The American Academy of Microbiology releases report

April 07, 2004

Washington, D.C. - Genomics has revolutionized the science of microbiology, and the authors of a new report from the American Academy of Microbiology (AAM) argue that this important analytical tool should now be more widely used to study microbes in their "real-world" setting, within microbial communities.

To date, microbial genomics has largely been applied to individual, isolated strains and then extrapolated to naturally occurring microbial communities. But just as human behavior can differ in individual versus group settings, so does that of microbes. For example, certain microbial communities are capable of breaking down hazardous chemicals that an individual species member cannot. Consortia of bacteria, such as in the human gut, are required to satisfy the nutritional requirements of many higher organisms.

Outside the laboratory, virtually all microorganisms exist in communities, where they exchange genetic material, nutrients, and biochemical signals. Most interactions, evolutionary processes, and biogeochemical activities in microorganisms occur at the community level and have immense impacts on human health and the planetary biosphere. Although genomic analysis of individual strains has had a significant payoff, progress can be significantly accelerated by studying microorganisms within the context of their communities, according to the report, "The Global Genome Question: Microbes as the Key to Understanding Evolution and Ecology."

"Microbial community genomics holds great promise for improving our world," comments colloquium co-chair David A. Relman, M.D., of Stanford University. "By allowing scientists to understand better the processes shaping and sustaining the microbial communities that, in turn, affect human health and the environment, genomics could substantially enhance our abilities to prevent and treat diseases and manage the precious natural resources and processes that maintain life on this planet."

The report points out that there are several hurdles to be overcome before genomics can be used most effectively in studying these communities, such as the challenges of coordinating research programs centered around critical biological questions and applying appropriate and cost-effective technologies to answer them. The tremendous complexity of microbial communities and the difficulties of measuring all the relevant internal and environmental variables associated with them pose additional challenges. Certain technical problems, such as identifying minority subpopulations, deciphering diverse chromosome structures, and complex genome assembly problems must be tackled to accelerate progress in microbial community genomics. The report also identifies a number of educational needs, including cross-disciplinary training at the graduate and postgraduate levels in fields melding biology and computer science or mathematics.

The report is based on an AAM-sponsored colloquium held in October 2002 in Longboat Key, FL, which brought together 27 scientists from academia and industry to discuss the current state of knowledge in microbial genomics. In focusing on the great potential of genomics to advance our understanding of microbial communities and ecosystems, it outlines future directions for research and recommends new solutions to the challenges of applying genomics to study microbial systems.
Support for the colloquium on which "The Global Genome Question" is based included the Ellison Medical Foundation; the National Science Foundation; the U.S. Department of Energy; the National Institute of Dental and Craniofacial Research, National Institutes of Health; and the National Institute of General Medical Sciences, National Institutes of Health.

The American Academy for Microbiology (AAM) is the honorific leadership group of the American Society for Microbiology. The mission of AAM is to recognize scientific excellence, as well as foster knowledge and understanding in the microbiological sciences. For more information about the American Society for Microbiology, contact Barbara Hyde at 202-942-9206 or visit

AAM reports can be downloaded free of charge at For more information or to receive a hard copy of "The Global Genome Question," contact Mimi Godfrey at the American Academy of Microbiology at 202-942-9292 or

American Society for Microbiology

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