Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes

doi:10.1186/gb-2009-10-3-r28

Genome Biology

Volume 10
Issue 3

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Schenk ME
Gasteiger J
Mewes HW

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Mewes HW
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Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes

Gabi Kastenmüller¹ , Maria Elisabeth Schenk¹ , Johann Gasteiger²^,3 and Hans-Werner Mewes¹^,4

¹Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstraße, D-85764 Neuherberg, Germany

²Computer-Chemie-Centrum, Universität Erlangen-Nürnberg, Nägelsbachstraße, D-91052 Erlangen, Germany

³Molecular Networks GmbH, Henkestraße 91, D-91052 Erlangen, Germany

⁴Chair for Genome-oriented Bioinformatics, Technische Universität München, Life and Food Science Center Weihenstephan, Am Forum 1, D-85354 Freising-Weihenstephan, Germany

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Genome Biology 2009, 10:R28doi:10.1186/gb-2009-10-3-r28


Published:	10 March 2009

Subject areas: Bioinformatics, Methods, Microbiology and parasitology

Abstract

Identifying the biochemical basis of microbial phenotypes is a main objective of comparative genomics. Here we present a novel method using multivariate machine learning techniques for comparing automatically derived metabolic reconstructions of sequenced genomes on a large scale. Applying our method to 266 genomes directly led to testable hypotheses such as the link between the potential of microorganisms to cause periodontal disease and their ability to degrade histidine, a link also supported by clinical studies.