adapted through countless individual generations and billions of years of environmental change. In addition to their essential activities throughout the biosphere, microbes have been the source of numerous technologies that have improved the human condition. They are used commercially to produce most of the antibiotics and many other drugs in clinical use, to remediate pollutants in soil and water, to enhance crop productivity, to produce biofuels, to ferment many human foods, and to provide unique signatures that form the basis of microbial detection in disease diagnosis and forensic analysis.

Historically, the study of microbes has predominantly focused on single species in pure laboratory culture, and so understanding of microbial communities lags behind understanding of their individual members. Only recently have the tools become available to study microbes in the complex communities where they actually live and thus to begin to understand what they are capable of and how they work. Traditional microbiological approaches have already shown how useful microbes can be; the new approach of metagenomics will greatly extend scientists’ ability to discover and benefit from microbial capabilities.

The opportunity that stands before microbiologists today is akin to a reinvention of the microscope in the expanse of research questions it opens to investigation. Metagenomics provides a new way of examining the microbial world that not only will transform modern microbiology but has the potential to revolutionize understanding of the entire living world. In metagenomics, the power of genomic analysis is applied to entire communities of microbes, bypassing the need to isolate and culture individual bacterial community members. The new approach and its attendant technologies will bring to light the myriad capabilities of microbial communities that drive the planet’s energy and nutrient cycles, maintain the health of its inhabitants, and shape the evolution of life. Metagenomics will generate knowledge of microbial interactions so that they can be harnessed to improve human health, food security, and energy production.

Metagenomics combines the power of genomics, bioinformatics, and systems biology. Operationally, it is novel in that it involves study of the genomes of many organisms simultaneously. It provides new access to the microbial world; the vast majority of microbes cannot be grown in the laboratory and therefore cannot be studied with the classical methods of microbiology. Although community ecology is not new to microbiology, the ability to bring to bear the power of genomics in the study of communities initiates an unparalled opportunity.

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