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Metabolites 2016, 6(1), 8; doi:10.3390/metabo6010008

The Time Is Right to Focus on Model Organism Metabolomes

1
Departments of Genetics and Biochemistry, Complex Carbohydrate Research Center and Institute of Bioinformatics, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
2
Wageningen University & Research Centre, PO Box 16, 6700AA Wageningen, The Netherlands
3
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
4
Bioinformatics Research Group, SRI International, 333 Ravenswood Avenue AE206, Menlo Park, CA 94025, USA
5
Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA
6
HighChem LLC, Leskova 11, 81105 Bratislava, Slovakia
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Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
8
RIKEN Center for Sustainable Resource Science, Yokohama 230-0045; Chiba University, Chiba 260-8675, Japan
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European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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University of Missouri, Department of Biochemistry, Columbia, MO 65211, USA
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School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
*
Author to whom correspondence should be addressed.
Academic Editor: Peter Meikle
Received: 18 December 2015 / Revised: 30 January 2016 / Accepted: 2 February 2016 / Published: 15 February 2016
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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. View Full-Text
Keywords: Escherichia coli; Saccharomyces cerevisiae; Caenorhabditis elegans; Danio rerio; Daphnia magna; Drosophila melanogaster; Mus musculus; Arabidopsis thaliana; Oryza sativa; Solanum lycopersicum Escherichia coli; Saccharomyces cerevisiae; Caenorhabditis elegans; Danio rerio; Daphnia magna; Drosophila melanogaster; Mus musculus; Arabidopsis thaliana; Oryza sativa; Solanum lycopersicum
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Edison, A.S.; Hall, R.D.; Junot, C.; Karp, P.D.; Kurland, I.J.; Mistrik, R.; Reed, L.K.; Saito, K.; Salek, R.M.; Steinbeck, C.; Sumner, L.W.; Viant, M.R. The Time Is Right to Focus on Model Organism Metabolomes. Metabolites 2016, 6, 8.

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