Genomics and the bacterial species problem

"The species problem is caused by two conflicting motivations; the drive to devise and deploy categories, and the more modern wish to recognize and understand evolutionary groups. As understandable as it might be that we try to equate these two, and as reasonable and correct as it might be to use taxa as starting hypotheses of evolutionary groups, the problem will endure as long as we continue to fail to recognize our taxa as inherently subjective, and as long as we keep searching for a magic bullet, a concept that somehow makes a taxon and an evolutionary group both one and the same."Jody Hey [1]Thus Jody Hey [1] dismisses the vast and highly philosophical literature on the meaning of the word 'species'. Of course, this literature overwhelmingly addresses species in the context of eukaryote (especially vertebrate) evolution, and seldom tackles the special problems that microbes pose. We microbiologists, to our credit, have often acknowledged that the exercise of formulating a useful 'species definition' and the quest for an underlying 'species concept' are not the exactly same [2-6]. But we too have a 'species problem'.What we want from a species definition is a set of easily applied and stable rules by which to decide when two organisms are similar enough in their genomic and/or phenotypic properties to be given the same name [5-8]. The needs for such a guide to taxonomic practice in medicine, biotechnology and defense are obvious, and even arbitrary rules to satisfy them would be better than no rules at all [9]. We look to a species concept, on the other hand, for a genetic and/or ecological model of bacterial diversification and adaptation. Ideally, this model would make sense of our definition, justifying the choice of one particular set of rules for defining species as less arbitrary, or more natural, than another [2-4,9-14]. Thus, while acknowledging the dual nature of our quest, we still hope for "a concept that somehow makes a taxon and an evolutionary grou