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The Microme Project: A Knowledge-Based Bioinformatics Framework for Microbial Pathway Genomics

The Microme Project: A Knowledge-Based Bioinformatics Framework for Microbial Pathway Genomics

Objective

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.
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Coordinator

EUROPEAN MOLECULAR BIOLOGY LABORATORY

Address

Meyerhofstrasse 1
69117 Heidelberg

Germany

Activity type

Research Organisations

EU Contribution

€ 876 000

Administrative Contact

Tom Ratcliff (Mr.)

Participants (15)

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COMMISSARIAT A L ENERGIE ATOMIQUE ET AUX ENERGIES ALTERNATIVES

France

EU Contribution

€ 567 000

ETHNIKO KENTRO EREVNAS KAI TECHNOLOGIKIS ANAPTYXIS

Greece

EU Contribution

€ 375 978

AGENCIA ESTATAL CONSEJO SUPERIOR DEINVESTIGACIONES CIENTIFICAS

Spain

EU Contribution

€ 375 979

FUNDACION CENTRO NACIONAL DE INVESTIGACIONES ONCOLOGICAS CARLOS III

Spain

EU Contribution

€ 250 481

LEIBNIZ-INSTITUT DSMZ-DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH

Germany

EU Contribution

€ 321 999

HELMHOLTZ-ZENTRUM FUR INFEKTIONSFORSCHUNG GMBH

Germany

Isthmus

France

EU Contribution

€ 242 480

MOLECULAR NETWORKS GMBH COMPUTERCHEMIE

Germany

EU Contribution

€ 239 800

SIB INSTITUT SUISSE DE BIOINFORMATIQUE

Switzerland

EU Contribution

€ 275 980

UNIVERSITE LIBRE DE BRUXELLES

Belgium

EU Contribution

€ 250 481

GENOME RESEARCH LIMITED

United Kingdom

EU Contribution

€ 321 756

TEL AVIV UNIVERSITY

Israel

EU Contribution

€ 417 152

Ceprodi Compagnie Europeenne de Produits Diabetiques

France

EU Contribution

€ 124 091,24

WAGENINGEN UNIVERSITY

Netherlands

EU Contribution

€ 464 476

AMABIOTICS SAS

France

EU Contribution

€ 159 496,76

Project information

Grant agreement ID: 222886

Status

Closed project

  • Start date

    1 December 2009

  • End date

    30 November 2013

Funded under:

FP7-KBBE

  • Overall budget:

    € 7 527 543,53

  • EU contribution

    € 5 263 150

Coordinated by:

EUROPEAN MOLECULAR BIOLOGY LABORATORY

Germany