The New Science of Metagenomics Revealing the Secrets of Our Microbial Planet (2007) / Chapter Skim
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7 A Balanced Portfolio: Multi-Scale Projects in the "Global Metagenomics Initiative"
7 A Balanced Portfolio: Multi-Scale Projects in the "Global Metagenomics Initiative"
Pages 107-123
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From page 107... ...
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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From page 108... ...
Providing a community data resource was the initial motivation, but the Human Genome Project and other model-organism genome projects have also spurred technological advances and inspired the development of new tools, common standards, and shared software resources. This chapter will argue that the potential value of large-scale metagenomics projects is substantial.
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From page 109... ...
WHY METAGENOMICS NEEDS A "BIG SCIENCE" COMPONENT Metagenomics has great promise, but is challenged by the extreme complexity of microbial communities, by the lack of sufficient data on many aspects of microbial communities (such as diversity and conservation of structure or function across geographic location) to support valid generalizations and, because of these factors, by the lack of unifying ecological principles that enable predictive modeling.
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From page 110... ...
? different times Do all human guts share a core Implement clustering methods for community?
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From page 111... ...
A global project might tackle one of these habitats from many angles -- sequencing, functional-expression analysis, genome reassembly, deep phylogenetic analysis, hybridization-based screening, and much more. A large-scale project could involve investigators in many disciplines such as genomicists, statisticians, geneticists, physicians, and sociologists.
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From page 112... ...
Information about habitat will also often need to include historical trends in these variables. Interoperable but separate model community databases would be the most efficient framework in which to develop the specific tools necessary to analyze data from the different environments and thereby maximize the utility of the data.
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From page 113... ...
Just as studies of different microbial communities face different technical challenges, they also raise different theoretical issues: • Study of a community in a natural environment would act as "proof of concept" for using metagenomics to understand the interaction between microbial communities and geochemical processes, eventually helping to understand change in global elemental cycles. • Study of a host-associated community would probe the interaction between a microbial community and the physiology and health of its host.
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From page 114... ...
These multidisciplinary groups would have the resources to develop new technical approaches useful to all metagenomics studies. The projects would also serve as incubators and evaluators of novel technologies, more precise and automated measures of conditions, 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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From page 115... ...
LEARNING FROM PREVIOUS LARGE-SCALE GENOMICS PROJECTS Several collaborative research projects comparable with the proposed global metagenomics projects yielded important transformative science, such as the human and Arabidopsis genome sequencing efforts. An examination of the history of these projects reveals factors that proved to be crucial to their success.
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From page 116... ...
Common data standards helped to enable this, and the discrete nature of chromosomes helped to organize the effort. Rapid data release and globally available databases ensured open sharing of information.
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From page 117... ...
Some members of the AGI lobbied for immediate data release as was the practice in the HGP, but there was considerable disagreement among the participants and their funders on this point, and public availability of data ranged from deposition of a draft sequence in GenBank within 24 hours of its generation to data release only when a sequence was finished and annotated. Data release was a subject of continuing discussion throughout the project, and the participants finally agreed to disagree about it.
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From page 118... ...
Through the implementation of open communication and clear procedures, a plan for a joint annotation effort between the Institute for Genomic Research and the Munich Information Center for Protein Sequences was established. LESSONS FOR METAGENOMICS The HGP and AGI provide valuable lessons for implementing a successful Global Metagenomics Initiative.
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From page 119... ...
, a specific model community will need to be chosen. The following criteria characterize communities that will yield the most useful data: • A community in which there is some fundamental understanding of the major functions and roles of the microbes and in which there would be a distinct benefit in improving that understanding, such as the microbial community colonizing the human gut or oral cavity.
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From page 120... ...
Model metagenomics communities should be chosen to leverage past knowledge and current research. Several funding agencies target long-term investigation of particular communities or environments, including NSF's LTER Network,1 NSF's and USDA's Microbial Observatories,2 and NSF's NEON.3 Phase I would include one or more workshops to develop a consensus on at least three and perhaps up to 10 communities as possible objects of a large-scale project.
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From page 121... ...
(>200,000) Determine how environmental Produce extensive sequence change affects substrate information about the use, polymer degradation, metagenome in soils under and secondary metabolite different regimes production Conduct a function-based Describe the distribution analysis of the metagenome of characteristics in the of soil under each regime community Microbial Conduct an extensive analysis Establish relationships between community of 16S rRNA sequences particular functions or associated Construct extensive members of the communities with managed metagenomic communities and community persistence ecosystems from habitat in various and collapse that perform a locations; characterize with Identify organisms, traits, service (such as sequencing and functional or chemical conditions bioremediation or analysis that prevent or reverse sludge processing)
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From page 122... ...
The Human Genome Project captured society's imagination with the promise of a deeper understanding of the basis of human health. Well-chosen metagenomics initiatives could similarly inspire with the promise of understanding of the microbial communities that contribute not only to human health but to the health of the biosphere (see Box 7-1)
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From page 123... ...
A BALANCED PORTFOLIO BOX 7-1 Key Outcomes of Large-Scale Projects in the Global Metagenomics Initiative • Broad principles and unifying theory for microbial-community ecology. • Large-scale, intensive studies of important habitats or questions.
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