title: The Time Is Right to Focus on Model Organism Metabolomes.
abstract: Model organisms are an essential component of biological and biomedical research that can be used to study specific biological processes. These organisms are in part selected for facile experimental study. However, just as importantly, intensive study of a small number of model organisms yields important synergies as discoveries in one area of science for a given organism shed light on biological processes in other areas, even for other organisms. Furthermore, the extensive knowledge bases compiled for each model organism enable systems-level understandings of these species, which enhance the overall biological and biomedical knowledge for all organisms, including humans. Building upon extensive genomics research, we argue that the time is now right to focus intensively on model organism metabolomes. We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to relate organism metabolic pathways within the context of evolutionary metabolomics, i.e., phylometabolomics. These efforts should focus on a series of established model organisms in microbial, animal and plant research.
authors.affiliation: Departments of Genetics and Biochemistry, Complex Carbohydrate Research Center and Institute of Bioinformatics, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA. aedison@uga.edu.
authors.forename: Arthur S
authors.initials: AS
authors.lastname: Edison
authors.affiliation: Wageningen University &amp; Research Centre, PO Box 16, 6700AA Wageningen, The Netherlands. robert.hall@wur.nl.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Hall
authors.affiliation: CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, CEA Saclay, Building 136, 91191 Gif-sur-Yvette cedex, France. christophe.junot@cea.fr.
authors.forename: Christophe
authors.initials: C
authors.lastname: Junot
authors.affiliation: Bioinformatics Research Group, SRI International, 333 Ravenswood Avenue AE206, Menlo Park, CA 94025, USA. pkarp@ai.sri.com.
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
authors.affiliation: Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA. irwin.kurland@einstein.yu.edu.
authors.forename: Irwin J
authors.initials: IJ
authors.lastname: Kurland
authors.affiliation: HighChem LLC, Leskova 11, 81105 Bratislava, Slovakia. robert.mistrik@highchem.com.
authors.forename: Robert
authors.initials: R
authors.lastname: Mistrik
authors.affiliation: Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA. lreed1@ua.edu.
authors.forename: Laura K
authors.initials: LK
authors.lastname: Reed
authors.affiliation: RIKEN Center for Sustainable Resource Science, Yokohama 230-0045; Chiba University, Chiba 260-8675, Japan. kazuki.saito@riken.jp.
authors.forename: Kazuki
authors.initials: K
authors.lastname: Saito
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. reza.salek@ebi.ac.uk.
authors.forename: Reza M
authors.initials: RM
authors.lastname: Salek
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. steinbeck@ebi.ac.uk.
authors.forename: Christoph
authors.initials: C
authors.lastname: Steinbeck
authors.affiliation: University of Missouri, Department of Biochemistry, Columbia, MO 65211, USA. sumnerlw@missouri.edu.
authors.forename: Lloyd W
authors.initials: LW
authors.lastname: Sumner
authors.affiliation: School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK. m.viant@bham.ac.uk.
authors.forename: Mark R
authors.initials: MR
authors.lastname: Viant
keywords: Arabidopsis thaliana; Caenorhabditis elegans; Danio rerio; Daphnia magna; Drosophila melanogaster; Escherichia coli; Mus musculus; Oryza sativa; Saccharomyces cerevisiae; Solanum lycopersicum