Taxonomy is the science of classification, identification, and nomenclature. For classification purposes, organisms are usually organized into subspecies, species, genera, families, and higher orders. For eukaryotes, the definition of the species usually stresses the ability of similar organisms to reproduce sexually with the formation of a zygote and to produce fertile offspring. However, bacteria do not undergo sexual reproduction in the eukaryotic sense. Other criteria are used for their classification.
Classification is the orderly arrangement of bacteria into groups. There is nothing inherently scientific about classification, and different groups of scientists may classify the same organisms differently. For example, clinical microbiologists are interested in the serotype, antimicrobial resistance pattern, and toxin and invasiveness factors in Escherichia coli, whereas geneticists are concerned with specific mutations and plasmids.
Identification is the practical use of classification criteria to distinguish certain organisms from others, to verify the authenticity or utility of a strain or a particular reaction, or to isolate and identify the organism that causes a disease.
Nomenclature (naming) is the means by which the characteristics of a species are defined and communicated among microbiologists. A species name should mean the same thing to all microbiologists, yet some definitions vary in different countries or microbiologic specialty groups. For example, the organism known as Clostridium perfringens in the United States is called Clostridium welchii in England.
A bacterial species is a distinct organism with certain characteristic features, or a group of organisms that resemble one another closely in the most important features of their organization. In the past, unfortunately, there was little agreement about these criteria or about the number of features necessary to distinguish a species. Species were often defined solely by such criteria as host range, pathogenicity, or ability to produce gas during the fermentation of a given sugar. Without a universal consensus, criteria reflected the interests of the investigators who described a particular species. For example, bacteria that caused plant diseases were often defined by the plant from which they were isolated; also, each new Salmonella serotype that was discovered was given species status. These practices have been replaced by generally accepted genetic criteria that can be used to define species in all groups of bacteria.