Antonie van Leeuwenhoek

, Volume 101, Issue 1, pp 35–43

What can genome-scale metabolic network reconstructions do for prokaryotic systematics?

  • Francisco Barona-Gómez
  • Pablo Cruz-Morales
  • Lianet Noda-García
Perspective

DOI: 10.1007/s10482-011-9655-1

Cite this article as:
Barona-Gómez, F., Cruz-Morales, P. & Noda-García, L. Antonie van Leeuwenhoek (2012) 101: 35. doi:10.1007/s10482-011-9655-1

Abstract

It has recently been proposed that in addition to Nomenclature, Classification and Identification, Comprehending Microbial Diversity may be considered as the fourth tenet of microbial systematics [Staley JT (2010) The Bulletin of BISMiS, 1(1): 1–5]. As this fourth goal implies a fundamental understanding of microbial speciation, this perspective article argues that translation of bacterial genome sequences into metabolic features may contribute to the development of modern polyphasic taxonomic approaches. Genome-scale metabolic network reconstructions (GSMRs), which are the result of computationally predicted and experimentally confirmed stoichiometric matrices incorporating all enzyme and metabolite components encoded by a genome sequence, provide a platform that can illustrate bacterial speciation. As the topology and the composition of GSMRs are expected to be the result of adaptive evolution, the features of these networks may provide the prokaryotic taxonomist with novel tools for reaching the fourth tenet of microbial systematics. Through selected examples from the Actinobacteria, which have been inferred from GSMRs and experimentally confirmed after phenotypic characterisation, it will be shown that this level of information can be incorporated into modern polyphasic taxonomic approaches. In conclusion, three specific examples are illustrated to show how GSMRs will revolutionize prokaryotic systematics, as has previously occurred in many other fields of microbiology.

Keywords

Genome-scale metabolic network reconstruction Chemotaxons Cardiolipin Menaquinones Natural products Streptomyces Actinobacteria 

Supplementary material

10482_2011_9655_MOESM1_ESM.docx (163 kb)
Supplementary Information. Details on the methods, organisms, genomes and genes analysed herein are provided as supplementary information (DOCX 162 kb)

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Francisco Barona-Gómez
    • 1
  • Pablo Cruz-Morales
    • 1
  • Lianet Noda-García
    • 1
  1. 1.Evolution of Metabolic Diversity Laboratory, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio)CINVESTAV-IPNIrapuatoMexico