Modern Classification Scheme of Microorganisms

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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%.

 

Phylum Proteobacteria

Class Alphaproteobacteria

Order Rickettsiales

Family Rickettsiaceae

Genus Rickettsia

Genus Orientia

Genus Wolbachia

Family Anaplasmataceae

Genus Anaplasma

Genus Neorickettsia

Genus Ehrlichia

Order Rhizobiales

Family Bartonellaceae

Genus Bartonella

Family Brucellaceae

Genus Brucella

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Burkholderia

Family Alcaligenaceae

Genus Alcaligenes

Genus Bordetella

Order Neisseriales

Family Neisseriaceae

Genus Neisseria

Genus Eikenella

Genus Kingella

Order Nitrozomonadales

Family Spirillaceae

Genus Spirillum

Class Gammaproteobacteria Order Thiotrichales

Family Francisellaceae

Genus Francisella

Order Legionellales

Family Legionellaceae

Genus Legionella

Family Coxiellaceae

Genus Coxiella

Order Pseudomonadales

Family Pseudomonadaceae

Genus Pseudomonas

Family Moraxellaceae

Genus Moraxella

Genus Acinetobacter

Order Vibrionales

Family Vibrionaceae

Genus Vibrio

Order Enterobacteriales

Family Enterobacteriaceae

Genus Enterobacter

Genus Calymmatobacterium

Genus Citrobacter

Genus Edwardsiella

Genus Erwinia

Genus Escherichia

Genus Hafnia

Genus Klebsiella

Genus Kluyvera

Genus Morganella

Genus Proteus

Genus Providencia

Genus Salmonella

Genus Serratia

Genus Shigella

Genus Yersinia

Order Pasteurellales

Family Pasteurellaceae

Genus Pasteurella

Genus Aggregatibacter

Genus Haemophilus

Class Epsilonproteobacteria

Order Campylobacteriales

Family Campylobacteriaceae

Genus. Campylobacter

Family Helicobacteriaceae

Genus Helicobacter

Genus Wolinella

Phylum Firmicutes

Class Clostridia

Order Clostridiales

Family Clostridiaceae

Genus Clostridium

Family Peptostreptococcaceae

Genus Peptostreptococcus

Family Peptococcaceae

Genus Peptococcus

Class Mollicutes

Order Mycoplasmatales

Family Mycoplasmataceae

Genus Mycoplasma

Genus Ureaplasma

Class Bacilli

Order Bacillales

Family Bacillaceae

Genus Bacillus

Family Listeriaceae

Genus Listeria

Family Staphylococcaceae

Genus Staphylococcus

Order Lactobacillales

Family Lactobacillaceae

Genus Lactobacillus

Family Enterococcaceae

Genus Enterococcus

Family Streptococcaceae

Genus Streptococcus

Phylum Actinobacteria

Class Actinobacteria

Subclass Actinobacteridae

Order Actinomycetales

Sub-order Actinomycineae

Family Actinomycetaceae

Genus Actinomyces

Genus Mobiluncus

Sub-order Micrococcineae

Family Micrococcaceae

Genus Micrococcus

Genus Stomatococcus

Sub-order Corynebacterineae

Family Corynebacteriaceae

Genus Corynebacterium

Family Mycobacteriaceae

Genus Mycobacterium

Family Nocardiaceae Genus Nocardia

Sub-order Propionibacterineae

Family Propionibacteriaceae

Genus Propionibacterium

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Bifidobacterium

Genus Gardnerella

Phylum Chlamydiae

Class Chlamydiae

Order Chlamydiales

Family Chlamydiaceae

Genus Chlamydia

Genus Chlamydophila

Phylum Spirochaetes

Class Spirochairtes

Order Spirochaetales

Family Spirochaetaceae

Genus Spirochaeta

Genus Borrelia

Genus Treponema

Family Leptospiraceae

Genus Leptospira

Phylum Bacteroidetes

Class Bacteroidetes

Order Bacteroidales

Family Bacteroidaceae

Genus Bacteroides

Family Porphyromonadaceae

Genus Porphyromonas

Family Prevotellaceae

Genus Prevotella

Phylum Fusobacteria

Class Fusobacteriia

Order Fusobacteriales

Family Fusobacteriaceae

Genus Fusobacterium

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.