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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.

Field of science

  • /natural sciences/computer and information sciences/databases
  • /natural sciences/biological sciences/genetics and heredity/genome
  • /engineering and technology/environmental biotechnology
  • /engineering and technology/industrial biotechnology/metabolic engineering

Call for proposal

FP7-KBBE-2007-2A
See other projects for this call

Funding Scheme

CP-IP - Large-scale integrating project

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)

COMMISSARIAT A L ENERGIE ATOMIQUE ET AUX ENERGIES ALTERNATIVES
France
EU contribution
€ 567 000
Address
Rue Leblanc 25
75015 Paris 15
Activity type
Research Organisations
Administrative Contact
Régis Copin (Mr.)
ETHNIKO KENTRO EREVNAS KAI TECHNOLOGIKIS ANAPTYXIS
Greece
EU contribution
€ 375 978
Address
Charilaou Thermi Road 6 Km
57001 Thermi Thessaloniki
Activity type
Research Organisations
Administrative Contact
Costas Kiparissides (Prof.)
AGENCIA ESTATAL CONSEJO SUPERIOR DEINVESTIGACIONES CIENTIFICAS
Spain
EU contribution
€ 375 979
Address
Calle Serrano 117
28006 Madrid
Activity type
Research Organisations
Administrative Contact
Carlos Manuel Abad Ruiz (Mr.)
FUNDACION CENTRO NACIONAL DE INVESTIGACIONES ONCOLOGICAS CARLOS III
Spain
EU contribution
€ 250 481
Address
Calle Melchor Fernandez Almagro 3
28029 Madrid
Activity type
Research Organisations
Administrative Contact
Ralf Dahm (Dr.)
LEIBNIZ-INSTITUT DSMZ-DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH
Germany
EU contribution
€ 321 999
Address
Inhoffenstrasse 7B
38124 Braunschweig
Activity type
Research Organisations
Administrative Contact
Heike Bauer (Dr.)
HELMHOLTZ-ZENTRUM FUR INFEKTIONSFORSCHUNG GMBH

Participation ended

Germany
Address
Inhoffenstrasse 7
38124 Braunschweig
Activity type
Research Organisations
Administrative Contact
Michael Stratz (Dr.)
Isthmus
France
EU contribution
€ 242 480
Address
Rue Saint Amand 31
75015 Paris
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Philippe Marlière (Dr.)
MOLECULAR NETWORKS GMBH COMPUTERCHEMIE
Germany
EU contribution
€ 239 800
Address
Neumeyerstr 28-34
90411 Nurnberg
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Christof H. Schwab (Dr.)
SIB INSTITUT SUISSE DE BIOINFORMATIQUE
Switzerland
EU contribution
€ 275 980
Address
Rue Michel Servet 1 Cmu
1206 Geneve
Activity type
Research Organisations
Administrative Contact
Jocelyne Bocquet (Ms.)
UNIVERSITE LIBRE DE BRUXELLES
Belgium
EU contribution
€ 250 481
Address
Avenue Franklin Roosevelt 50
1050 Bruxelles
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Jacques Van Helden (Prof.)
GENOME RESEARCH LIMITED
United Kingdom
EU contribution
€ 321 756
Address
The Gibbs Building, Euston Road 215
NW1 2BE London
Activity type
Research Organisations
Administrative Contact
David Davison (Mr.)
TEL AVIV UNIVERSITY
Israel
EU contribution
€ 417 152
Address
Ramat Aviv
69978 Tel Aviv
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Lea Pais (Ms.)
Ceprodi Compagnie Europeenne de Produits Diabetiques

Participation ended

France
EU contribution
€ 124 091,24
Address
Bd De Courcelles 67
75008 Paris
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
David Dieumegard (Mr.)
WAGENINGEN UNIVERSITY
Netherlands
EU contribution
€ 464 476
Address
Droevendaalsesteeg 4
6708 PB Wageningen
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Tom Bessems (Mr.)
AMABIOTICS SAS
France
EU contribution
€ 159 496,76
Address
Rue Gaston Cremieux 2
91000 Evry
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Chantal Rougier (Ms.)