Project objectives and structure
The Microme project is a four-year collaborative project funded from December 2009-Framework Programme 7 of the European Commission, and developed around eight work packages. Microme will produce four primary products:
(i) a curated database of reference pathways and variants
(ii) a set of genome-scale metabolic networks, each for a given bacterial species; these so-called pathway assemblies will be structured in terms of the pathway variants represented in that organism
(iii) a set of genome-scale, constraint-based metabolic models derived from the networks
(iv) a publicly accessible web portal, where Microme data can be interactively explored, comparative analyses of pathways and online simulations with models performed, and from which Microme data can be downloaded.
WP1 and WP2 are focused on the establishment of the pathway repository and projection system. WP3 is focused on using these projected networks to construct metabolic models. WP4 is focused on the comparative and evolutionary analysis of metabolic pathways, developing methods and software, and producing targeted case studies that will demonstrate the utility of the database and associated tools. WP5 develops metabolic engineering strategies to exploit the Microme resource in the service of white biotechnology and environmental sustainability objectives. The work performed in the context of WPs 3, 4 and 5 will not only feed off the pathways repository established in WP1 and 2, but also contribute the repository’s content, and to the development of new/improved tools for pathway integrity checking and projection. WP6 integrates this content in a single web portal. WP 7 and 8 address outreach/training, and internal project management, respectively.
Expected final results and their potential impact and use
The development of high throughout genome sequencing technologies has enormous potential to increase our understanding of basic biology and to develop biotechnological applications. However, genome sequence alone does not tell us how an organism responds to its environment, or and what catalytic activities is uses (and in which combination) to do so. Microme will develop both a data set and a tool set to address these questions, tested in the context of specific in vivo and in silico experimental data generated in the course of the project. The outputs will be a sustainable infrastructure for the integrated storage, analysis and dissemination of molecular, pathway and genome data, integrated with other reference resources and capable of scaling to thousands of genome sequences; a set of novel methodologies exploiting the existence of data from many species for the understanding of individual species or biological problems, utilising systems biology and evolutionary approaches; and a set of tools for the application of this knowledge for the design of biosynthetic strategies capable of utilising the natural repertoire of chemical transformations for applications in green and white biotechnology.