into the workings of these microbial communities, called microbiomes. The new papers “are very thoughtful and have a lot to tell us,” said Jo Handelsman, the associate director of the White House Office of Science and Technology Policy and herself a microbiologist.

As to whether there will be a national microbiome initiative, she said, “We don’t have anything to announce today.”

Microbiomes have become the focus of intense study and public interest. The trillions of microbes that live inside the human body, for example, play important roles in health, from fighting diseases to maintaining a balanced immune system.

But the planet is home to a vast number of other microbiomes, from the microbial communities that live in undersea volcanoes to microbes that cling to existence in Antarctic deserts. These play an instrumental role in the environment: Ocean microbes, for example, produce half of the oxygen we breathe.

Dr. Miller said a microbiome initiative could uncover fundamental explanations for why things are the way they are. “It’s like we’re looking up in the sky with a refractive telescopic for the first time and saying, ‘Wow, it’s amazing what’s up there. What is all this doing? How does it work?’ ” he said.

Researchers have been investigating microbes for centuries, ever since Antonie van Leeuwenhoek peered into a crude microscope in the mid-1600s and discovered that a drop of water was full of tiny swimming creatures.

In recent decades, microbiologists have begun to map their astonishing diversity. The animal kingdom contains about 40 major groups, or phyla. Microbiologists now recognize upward of 1,000 phyla of microbes.

“Plants and animals are a patina on the microbial world,” said Margaret J. McFall-Ngai of the University of Hawaii, a co-author on both new papers.

Each of these communities of microbes can be dizzyingly complex. A single human microbiome can be made up of trillions of microbes divided into thousands of species.

Scientists cannot yet answer even basic questions about how these communities function. In Science, 48 scientists described some of the most pressing mysteries.

All microbiomes can change, for example, sometimes drastically. The Deepwater Horizon oil spill altered the diversity of microbes in the Gulf of Mexico. Likewise, a bad intestinal infection can drive out common gut species that maintain human health.

These disturbances may seem dissimilar, but microbiologists believe that unhealthy microbiomes may share certain universal signatures. Understanding patterns like these might allow us to control the communities.

As yet, there are few examples of successful manipulation of microbiomes. The best documented is a medical procedure known as fecal transplant. Patients with life-threatening gut infections can be cured by receiving intestinal bacteria from a healthy donor.

Yet scientists are still at a loss to explain how individual species of bacteria in such a transplant help battle infections. A fuller understanding might open the way to using microbiome-based treatments for other ailments, from tooth decay to obesity.

Dr. Miller said it might also be possible to tend to microbiomes outside our bodies. Manipulating microbes in farm fields could increase the productivity of crops, for example.

The tundra, too, contains vast amounts of methane-generating microbes that could accelerate global warming. Understanding how that microbiome works might lead to ways to control its effects on the climate.

Microbiomes are so complex, Dr. Miller cautioned, that it will take years to achieve such a level of understanding. “This has to be structured as a long-term effort,” he said. “We are looking off in the distance, but along the way there are many milestones.”

Answering the questions will demand new tools to gather and analyze data, Dr. McFall-Ngai said. To understand how microbes behave, for instance, scientists need a better way to see the molecular activity inside them.

“We want to pull out individual cells and ask, ‘What are they doing?’ ” Dr. McFall-Ngai said. “We have no methods for that.”

In their commentary for Nature, Dr. McFall-Ngai and her co-authors, Nicole Dubilier of the Max Planck Institute for Marine Microbiology in Germany and Liping Zhao of Shanghai Jiao Tong University in China, urged the United States to coordinate research efforts on microbiomes with other countries.

“Earth’s biome is not defined by national borders,” they wrote.

Over the past year, the Kavli Foundation, a philanthropic science organization based in California, has hosted a series of meetings for microbiome experts, where they discussed the best way to move their research forward. The foundation had organized a similar set of workshops about neuroscience, which ultimately led to the Brain Initiative.

The White House Office of Science and Technology Policy joined the effort with a series of its own meetings and a public request for information for “an effort to unify and focus microbiome research across sectors” of the government.

The National Science and Technology Council will release a report on these efforts by the end of the year, which will address how federal agencies can coordinate the research they fund on the microbiome.

“We need to make sure that the federal investments are meeting the needs of the science and advancing the science as fast as possible towards applications,” Dr. Handelsman said.