Microbial Taxonomy

Published on 08/02/2015 by admin

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Last modified 22/04/2025

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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.

Identification

Microbial identification is the process by which a microorganism’s key features are delineated. Once those features have been established, the profile is compared with those of other previously characterized microorganisms. The organism can then be assigned to the most appropriate taxa (classification) and can be given appropriate genus and species names (nomenclature); both are essential aspects of the role taxonomy plays in diagnostic microbiology and infectious diseases (Box 1-1).

Box 1-1   Role of Taxonomy in Diagnostic Microbiology

• Establishes and maintains records of key characteristics of clinically relevant microorganisms

• Facilitates communication among technologists, microbiologists, physicians, and scientists by assigning universal names to clinically relevant microorganisms. This is essential for:

• Establishing an association of particular diseases or syndromes with specific microorganisms

• Epidemiology and tracking outbreaks

• Accumulating knowledge regarding the management and outcome of diseases associated with specific microorganisms

• Establishing patterns of resistance to antimicrobial agents and recognition of changing microbial resistance patterns

• Understanding the mechanisms of antimicrobial resistance and detecting new resistance mechanisms exhibited by microorganisms

• Recognizing new and emerging pathogenic microorganisms

• Recognizing changes in the types of infections or diseases caused by characteristic microorganisms

• Revising and updating available technologies for the development of new methods to optimize the detection and identification of infectious agents and the detection of resistance to antiinfective agents (microbial, viral, fungal, and parasitic)

• Developing new antiinfective therapies (microbial, viral, fungal, and parasitic)

Identification Methods

A wide variety of methods and criteria are used to establish a microorganism’s identity. These methods usually can be separated into either of two general categories: genotypic characteristics and phenotypic characteristics. Genotypic characteristics relate to an organism’s genetic makeup, including the nature of the organism’s genes and constituent nucleic acids (see Chapter 2 for more information about microbial genetics). Phenotypic characteristics are based on features beyond the genetic level and include both readily observable characteristics and characteristics that may require extensive analytic procedures to be detected. Examples of characteristics used as criteria for bacterial identification and classification are provided in Table 1-1. Modern microbial taxonomy uses a combination of several methods to characterize microorganisms thoroughly so as to classify and name each organism appropriately.

TABLE 1-1

Identification Criteria and Characteristics for Microbial Classification

Phenotypic Criteria Examples Principles
Macroscopic morphology Characteristics of microbial growth patterns on artificial media as observed when inspected with the unaided eye. Examples of such characteristics include the size, texture, and pigmentation of bacterial colonies.
Microscopic morphology Size, shape, intracellular inclusions, cellular appendages, and arrangement of cells when observed with the aid of microscopic magnification.
Staining characteristics Ability of an organism to reproducibly stain a particular color with the application of specific dyes and reagents. Staining is used in conjunction with microscopic morphology for bacterial identification. For example, the Gram stain for bacteria is a critical criterion for differential identification.
Environmental requirements Ability of an organism to grow at various temperatures, in the presence of oxygen and other gases, at various pH levels, or in the presence of other ions and salts, such as NaCl.
Nutritional requirements Ability of an organism to utilize various carbon and nitrogen sources as nutritional substrates when grown under specific environmental conditions.
Resistance profiles Exhibition of a characteristic inherent resistance to specific antibiotics, heavy metals, or toxins by certain microorganisms.
Antigenic properties Establishment of profiles of microorganisms by various serologic and immunologic methods for determining the relatedness among various microbial groups.
Subcellular properties Establishment of the molecular constituents of the cell that are typical of a particular taxon, or organism group, by various analytic methods. Some examples include cell wall components, components of the cell membrane, and enzymatic content of the microbial cell.
Genotypic Criteria Examples Principles
Deoxyribonucleic acid (DNA) base composition ratio DNA comprises four bases (guanine, cytosine, adenine, and thymine). The extent to which the DNA from two organisms is made up of cytosine and guanine (i.e., G + C content) relative to their total base content can be used as an indicator of relatedness or lack thereof. For example, an organism with a G + C content of 50% is not closely related to an organism with a G + C content of 25%.
Nucleic acid (DNA and ribonucleic acid [RNA]) base sequence analysis, including hybridization assays. The order of bases along a strand of DNA or RNA is known as the base sequence. The extent to which sequences are similar (homologous) between two microorganisms can be determined directly or indirectly by various molecular methods. The degree of similarity in the sequences may be a measure of the degree of organism relatedness, specifically, the ribosomal RNA (rRNA) sequences that remain stable in comparison to the genome as a whole.

Although the criteria and examples in Table 1-1 are given in the context of microbial identification for classification purposes, the principles and practices of classification parallel the approaches used in diagnostic microbiology for the identification and characterization of microorganisms encountered in the clinical setting. Fortunately, because of the previous efforts and accomplishments of microbial taxonomists, microbiologists do not have to use several burdensome classification and identification schemes to identify infectious agents. Instead, microbiologists use key phenotypic and genotypic features on which to base their identification in order to provide clinically relevant information in a timely manner (see Chapter 13). This should not be taken to mean that the identification of all clinically relevant organisms is easy and straightforward. This is also not meant to imply that microbiologists can only identify or recognize organisms that have already been characterized and named by taxonomists. Indeed, the clinical microbiology laboratory is well recognized as the place where previously unknown or uncharacterized infectious agents are initially encountered, and as such it has an ever-increasing responsibility to be the sentinel for emerging etiologies of infectious diseases.

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