New approaches to improve the bacterial species definition

Abstract

Taxonomy is a scientific specialty that, as a final goal, produces a classification system of biological units that serves as a communication tool among scientists of different disciplines. The research activities in the taxonomy of prokaryotes have improved concurrently with technological developments, especially in molecular biology. For many years, microbiologists have recognised that the number of described microbial/bacterial species is much too small in comparison with the expected diversity thriving in the biosphere. There is general agreement that taxonomists need to speed up the process of classifying prokaryotes. However, it seems that, at least, in western countries, the number of taxonomists is suffering a decline in promoting taxonomic expertise [1]. Contrarily, there is a significant increase in taxonomic activities in eastern countries, which has been responsible for most of the current growth in new microbial descriptions in taxonomic journals. Unfortunately, most of the new classifications are based on single isolates and often are restricted to the minimal standards guaranteeing the publication. Both of these recent practices create significant problems for the stability and operationality of the classification system. The new ‘-omic’ technologies offer important advantages also for taxonomy [2]. The generation of extensive databases that can be used interactively can help in modernizing taxonomy. In this regard, genetic tools, such as the LTP [3] and JSpecies [4] can improve and enhance the species descriptions at the genotypic level. However, phenotypic-based methods, such as MALDI-TOF Mass Spectrometry of whole cell profiles [5] and metabolic profiling by means of high-resolution mass spectrometry [6] seem to be promising tools for classification and identification