• Biotechnology: The identification and exploitation of the biosynthetic and biocatalytic capacities of microbial communities to generate beneficial industrial, food, and health products (pharmaceuticals, antibiotics, and probiotics).

  • Agriculture: The development of more effective and comprehensive methods for early detection of threats to food production (crop and animal diseases) and food safety (monitoring and early detection of dangerous microbial contaminants) and the development of management practices that maximize the benefit from microbial communities in and around domestic plants and animals.

  • Biodefense and Microbial Forensics: the development of more effective vaccines and therapeutics against potential bioterror agents, the deployment of genomic biosensors to monitor microbial ecosystems for known and potential pathogens, and the ability to precisely identify and characterize microbes that have played a role in war, terrorism, and crime events, thus contributing to discovering the source of the microbes and the party responsible for their use.

Meeting these challenges will require progress on several fronts. Technological, methodological, computational, and conceptual advances will be needed to develop the potential of metagenomics fully.

Furthermore, as microbiologists turn their attention to the study of microbes in their natural environments, it is likely that many of biology’s most basic organizing concepts will be affected by deeper understanding of life at the microbial level. Metagenomics will probably expand answers to questions like, What is a species?, What is the role of microbes in maintaining the health of their host?, How diverse is life?, and What ecological and evolutionary roles do viruses play? The metagenomics approach is uniquely well suited to gathering the information necessary to make progress on such basic conceptual questions.


The opportunity intrinsic to a new frontier of science is accompanied by new challenges that were not anticipated by prior research. Metagenomics is no exception. Current metagenomics researchers face several difficulties and obstacles. Early metagenomics studies have been able to survey the metagenomes of complex microbial communities, but have been able to characterize in depth only the simplest communities. Generating massive sequence databases is not the limiting step; using the databases to determine the complete genomes of community members and to understand a community’s metabolic capabilities or potential responses to environmental change is still beyond the field’s capabilities in even moderately complex

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