The New Science of Metagenomics Revealing the Secrets of Our Microbial Planet (2007) / Chapter Skim
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8 Recommendations
8 Recommendations
Pages 124-133
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From page 124... ...
Because so little is known about microbial communities, the potential for discovery is great in any habitat chosen for study. The committee identified eight potential opportunities in different application areas that can be addressed with metagenomics: • Earth Sciences: The development of genome-based microbial ecosystem models to describe and predict global environmental processes, change, and sustainability.
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From page 125... ...
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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From page 126... ...
The medium-sized projects will provide centers of study that unite diverse techniques and disciplines to study numerous habitats encompassing diverse organisms, scientific questions, and technical challenges. The large-scale projects will characterize a few microbial habitats in great depth, using large multidisciplinary and multinational teams to address challenges in metagenomics that require massive datasets or highly diversified scientific approaches and engaging more investigators than would typically participate in a medium-sized center.
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From page 127... ...
To maximize the benefits and knowledge gained from the large-scale projects, they should represent a breadth of habitat type, including: • A community in a natural environment, to understand the interactions between microbial communities and geochemical processes or global nutrient cycles. • A host-associated community, to probe the interactions between a microbial community and the physiology and health of its host.
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From page 128... ...
Scientific societies also can play a critical role in ensuring broad participation. RECOMMENDATION 2 The committee recommends that an interagency working group like the Microbe Project take responsibility for ensuring open communication about the metagenomics portfolios of relevant agencies and for facilitating the organization of workshops and meetings to bring together metagenomics researchers who are working on different types of communities.
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From page 129... ...
RECOMMENDATION 3 The committee recommends establishing several types of training programs to encourage scientists to develop the skills needed for metagenomics research. The following mechanisms have been successful in providing cross-disciplinary training: interdisciplinary training to augment traditional
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From page 130... ...
No one metadata standard will be appropriate for all samples, which will come from extremely diverse environments, but there should be close collaboration and coordination among the communities of scientists developing metadata standards. One major challenge faced by metagenomics databases compared with "conventional" genomics databases will be the demand for community input into the annotation process.
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From page 131... ...
Funding for databases requires a different approach than that for research projects: the committee recommends the development of mechanisms for long-term funding, coupled with community oversight and evaluation. The enormous amounts of data generated by metagenomics should be made available as rapidly as possible, and deposition into the international sequence archives should be required.
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From page 132... ...
And expression systems for functional metagenomics are not yet sufficiently robust and flexible to express most genes in most metagenomes. RECOMMENDATION 6 The committee recommends investment in the following because improvements would enhance the productivity of many metagenomics projects: new or improved technologies for appropriate habitat sampling, macromolecule recovery, and habitat characterization, depending on habitat; new approaches to deal with the unevenness of population sizes in communities and to target populations of interest within complex communities; development of measures of community diversity to supplement 16S rRNA gene surveys, including arrays and additional phylogenetically informative genetic markers; and development of diverse host species and expression strategies for functional-expression analyses.
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From page 133... ...
RECOMMENDATION 8 The committee recommends that education and public outreach be components of all metagenomics projects. Both large and small projects can be used as catalysts for teaching microbiology.
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