Objectif
The exponential increase in microbial genome and metagenome sequencing throughput has widened the gap between sequence and functional understanding. A clear picture of metabolic processes across the spectrum of bacterial species is essential to enable the exploitation of microbial genomics for the purposes of environmental biotechnology. The Microme project endeavors to extend the scope of microbial genome annotation from functional assignment at the gene level to the systematic generation of pathway assemblies and genome-scale metabolic models. A few key ideas and design principles will enable the Microme reconstruction pipeline to achieve this ambitious goal.A clear definition of a metabolic pathway as a collection of reaction sets, each of which convert the same defined inputs into the same outputs, will allow species-specific pathway variants to be identified, assembled into networks, compared across species, and used for downstream computations. A unique pathways projection, curation and assembly cycle, feeding directly into the flow of newly sequenced genomes, will allow a qualitative increase in the speed and reliability of the pathway generation process. Pathways and models produced the pipeline will be accessible to the scientific community as an integrated resource via the Microme portal. Finally, taking advantage of the availability of pathway assemblies from a large sample of genomes, methods for comparative and phylogenetic analyses and novel metabolic engineering strategies for environmental biotechnology goals will be developed, applied to proof-of-concept studies, and integrated to the resource as an analytical tool layer. Microme will be supported by a robust bioinformatics infrastructure, developed by integrating a set of established European databases and tools, integrated with reference protein annotation, metabolites and reactions databases, and interfaced with the annotation pipelines of the two main European sequencing centers.
Champ scientifique
Thème(s)
Appel à propositions
FP7-KBBE-2007-2A
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Régime de financement
CP-IP - Large-scale integrating projectCoordinateur
69117 Heidelberg
Allemagne
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Participants (15)
75015 PARIS 15
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57001 Thermi Thessaloniki
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28006 Madrid
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28029 Madrid
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38124 Braunschweig
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Participation terminée
38124 Braunschweig
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75015 Paris
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90411 Nurnberg
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1206 Geneve
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1050 Bruxelles / Brussel
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CB10 1SA SAFFRON WALDEN
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69978 Tel Aviv
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Participation terminée
75008 Paris
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6708 PB Wageningen
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91000 EVRY
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