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Microbial taxonomy in the post-genomic era: rebuilding from scratch?
Cristiane C Thompson1, Gilda R Amaral, Mariana Campeão
1Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil, thompsoncristiane@gmail.com.
Archives of Microbiology
|December 24, 2014
Summary
Microbial taxonomy needs an update to accurately describe diverse microbes. A shift towards genomic-based classification using high-quality genome sequences is proposed as the new standard.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Current microbial taxonomy struggles to adequately describe bacterial, archaeal, and eukaryotic microbial diversity.
- The prokaryote species concept, central to taxonomy, has undergone re-evaluation twice.
- Polyphasic taxonomy, its principles, and its pragmatic species concept require revisiting.
Purpose of the Study:
- To propose a re-evaluation of polyphasic taxonomy.
- To advocate for a transition towards a genomic-based microbial taxonomy.
- To establish high-quality complete genome sequences as the new gold standard.
Main Methods:
- Review of current taxonomic principles and practices.
- Analysis of the pragmatic species concept in microbial taxonomy.
- Proposal for a future genomic-based approach.
Main Results:
- Identification of limitations in current polyphasic taxonomy.
- A clear need for a revised approach to microbial species definition.
- The potential for genomic data to revolutionize microbial classification.
Conclusions:
- A genomic-based microbial taxonomy is achievable and necessary.
- Standardized and automated curation of complete genome sequences is crucial.
- This approach fulfills a long-standing goal in microbial taxonomy.
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