Modern Classification Scheme of Microorganisms
Now all cellular forms of living world are grouped into major clusters known as domains. Domain is the highest taxon of current biological classification.
There are 3 domains: Bacteria, Archaea, Eukarya.
Domains Bacteria and Archaea comprise microbial agents without cell nucleus (prokaryotic domains).
Domains Bacteria and Archaea are divided into phyla. Domain Bacteria now includes 23 bacterial phyla.
Domain Eukarya (or Eukaryota) contains biological organisms with cellular nucleus. Until quite recently this domain was divided into kingdoms: Fungi, Protista, Cromista, Plantae, and Animalia.
Kingdom Fungi encompasses 7 phyla. The phyla Ascomycota and Basidiomycota harbor the certain fungal agents that cause the disorders in humans. The members of phyla Ascomycota and Basidiomycota are separately placed into sub-kingdom Dikarya as the fungi with sexual reproduction and dicaryon formation.
The most entangled is the situation with protozoan taxonomy. Protozoa were primarily placed into separate kingdom Protista. In 2005 International Society of Protistologists proposed to re-classify all the domain Eukarya on monophyletic principle. Monophyletic principle presumes hierarchic division of biological objects originated from common ancestor (phylogenetic tree). Phylogenetic relationships (distances) between various groups of organisms are determined by molecular genetic methods. Last revision of new classification was published in 2012.
On this ground, the whole domain of Eukarya was re-exposed as 5 great genetic clusters termed as super-groups (or genetic clades). Former kingdom Protista was proven to be polyphyletic. Thus, various groups of protozoans were spread throughout clades Alveolata (with phyla Apicomplexa and Ciliophora), Excavata (phylum Metamonada), and Amoebozoa.
As the result of rapid progress of molecular genetic analysis, this division is not stable yet and can be regarded as provisional. Following the gain of new experimental data, this classification should be re-ascertained.
Subsequent more low taxonomy units for bacteria are: class, order, family, genus, and species.
Species is the most common unit in microbial taxonomy. In contrast with higher organisms, bacterial species is unstable category. It is the subject of permanent evolution resulting in rapid environmental adaptation of bacteria. Species ability of easy alterations is largely based on lateral gene transfer that occurs not only among related bacterial species but also between distant microbial groups (genera or families).
The correct definition of a species is always a difficult problem in microbial classification, thereby many variations of species definition were proposed.
In medical microbiology species presumes the populations of microorganisms of the common origin with closely related genotypes, properties and area of habitation, which possess genetically fixed ability to induce similar reactions in the affected organism or in the external environment.
For microbial designation the binominal nomenclature is accepted where each species has a generic and a specific name. The generic name is written in italicized upper case, and the specific name – in lower case. For instance, pathogenic staphylococcus of golden color is called Staphylococcus aureus, the anthrax bacillus – Bacillus anthracis, the diphtheria causative agent – Corynebacterium diphtheriae, etc.
If the differences with the typical species characteristics are found on examination of isolated bacteria, the culture is regarded as subspecies. Subspecies is the lowest taxonomic rank in official nomenclature.
The term strain designates a microbial population of the same species isolated from different sources, or even from the same source, but in a different period of time.
Strains are identified by all properties, thoroughly described, acquire legend with number, date and site of isolation and placed into strain collection. Usually the members of the same strain demonstrate homology of genomic DNA more than 95%.
Class Gammaproteobacteria Order Thiotrichales
Family Nocardiaceae Genus Nocardia
If the description is not completed, the strain is termed as bacterial isolate (clinical or environmental).
Other infraspecies subdivisions in bacteria are known as variants (suffix –var for short). Usually they are beyond the lines of official classification indicating the differences in certain microbial properties like antigenic – serovar (syn. serotype), or morphological – morphovar, chemical – chemovar, biochemical or physiological – biovar, pathogenic – pathovar, bacteriophage susceptibility – phagovar, etc.