Christopher D. Doern - Pocket Guide to Clinical Microbiology

It should be appreciated that despite appearances, changes in nomenclature are regulated by a system of rules with oversight governed by the International Code of Biological Nomenclature ( www.biosis.org.uk/zrdocs/codes/codes.htm). The International Code of Nomenclature of Bacteria governs bacterial taxonomy, and all bacteria named after 1980 must be validly published in the International Journal of Systematic and Evolutionary Microbiology . A current listing of bacteria can be found at http://www.bacterio.net, http://www.bacterio.cict.fr/, and https://www.dsmz.de/. The International Committee on Taxonomy of Viruses (ICTV) governs viral taxonomy, and all currently recognized viruses can be found at https://talk.ictvonline.org//. The International Code of Botanical Nomenclature governs fungal classification, and additional information can be found at http://www.iapt-taxon.org/nomen/main.php/.

Classification and taxonomy of prokaryotes (bacteria) is complicated and is governed by the International Code of Nomenclature of Bacteria (last revised in 1990). By definition, each prokaryotic species must include a genus-level name that is included within a hierarchy or ranks, which includes (from highest to lowest rank) subtribe, tribe, subfamily, family, suborder, order, subclass, class, division (or phylum), and domain (or empire). To further complicate matters, the tribe and subtribe do not actually include names and are therefore not used.

Most importantly, there is no such thing as an 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