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Exploiting the huge amount of information that is being generated by genome-sequencing projects represents one of the more significant challenges facing microbiologists today. Using 'static' DNA sequences to build an integrated view of microbial life has enormous potential, both to illuminate the fundamental principles of life and to harness the capabilities of microorganisms in tackling problems of an environmental, industrial and clinical nature.

Since the landmark publication of the genome sequence of Haemophilus influenzae in 1995, over 300 microbial genomes have been sequenced to completion. The investment in resources, financial and otherwise, required to achieve this startling progress has been both considerable and unheralded in recent times. This fundamental shift in the microbiology funding landscape has been accompanied by an equally far-reaching change in the research landscape, and it is difficult to argue that some of the more traditional areas of microbiological research have not suffered as a consequence of this new focus. A timely question on the lips of many microbiologists, therefore, is whether the end results have justified the means?

The ultimate goal is the realization of a predictive, systems-level understanding of microorganisms

There is little doubt that the insights gained from genomic information have revolutionized our understanding of the complexity and biology of microbial life. However, these insights represent only a fraction of the potential knowledge waiting to be unlocked. The accurate determination and initial interpretation of the complete DNA sequence of an organism is only the starting point for an integrated understanding of biological function. The ultimate goal is the realization of a predictive, systems-level understanding of microorganisms, derived directly from the genome sequence. The stages in achieving this goal must encompass an understanding of microorganisms at the molecular level, at the whole-cell level and, finally, at the microbial-community and environmental level. Of course, surmounting the technical challenges presented by these multi-scale explorations is a daunting prospect and will require new capabilities in computation, modelling and simulation — all integral parts of a systems-biology approach to understanding microbial life.

With these challenges in mind, one particularly welcome initiative aimed at exploiting genomic investment and ushering in a new 'systems microbiology' era is the United States Department of Energy (DoE) Genomics: Genomes to Life (GTL) Roadmap. Formulated over the past 3 years and drawing on the expertise of >800 scientists, this programme aims to achieve a predictive understanding of the microbial capabilities for applications in energy production, bioremediation and global carbon cycling and sequestration. To achieve this, the roadmap outlines a research programme comprising three phases.

The first phase, projected to last 8 years and with the goal of promoting the transition from genomics to systems biology, will include key proof-of-principle experiments on complex energy and environmental systems. Computing and information technologies will be developed to provide the foundation for data management, analysis and modelling. In the second phase, also envisaged to last 8 years, the high-throughput tools developed will provide an integrated computational environment that links experimental data with the modelling and simulation of microbial systems. To facilitate these processes, the plan calls for the establishment of facilities that will provide the required technologies and state-of-the-art computing to develop a predictive systems-level understanding of microbial life. These facilities would be available to the broader research community and to industry and would have the potential to dramatically increase the pace of translation of basic science into new applications. The end result of this phase should be a reduction in the timeframe for complete analysis of any microbial system from years to months. The final phase of the programme will be the application of the knowledge and capabilities developed in the earlier phases to achieving a fuller understanding of microbial processes, especially those relevant to energy and environmental requirements.

Although the Genomics:GTL Roadmap clearly addresses the needs of one area of microbiology, the opportunities, strategies and solutions outlined could be applied to any field within the microbial sciences in which there has been significant genome-project investment. The plan is currently undergoing review and refinement at the National Academy of Sciences, and the DoE has recently solicited comment and feedback (go to: http://www.doegenomestolife.org/roadmap). As this strategy and its ramifications are of undoubted importance to the future conduct of microbiological research, and to ensure a resounding 'yes' to the question of whether the ends have justified the means, we encourage all interested microbiologists to participate in this process.