The New Science of Metagenomics Revealing the Secrets of Our Microbial Planet (2007) / Chapter Skim
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We also depend on microbes to clean up pollutants in the environment, such as oil and chemical spills. All these activities are carried out by complex microbial communities -- intricate, balanced, and integrated entities that adapt swiftly and flexibly to environmental change.
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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.
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In the second sense, meta also recognizes the need to develop computational methods that maximize understanding of the genetic composition and activities of communities so complex that they can only be sampled, never completely characterized. Metagenomics, still a very new science, has already produced a wealth of knowledge about the uncultured microbial world because of its radically new ways of doing microbiology.
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Microbial communities live virtually everywhere, and we are largely ignorant of their inhabitants and ecology; so there are literally millions of potential metagenomics projects. Each project would generate massive amounts of DNA sequence and functional data.
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MAJOR ACADEMIC, GOVERNMENTAL, AND COMMERCIAL STAKEHOLDERS There are many potentially beneficial collaborations among various academic disciplines in metagenomics projects, including atmospheric, ocean, soil, and water studies; geology; medicine; veterinary science; agricultural science; environmental; and bioengineering. It is, however, perhaps the field of biology that will be most affected by increasing knowledge of microbes.
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DIFFICULTIES FACING CURRENT RESEARCHERS The sequence-based metagenomics approach has already been applied to many environments, including the ocean, many soils, coral reefs, whale carcasses, thermal vents, and hot springs. The microbial communities associated with different organisms -- including humans, termites, aphids, and worms -- have been studied.
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The diversity of habitats on Earth, the complexity of microbial communities, and the myriad functions governed by microbes suggest that highly productive metagenomics research will be possible in decentralized, small-project settings. However, no individual researcher is likely to have the capability and resources to achieve a comprehensive characterization of a complex microbial community.
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Large-scale projects could unite scientists of multiple disciplines around the study of a particular sample, habitat, function, or analytical challenge -- an approach that is more likely to illuminate themes and advance technical approaches than would a disparate group of small projects by researchers with different goals and nonuniform methods. These large-scale projects would also serve as incubators for the development of novel technologies, analytical techniques, and community databases and would equip smaller-scale projects with the knowledge to design efficient sampling schemes, make informed choices about habitats to study, and identify fruitful strategies for identifying specific functions.
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In the genomic-sequencing community, many of the major species being studied have special community genomics databases, for example, FlyBase for the fruitfly Drosophila,1 and TAIR for the model plant Arabidopsis.2 This model -- community databases organized to accommodate metagenomics data from particular environments or organisms -- appears to be a promising approach to providing convenient access to the data of metagenomics projects. One major challenge faced by metagenomics databases in contrast with "conventional" genomics databases will be the demand for community input into the annotation process.
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TRAINING AND PUBLIC OUTREACH Metagenomics presents some specific challenges for training experts and some global opportunities for educating the public about microbiology. The interdisciplinary nature of the science of metagenomics necessitates deployment of new training programs to encourage scientists to broaden their skills beyond those learned in their own disciplines.
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SUMMARY explain its scientific basis and implications in accessible and interesting ways. All metagenomics scientists should be encouraged to teach about their science in their local communities.
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