Microbial Taxonomy



Microbial Taxonomy



Objectives



1. Define classification, identification, species, genus, and binomial nomenclature.


2. Properly use binomial nomenclature in the identification of microorganisms, including syntax, capitalization, and punctuation.


3. Identify a microorganism’s characteristics as either phenotypic or genotypic.


4. Describe how the classification, naming, and identification of organisms play a role in diagnostic microbiology in the clinical setting.


Taxonomy is the area of biologic science comprising three distinct but highly interrelated disciplines: classification, nomenclature (naming), and identification of organisms. Applied to all living entities, taxonomy provides a consistent means to classify, name, and identify organisms. This consistency allows biologists worldwide to use a common label for every organism studied within the multitude of biologic disciplines. The common language that taxonomy provides minimizes confusion about names, allowing more attention to be focused on other important scientific issues and phenomena. The importance of taxonomy is realized not only in phylogeny (the evolutionary history of organisms), but also in virtually every other biologic discipline, including microbiology.


In diagnostic microbiology, classification, nomenclature, and identification of microorganisms play a central role in providing accurate and timely diagnosis of infectious diseases. A brief, detailed discussion of the three major components of taxonomy is important for a thorough understanding of bacterial identification and application to diagnostic microbiology.



Classification


Classification is a method for organizing microorganisms into groups or taxa based on similar morphologic, physiologic, and genetic traits. The hierarchical classification system consists of the following taxa designations:




Species


Species (abbreviated as sp., singular, or spp., plural) is the most basic of the taxonomic groups and can be defined as a collection of bacterial strains that share common physiologic and genetic features and differ notably from other microbial species. Occasionally, taxonomic subgroups within a species, called subspecies, are recognized. Furthermore, designations such as biotype, serotype, or genotype may be given to groups below the subspecies level that share specific but relatively minor characteristics. For example, Klebsiella pneumoniae and Klebsiella oxytoca are two distinct species within the genus Klebsiella. Serratia odorifera biotype 2 and Treponema pallidum subsp. pallidum are examples of a biotype and a subspecies designation. A biotype is considered the same species with the same characteristic genetic makeup that displays differential physiologic characteristics. Subspecies are typically environmentally isolated from the original species but do not display significant enough divergence to be classified as a biotype or a new species. Although these subgroups may have some taxonomic importance, their usefulness in diagnostic microbiology is limited.



Genus


Genus (plural, genera), the next taxon, contains different species that have several important features in common. Each species within a genus differs sufficiently to maintain its status as an individual species. Placement of a species within a particular genus is based on various genetic and phenotypic characteristics shared among the species. Microorganisms do not possess the multitude of physical features exhibited by higher organisms such as plants and animals. For instance, they rarely leave any fossil record, and they exhibit a tremendous capacity to intermix genetic material among supposedly unrelated species and genera. For these reasons, confidently establishing a microorganism’s relatedness in higher taxa beyond the genus level is difficult. Although grouping similar genera into common families and similar families into common orders is used for classification of plants and animals, these higher taxa designations (i.e., division, class, order) are not useful for classifying bacteria.



Family


A family encompasses a group of organisms that may contain multiple genera and consists of organisms with a common attribute. The name of a family is formed by adding the suffix -aceae to the root name of the type genus; for example, the Streptococcaceae family type genus is Streptococcus. One exception to the rule in microbiology is the family Enterobacteriaceae; the type species is Escherichia coli. Bacterial (prokaryotic) type species or strains are determined according to guidelines published by the International Committee for the Systematics of Prokaryotes. Species definitions are distinguished using DNA profiling, including a nearly complete 16S rRNA sequence with less than 0-5% ambiguity in combination with phenotypic traits. Type species should also be described in detail using diagnostic and comparable methods that are reproducible.



Nomenclature


Nomenclature is the naming of microorganisms according to established rules and guidelines set forth in the International Code of Nomenclature of Bacteria (ICNB) or the Bacteriological Code (BC). It provides the accepted labels by which organisms are universally recognized. Because genus and species are the groups commonly used by microbiologists, the discussion of rules governing microbial nomenclature is limited to these two taxa. In this binomial (two name) system of nomenclature, every organism is assigned a genus and a species of Latin or Greek derivation. Each organism has a scientific “label” consisting of two parts: the genus designation, in which the first letter is always capitalized, and the species designation, in which the first letter is always lower case. The two components are used simultaneously and are printed in italics or underlined in script. For example, the streptococci include Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus agalactiae, and Streptococcus bovis, among others. Alternatively, the name may be abbreviated by using the upper case form of the first letter of the genus designation followed by a period (.) and the full species name, which is never abbreviated (e.g., S. pneumoniae, S. pyogenes, S. agalactiae, and S. bovis). Frequently an informal designation (e.g., staphylococci, streptococci, enterococci) may be used to label a particular group of organisms. These designations are not capitalized or italicized.


As more information is gained regarding organism classification and identification, a particular species may be moved to a different genus or assigned a new genus name. The rules and criteria for these changes are beyond the scope of this chapter, but such changes are documented in the International Journal of Systemic and Evolutionary Microbiology. In the diagnostic laboratory, changes in nomenclature are phased in gradually so that physicians and laboratorians have ample opportunity to recognize that a familiar pathogen has been given a new name. This is usually accomplished by using the new genus designation while continuing to provide the previous designation in parentheses; for example, Stenotrophomonas (Xanthomonas) maltophilia or Burkholderia (Pseudomonas) cepacia.

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Aug 25, 2016 | Posted by in MICROBIOLOGY | Comments Off on Microbial Taxonomy

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