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Workflow for Reconstructing Metabolic Models from Metagenomic Data

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The 2010 DOE Systems Biology Knowledgebase Implementation Plan describes scientific objectives the Knowledgebase will support in microbial, plant, and metacommunity research areas. Illustrated in this figure is an example workflow for metacommunity scientific objective 1, Model Metabolic Processes within Microbial Communities. Characterization of environmental microbial physiology can proceed through two broad approaches: (1) the “bottom-up” approach in which microbes are isolated and cultured in the laboratory and then integrated, evaluated, and modeled in a defined community and (2) the “top-down,” metagenome-based approach in which DNA from environmental samples is directly sequenced for understanding the community’s metabolic potential through bioinformatics and pathway reconstruction. The “bottom-up” approach involves data from individual species or members, and the “top-down” approach relies on whole-metacommunity analysis. This figure illustrates a simplified version of a top-down workflow. Green modules represent capabilities that are reasonably well established. The orange box represents an available method that needs more development. Red boxes show capabilities that still require significant new development.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science.


U.S. DOE. 2010. DOE Systems Biology Knowledgebase Implementation Plan. U.S. Department of Energy Office of Science (p. 64) ( website)

Biological and Environmental Research Information System, Oak Ridge National Laboratory, and