Mapping the Earth’s microbiomes: federal agencies join forces to explore the microbial world

Jo Handelsman explaining the microbial world during her Patrusky Lecture at CASW’s New Horizons in Science 2015. (CASW photo by Mark Bennington.)

Microbes are organisms that are invisible to the naked eye. They surround us but usually go unnoticed. Now the federal government has a new focus on microbes, said Jo Handelsman, associate director of the White House Office of Science and Technology Policy, speaking Oct. 11 during CASW’s New Horizons in Science program at the Massachusetts Institute of Technology. More than 10 federal agencies and departments recently joined forces to share data and draft a coordinated plan to map the Earth’s microbiomes, the collections of microbes that live in particular habitats such as in the ocean or on your skin.

Microbes have often been thought of only as germs, pathogens that cause disease. Pathogens are an important subset of microbes. Yet, the majority of microbes are harmless and microbes influence all natural processes on Earth, said Handelsman, who is also professor of molecular, cellular, and developmental biology at Yale University. Handelsman delivered the third Patrusky Lecture to an audience of sciencewriters during the ScienceWriters2015 conference.

Microbes rule

“Why is it the world doesn’t appreciate that we are run by microbes?” Handelsman asked rhetorically. Before the late 20th century, scientists did not have the tools to investigate the complexity and dynamic nature of microbiomes. Today, researchers use DNA-based techniques, such as metagenomics, to conduct a thorough census of a microbial community. They also apply machine learning, an approach that harnesses the artificial intelligence of computers to make sense of complicated data. These innovations have revealed previously unfathomed ways that microbiomes relate to the health of human beings and the planet.

All organisms and ecosystems have microbiomes that provide many protective qualities, Handelsman said. We now know that a plant’s microbiome influences its ability to withstand environmental stresses like drought. The unique microbial communities of the oceans not only protect the atmosphere by trapping carbon dioxide but also help transform plant and animal remains into fossil fuels within the cracks of the ocean floor.

A similar symbiotic relationship exists between microbes and humankind. Scientists now recognize that a human body is 90 percent microbial. When you examine the whole body with a microscope, you see that microbial cells outnumber human cells at a rate of about 10 to one. In the past decade, medical researchers have reported connections between microbes in the human intestines and health conditions never before linked to microbes such as obesity and autism, Handelsman said. These surprising discoveries have led her to wonder how much disease is due to one’s own physiology and personal choices and how much is due to “the chemistry of our microbial benefactors.”

Citizen science: crowdsourcing microbiome research

In 2007, the National Institutes of Health (NIH) launched the Human Microbiome Project to create public datasets of the human microbiome and study its relationship with human health. The Human Microbiome Project continues the legacy of the NIH’s Human Genome Project, which raced against the private company Celera Genomics in the early 2000s to complete the map of the human genetic code.

When it comes to mapping microbiomes, the U.S. government faces no serious competition from the private sector. Instead, microbiome researchers have established complementary initiatives, such as American Gut and the Earth Microbiome Project. Both are open-sourced and open access, meaning anyone can contribute and access data. For $99 and a stool sample, American Gut provides you with a report on your gut microbiome and inputs your anonymous information into its database. The Earth Microbiome Project aims to become a vast catalog of microbial communities worldwide that is available to the public as wellResearchers contribute, but all of society may benefit from the potential results because the most powerful sets of data are usually the largest ones.

“A global issue across microbiomes is the precision question,” said Handelsman, explaining that researchers need to hone in on which factors, if any, can be modified within a human microbiome to either prevent or treat disease.

Although the future of microbiome-based cures for human disease is fuzzy, Handelsman made it clear that the notion of microbes as purely pathogenic is outdated. “The vast majority of life is microbial. You’ve got to face that fact,” she said. Given the incredible contribution people are making to crowdsourced microbiome research, it appears that many have already embraced the microbial frontier.

Cora Best is a Ph.D. candidate in human nutrition at Cornell University and a recipient of a NIH nutrition training grant for training in translational science. Cora likes to work toward increased public understanding of science, nutrition science in particular. She has dedicated her professional life to finding and supporting good solutions for improving public health and nutrition. Follow her on Twitter: @CoraMBest