official classification of prokaryotes. This is because in contrast to eukaryotes, the prokaryotic designations are a matter of scientific judgment. Therefore, the closest things that we have to “official” taxonomic designations are those names that are generally accepted by the microbiology community. Despite this fact, microbiologists have achieved some amount of consensus by relying on resources such as the International Journal of Systematic and Evolutionary Microbiology and Bergey’s Manual of Systematic Bacteriology.
As of the writing of this fourth edition Pocket Guide, the prokaryotes were divided into 2 domains, 35 phyla, 80 classes, 1 subclass, 178 orders, 20 suborders, 402 families, and 2,552 genera. The following is a consolidated taxonomic outline, which will focus on the taxonomic organization or those organisms that are most likely to be encountered in the clinical microbiology laboratory. This is not meant to be an exhaustive list of all bacteria. Rather, it is intended to provide some context to the relationships between some of the most commonly encountered organisms in human clinical specimens.
The taxonomy of bacterial classification is arranged in the following way…
DomainPhyla ClassSubclassOrderSuborderFamilyGenera
Domain: BacteriaClass. ActinobacteriaFamily. ActinomycetaceaeGenus. ActinobaculumGenus. ActinomycesGenus. ArcanobacteriumGenus. MobiluncusGenus. TrueperellaFamily. CorynebacteriaceaeGenus. CorynebacteriumGenus. TuricellaFamily. DietziaceaeGenus. DietziaFamily. MycobacteriaceaeGenus. MycobacteriumFamily. NocardiaceaeGenus. GordoniaGenus. NocardiaGenus. RhodococcusFamily. TsukamurellaceaeGenus. TsukamurellaFamily. PropionibacteriaceaeGenus. PropionibacteriumFamily. StreptocmycetaceaeGenus. StreptomycesFamily. NocardiopsaceaeGenus. NocardiopsisFamily. BifidobacteriaceaeGenus. AlloscardoviaGenus. BifidobacteriumGenus. GardnerellaFamily. BrevibacteriaceaeGenus. BrevibacteriumFamily. CellulomonadaceaeGenus. CellulomonasGenus. OerskoviaGenus. TropherymaFamily. DermabacteraceaeGenus. DermabacterGenus. HelcobacillusFamily. DermacoccaceaeGenus. DermacocccusGenus. KytococcusFamily. MicrobacteriaceaeGenus. LeifsoniaGenus. MicrobacteriumFamily. MicrococcaceaeGenus. ArthrobacterGenus. KocuriaGenus. MicrococcusGenus. RothiaGenus. StomatococcusClass. CoriobacteriiaFamily. AtopobiaceaeGenus. AtopobiumFamily. EggerthellaceaeGenus. EggerthellaGenus. SlackiaClass. BacteroidiaFamily. BacteroidaceaeGenus. BacteroidesFamily. PorphyromonadaceaeGenus. DysgonomonasGenus. MicrobacterGenus. ParabacteroidesGenus. PorphyromonasGenus. TannerellaFamily. PrevotellaceaeGenus. PrevotellaClass. FlavobacteriiaFamily. FlavobacteriaceaeGenus. BergeyellaGenus. CapnocytophagaGenus. ChryseobacteriumGenus. ElizabethkingiaGenus. EmpedobacterGenus. FlavobacteriumGenus. WeeksellaClass. SphingobacteriiaFamily. SphingobacteriaceaeGenus. SphingobacteriumClass. ChlamydiaeFamily. ChlamydiaceaeGenus. ChlamydiaGenus. ChlamydophilaClass. Bacilli or FibribacteriaFamily. BacillaceaeGenus. BacillusFamily. ListeriaceaeGenus. ListeriaFamily. PaenibacillaceaeGenus. PaenibacillusFamily. StaphylococcaceaeGenus. StaphylococcusFamily. Unassigned Genus.GemellaFamily. AerococcaceaeGenus. AbiotrophiaGenus. AerococcusGenus. DolosicoccusGenus. FacklamiaGenus. GlobicatellaFamily. CarnobactericeaeGenus. AlloiococcusGenus. DolosigranulumGenus. GranulicatellaFamily. EnterococcaceaeGenus. EnterococcusGenus. VagococcusFamily. LactobacillaceaeGenus. LactobacillusGenus. PediococcusFamily. LeuconostocaceaeGenus. LeuconostocGenus. WeissellaFamily. StreptococcaceaeGenus. LactococcusGenus. StreptococcusClass. ClostridiaFamily. ClostridiaceaeGenus. ClostridiumGenus. SarciniaFamily. PeptococcaceaeGenus. PeptococcusFamily. PeptostreptococcaceaeGenus. PeptostreptococcusFamily. UnassignedGenus. AnaerococcusGenus. FinegoldiaGenus. HelcococcusGenus. PeptoniphilusClass. ErysipelotrichiaFamily. ErysipelotrichaceaeGenus. ErysipelothrixClass. NegativicutesFamily. VeillonellaceaeGenus. VeillonellaClass. FusobacteriiaFamily. FusobacteriaceaeGenus. FusobacteriumFamily. LeptotrichiaceaeGenus. LeptotrichiaGenus. SneathiaGenus. StreptobacillusClass. AlphaproteobcteriaFamily. CaulobacteraceaeGenus. BrevundimonasFamily. BartonellaceaeGenus. BartonellaFamily. BrucellaceaeGenus. BrucellaGenus. OchrabactrumFamily. RhizobiaceaeGenus. AgrobacteriumGenus. RhizobiumFamily. RhodobacteraceaeGenus. ParacoccusFamily. AcetobacteraceaeGenus. RoseomonasFamily. RhodospirllaceaeGenus. InquilinusFamily. AnaplasmataceaeGenus. AnaplasmaGenus. EhrlichiaGenus. WolbachiaFamily. RickettsiaceaeGenus. OrientiaGenus. RickettsiaFamily. SphingomonadaceaeGenus. SphingomonasClass. BetaproteobacteriaFamily. AlcaligenaceaeGenus. AchoromobacterGenus. AlcaligenesGenus. BordetellaGenus. OligellaFamily. BurkholderiaceaeGenus. BurkholderiaGenus. CupriavidisGenus. PandoraeaGenus. RalstoniaFamily. ComamonadaceaeGenus. AcidovoraxGenus. ComamonasGenus. DefltiaFamily. OxalobacteraceaeGenus. HerbaspirillumFamily. NeisseriaceaeGenus. EikenellaGenus. KingellaGenus. NeisseriaFamily. SprillaceaeGenus. Genera Genus. SprilliumClass. EpsilonproteobacteriaFamily. CampylobacteraceaeGenus. ArcobacterGenus. CampylobacterFamily. HelicobacteraceaeGenus. HelicobacterClass. GammaproteobacteriaFamily. EnterobacteriaceaeGenus. CedeceaGenus. CitrobacterGenus. CronobacterGenus. EdwardsiellaGenus. EnterobacterGenus. ErwiniaGenus. EscherichiaGenus. HafniaGenus. KlebsiellaGenus. KluyberaGenus. LeclerciaGenus. MorganellaGenus. PantoeaGenus. PlesiomonasGenus. ProteusGenus. ProvidenciaGenus. RaoltellaGenus. SalmonellaGenus. SerratiaGenus. ShigellaGenus. YersiniaGenus. YokenellaFamily. VibrionaceaeGenus. VibrioFamily. AeromonadaceaeGenus. AeromonasFamily. ShewanellaceaeGenus. ShewanellaFamily. CardiobacteriaceaeGenus. CardiobacteriumGenus. SuttonellaFamily. CoxiellaceaeGenus. CoxiellaFamily. LegionellaceaeGenus. LegionellaFamily. PasteurellaceaeGenus. ActinobacillusGenus. AggregatibacterGenus. HaemophilusGenus. PasteurellaFamily. MoraxelaceaeGenus. AcinetobacterGenus. BranhamellaGenus. MoraxellaFamily. PseudomonadaceaeGenus. ChryseomonasGenus. FlavimonasGenus. PseudomonasFamily. FrancisellaceaeGenus. FrancisellaClass. SpirochaetesFamily. BrachyspiraceaeGenus. BrachyspiraFamily. LeptospiraceaeGenus. LeptospiraFamily. BorreliaceaeGenus. BorreliaFamily. SpirochaetaceaeGenus. TreponemaClass. MollicutesFamily. MycoplasmataceaeGenus. MycoplasmaGenus. Ureaplasma
Taxonomic Classification of Human Viruses
The taxonomy of viral classification is arranged in the following way…
OrderFamilySubfamilyGenusSpecies
Practically speaking, most clinical microbiologists organize viruses in terms of genome structure, family, and genus, and only rarely are the subfamily or species designations utilized. As such, the following taxonomic structure is presented in terms of what would be most useful to the practicing clinical microbiologist.
Single-stranded, nonenveloped DNA virusesFamily. ParvoviridaeGenus. ErythrovirusSpecies. Human parvovirus B19 virus
Double-stranded, nonenveloped DNA virusesFamily. PolyomaviridaeGenus. PolyomavirusSpecies. JC polyomavirus, BK polyomavirusFamily. PapillomaviridaeGenus. PapillomavirusSpecies. Human papillomavirusFamily. AdenoviridaeGenus. MastadenovirusSpecies. Human adenoviruses (species A to G)
Double-stranded, enveloped DNA virusesFamily. PoxviridaeGenus. OrthopoxvirusSpecies. Vaccinia virus, variola virus smallpox virus, cowpox virus, monkeypox virusGenus. MolluscipoxvirusSpecies. Molluscum contagiosum virusGenus. ParapoxvirusSpecies. Orf virusFamily. HepadnaviridaeGenus. OrthohepadnavirusSpecies. Hepatitis B virusFamily. HerpesviridaeGenus. SimplexvirusSpecies. Human herpesvirus 1 (herpes simplex virus type 1; HHV-1), human herpesvirus 2 (herpes simplex virus type 2; HHV-2)Genus. VaricellovirusSpecies. Human herpesvirus 3 (varicella-zoster virus [VZV]; HHV-3)Genus. LymphocryptovirusSpecies. Human herpesvirus 4 (Epstein-Barr virus [EBV]; HHV-4)Genus. CytomegalovirusSpecies. Human herpesvirus 5 (CMV; HHV-5)Genus. RoseolovirusSpecies. Human herpesvirus 6 (roseola virus; HHV-6), human herpesvirus 7 (HHV-7)Genus. RhadinovirusSpecies. Human herpesvirus 8 (HHV-8)
Single-stranded, positive-sense, nonenveloped RNA viruses
Family. PicornaviridaeGenus. EnterovirusSpecies. Enterovirus A (human coxsackievirus A2, human enterovirus 71) Enterovirus B (human coxsackievirus B1, human echovirus), Enterovirus C (human poliovirus 1 to 3, human coxsackievirus A1), Enterovirus D (human enterovirus 68, 70, and 94), Rhinovirus A, B, and C.Genus. AphthovirusSpecies. Foot-and-mouth disease virusGenus. HepatovirusSpecies. Human hepatitis A virus (HHAV)
Family.
