The problem of species and in particular microbial species is central in biology. An active collaboration of
various specialists such as taxonomists, epistemologists, mathematicians and bioinformatics experts is desirable for its
This article intended to show the possibilities and perspectives of bioinformatics research in understanding the ontological
problem of species, i.e. the problem of the existence of the microbial species. The approach undertaken of this paper is
based on the concept that if microbial species exist, then there should be detectable discontinuities or disconnections
between microorganisms assigned to different species. A yeast model has been used to show how the distances from a
reference organism raise with the increase of the number of different strains included in the study.