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What can genome-scale metabolic network reconstructions do for prokaryotic systematics?
Francisco Barona-Gómez1, Pablo Cruz-Morales, Lianet Noda-García
1Evolution of Metabolic Diversity Laboratory, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), CINVESTAV-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato, Mexico. fbarona@langebio.cinvestav.mx
Antonie Van Leeuwenhoek
|October 22, 2011
Summary
Understanding microbial diversity is the fourth tenet of microbial systematics. Genome-scale metabolic network reconstructions (GSMRs) translate bacterial genomes into metabolic features, aiding in microbial speciation and modern taxonomy.
Area of Science:
- Microbial Systematics
- Computational Biology
- Genomics
Background:
- Microbial systematics traditionally includes nomenclature, classification, and identification.
- Comprehending microbial diversity is proposed as a fourth tenet, requiring a deeper understanding of microbial speciation.
- Bacterial genome sequences offer a potential source of information for advancing microbial systematics.
Purpose of the Study:
- To argue that translating bacterial genome sequences into metabolic features can advance modern polyphasic taxonomic approaches.
- To demonstrate how Genome-scale Metabolic Network Reconstructions (GSMRs) can illustrate bacterial speciation.
- To explore the utility of GSMRs as novel tools for prokaryotic taxonomists.
Main Methods:
- Utilizing Genome-scale Metabolic Network Reconstructions (GSMRs) based on computationally predicted and experimentally confirmed stoichiometric matrices.
- Analyzing the topology and composition of GSMRs as products of adaptive evolution.
- Applying GSMRs to selected examples from Actinobacteria, with experimental phenotypic characterization for confirmation.
Main Results:
- GSMRs provide a platform to illustrate bacterial speciation.
- Features of GSMRs offer novel tools for prokaryotic taxonomy.
- Information from GSMRs, when experimentally confirmed, can be integrated into modern polyphasic taxonomic approaches.
Conclusions:
- GSMRs have the potential to revolutionize prokaryotic systematics.
- The translation of genomic information into metabolic features is key to understanding microbial diversity.
- GSMRs offer a powerful approach to achieving the fourth tenet of microbial systematics.
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