Metagenomics is an emerging field in which the power of genomic analysis (the analysis of all the DNA in an organism) is applied to entire communities of microbes, bypassing the need to isolate and culture individual microbial species.
The Metagenomics Process [top]
Metagenomics includes a wide variety of novel techniques and approaches, and it is likely that other new methods will arise as the field progresses. Here are some of the basic steps:
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- Researchers often start a metagenomics project by taking a sample of a particular environment (such as soil, seawater, or the human mouth) and extracting the DNA from all the microbes in the sample.
- This genetic information is then studied to reveal important characteristics of the microbial community.
- In sequence-based metagenomics, researchers study the entire genetic sequence-the pattern of the four different nucleotide bases (A, C, G, and T) in the DNA strands-found in a sample.
- In function-based metagenomics, researchers screen the extracted genes for various functions, such as vitamin or antibiotic production. New antibiotics have already been discovered using this approach.
Why Metagenomics? [top]
What's so exciting about metagenomics? A lot.
- The tools of classical genomics and microbiology largely rely on isolating individual microbial species in pure cultures—that is, cultures containing only microbes of a particular species.
- This means that the vast majority of the microbial world has been inaccessible to science because merely a miniscule fraction—most scientists estimate less than 1%—of the estimated millions of microbial species on Earth can be cultured.
- By allowing scientists to access a community's genome without relying on pure cultures, metagenomics transcends the limitations of classical genomics and microbiology.
- Metagenomics gives scientists access to millions of microbes that have not previously been studied.
Applications [top]
The possibilities this new field offers are mind-boggling. Studying microbial communities can lead to advances in...
Challenges and Needs [top]
The National Research Council report
The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet (2007) addresses the challenges and opportunities metagenomics holds for the future of microbiology. The report describes a number of technological, methodological, and computational advances that are needed before metagenomics can reach its full potential. Below are some of the report's conclusions. For full discussion of these issues, please
see the report.
Development of improved tools and methods:
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- Scientists must determine how to best sample an environment, how many times samples should be taken, and whether a sample is representative of the environment.
- Improved DNA extraction techniques could help ensure that the DNA extracted from a sample adequately represents the entire community's genome and has little or no contamination.
- Studying the proteins and metabolites (the products of cellular processes) generated by a microbial community will help describe how the community operates and interacts with its habitat.
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Data management and bioinformatics needs:
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- Metagenomics data should be stored in databases that use common standards and are freely accessible to all.
- Databases should include specialized tools that enable different scientists to analyze the data in different ways.
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Institutional frameworks:
- A broad range of fields; including chemistry, genetics, microbiology, biochemistry, pathology, ecology, evolution, soil and atmospheric sciences, geology, oceanography, statistics, computer sciences, database development, mathematics, engineering, and others have applicability to metagenomics.
- Universities will need to rapidly evolve their educational, administrative, and mentoring structures to facilitate interdisciplinary collaboration to help metagenomics reach its full potential.
- Communication and coordination across the relevant state and federal government agencies would be extremely useful in advancing the field.
Establishing a "Global Metagenomics Initiative"
- A Global Metagenomics Initiative should be established that includes a small number of large-scale, comprehensive projects, a larger number of medium-sized projects, and many small-scale projects.
- Large-scale projects will each explore a microbial community in great depth, analyzing a habitat with attention to potential for discovery, variation, commonalities, and detailed investigation. Possible candidate communities include:
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 A community in a natural environment (such as seawater or soil),
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A host-associated community (such as the microbes in the human gut or mouth), and
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A "managed" environment community (such as a sewage treatment facility or bioremediation site).
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- Medium-sized projects will encompass the greater diversity of microbial habitat types and should include a multidisciplinary approach.
- Small-scale projects will be initiated by individual scientists to examine a slice of a community, a particular function in multiple communities, or a specific technical advance.
For More Information [top]
The information on this Web page was derived from the National Research Council report The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet (2007) and the 20-page educational booklet derived from that report, Understanding Our Microbial Planet: The New Science of Metagenomics.
PHOTO CREDITS: (from top) Metagenomics at work in the laboratory of Jo Handelsman photo courtesy Jeff Miller, University of Wisconsin-Madison; Microbes photos courtesy (from left) Michael Abbey, Pacific Northwest National Laboratory, NASA, UCMP Berkeley; Metagenomics at work in the laboratory of Jo Handelsman photo courtesy Jo Handelsman, University of Wisconsin-Madison.
Support for this web publication was provided by the Presidents' Circle Communication Initiative of the National Academies.
