Revealing Our Microbial Planet

New Science May Revolutionize Understanding of the Living World

A n emerging field of science called metagenomics offers a revolutionary new approach to studying microbes by applying genomic analysis to entire microbial communities. Just as 17th-century microscopes gave scientists their first glimpse of the microbial world, metagenomics gives today's scientists a new tool for the study of complex communities of microorganisms, opening the door to a realm that was previously inaccessible to science.

"Metagenomics may be the most important event in microbiology since the invention of the microscope," suggested Jo Handelsman, co-chair of the National Research Council's new report on metagenomics, during an interview with Public Radio International's Living on Earth. And a greater understanding of microbes could be key to addressing some of today's most complex medical, environmental, agricultural, and economic challenges, the report says.

A miniscule fraction of the microbial species on Earth -- most scientists estimate less than 1 percent -- can be cultured using current methods. Metagenomics allows researchers to access the genomes of an entire microbe community without the need to culture individual organisms, making it possible to simultaneously study millions of species that cannot be examined in the laboratory.

Metagenomics studies begin by obtaining a sample from a particular environment such as seawater, soil, or the human gut, extracting genetic material from all the organisms in the sample, and then analyzing it to gain insights on how members of the community interact and perform complex functions. One of the biggest challenges will be manipulating the enormous amount of data that is generated to better understand single species, selected parts of the sample, or the dynamics of the entire community.

Shedding light on thousands of new microorganisms may change the way scientists understand fundamental biological concepts as well as lead to practical applications for human health, agriculture, and environmental stewardship, according to the report. Microbes naturally perform complex biochemical transformations that help clean up such hazardous pollutants as gasoline leaks, oil spills, sewage, and nuclear waste. Some microbes create byproducts such as hydrogen, methane, and butanol -- potential sources of renewable energy. Studying the characteristics of such microbes can help scientists learn to channel microbial capabilities to help us manage tough environmental and economic problems.

Microbes even play a major role in maintaining human health. "We have 10 times more bacterial cells in our bodies than human cells, so we're 90 percent bacteria," said Handelsman. These microbial inhabitants help our bodies digest food and even defend us from pathogens. Given that hundreds of drugs available today were derived from chemicals first found in microbes, studying microbial communities holds great potential for developing new ways to diagnose, treat, and prevent disease.

The Research Council report was requested by several federal agencies interested in the potential of metagenomics and how best to encourage its success. In particular, the committee was asked to recommend promising directions for future studies. It concluded that the most efficient way to boost the field of metagenomics overall would be to establish a Global Metagenomics Initiative that includes a few large-scale, internationally coordinated projects and numerous medium- and small-size studies.

"Because the challenges and opportunities presented by metagenomics are so enormous, a large-scale commitment equivalent to that of the Human Genome Project is both justified and necessary," said committee co-chair James M. Tiedje. Interdisciplinary collaboration and an array of federal agencies would help to build the foundation of standard methods and databases necessary for this new field to reach its full potential.   -- Anne Jurkowski

The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Committee on Metagenomics: Challenges and Functional Applications, Board on Life Sciences, Division on Earth and Life Studies (2007, 170 pp.; ISBN 0-309-10676-1; available from the National Academies Press, tel. 1-800-624-6242; $36.50 plus $4.50 shipping for single copies).

The committee was co-chaired by Jo Handelsman, professor of plant pathology, University of Wisconsin, Madison, and James M. Tiedje, University Distinguished Professor and director, Center for Microbial Ecology, Michigan State University, East Lansing. The study was funded by the National Institutes of Health, National Science Foundation, and U.S. Department of Energy.