MICROBIAL TAXONOMY

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Taxonomy can be defined as the scientific system of classifying biological organisms into taxa (singular: taxon). Taxonomy is generally the science of biological classification; and it is the grouping of living organisms inclusive of microorganisms according to some characteristics which they share. Scientists that specialize in the classification of organisms are known as taxonomists. Taxonomy is the system of classifying organisms in orderly manner into categories known as taxon. Taxa are other terms used for groups in scientific classification. A taxon is a group of strains, species or genera that have similar morphologic or physiological characteristics different from other category of organisms in a given taxonomic classification. Taxonomy is all about putting a name to an organism. It is the science of identifying and naming species of organisms and arranging same into a classification system. Because of the diversity of organisms on planet earth, living organisms including microorganisms are therefore grouped together, and are further arranged into a hierarchical arrangement based on some mutual similarity or evolutionary similarities that exist amongst these organisms. This type of identification and classification of living organisms makes a good sense of them since they are arranged into groups based on some unique features that they share together.

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Taxonomy is very significant to the microbiologists and other biological and medical sciences because it makes their work a little bit easier in terms of identifying, naming and grouping isolated organisms. It helps for accurate identification of microorganisms; better understanding of microbes because of their allotment to a given group, and it enhances better communication amongst scientists working with these organisms. It is noteworthy that in microbiology, especially in the clinical aspect of it, working with an unidentified pathogenic microorganism could not just be only difficult for the physician to treat a given infection but also, the wellness of the patient will be in jeopardy. Thus, taxonomy helps to make straightforward the classification of the ever-increasing diversity of the microbial world – so that therapeutic measures can be better informed, optimized and produce good prognosis in patients.

The classification of organisms has various hierarchical categories which outlines the different group to which every living organism belongs to. These hierarchical categories are divided into eight; and they are domain, kingdom, phylum, class, order, family, genus, and species. While the species level represents the lowest category of organisms, the kingdom is the highest classification category. The two domains into which living organisms are classified into are eukaryotic domain and prokaryotic domain. The other classification is the Archaea domain – to which organisms that do not classify as eukaryotes or prokaryotes are classified into. The archaea, eukaryotic and prokaryotic domains are usually the three major domains of the tree of life (as reported by biologists in the taxonomical classification of living organisms including microorganisms). These three categories into which living organisms are classified into include: identification, classification, and nomenclature, and they are discussed in the later part of this section.

In microbial taxonomy, inferences are usually drawn from the latest and updated edition of the “Bergey’s Manual of Systematic Bacteriology” (which was originally designed by Professor David Bergey and colleagues in 1923) when classifying, identifying or naming a bacterium. The Bergey’s manual of systematic bacteriology is a reference standard that is used to classify microorganisms (bacteria) based on certain physiological, functional and structural features that they share. It allows microbiologist to place microbes (especially newly identified bacteria) into a particular group or category that contain the attributes of these newly identified organisms. Information from this manual gives microbiologists a clue and an internationally acceptable system of classifying prokaryotes. It also provides a precise method of classifying bacteria. However, the information in the Bergey’s Manual of Systematic Bacteriology is only provisional and is subject to change due to emerging information about the phylogenetic relationships of microorganisms.

The identification and classification of microorganisms is a continuum, and readers are advised to always ensure that they refer to the Bergey’s Manual of Systematic and Determinative Bacteriology for updated information regarding the phylogenetic relationships of microorganisms. However, readers are also advised to make use of other available systems of classifying microorganisms that have been updated and approved by the scientific and/or medical community whenever the issue of microbial taxonomy arises. The standard ranking used in the taxonomy of bacteria is listed in Table 1, and this serves as a guide to beginners who seeks to attempt and understand the underlying principles of bacterial classification using already identified organisms. The organism used here is Klebsiella pneumoniae, a Gram negative bacterium. Beginners can attempt to classify a different organism (for example, a Gram positive bacterium) in order to master the process of bacterial and/or microbial classification.Only the rank of family, genus and species are normally used when categorizing a bacterium for practical purposes and for easy comprehension. There are different categories of taxonomy; and this includes: classification, identification and nomenclature.

Table 1. Taxonomic organizations of bacteria (e.g. Klebsiella pneumoniae)

Standard rankingExample
KingdomProkaryote (Bacteria)
DivisionProteobacteria
Classγ-Proteobacteria
OrderEnterobacteriales
FamilyEnterobacteriaceae
GenusKlebsiella
SpeciesKlebsiella pneumoniae

CATEGORIES OF TAXONOMY

Taxonomy, which is the science of biological classification, is divided into 3 main interconnected parts that include identification, classification and nomenclature.

  • Identification: This is the practical side of taxonomy which helps to determine that a particular microorganism isolated from a given sample or environment belongs to a recognized taxon (group) of organisms. In identifying an organism, varying experiments are often undertaken in order to characterize and designate the organism to a given taxon following already laid down classification scheme.   
  • Classification: This is the arrangement of living organisms into different groups (or taxa) based on some shared similarity or evolutionary relatedness shared by the organisms being classified. In classifying a microorganism (for example, bacteria), an understanding of the results obtained from observational, experimental, biochemical, morphologic and physiological examinations carried out on the microorganism is always taken into consideration when assigning an organism to a given taxon. 
  • Nomenclature: This is the component of taxonomy that assign names to already identified and classified organisms based on already published guidelines or principles. Drawing inferences from the Bergey’s manual of systematic bacteriology can also aid in this art of giving a name to a bacterium. The morphological and/or physiological characteristics, as well as the biochemical characteristics of a given microorganism (for example, bacteria) are also taken into consideration when assigning it a name.  

Microorganisms have wide taxonomic distribution and this includes organisms such as viruses, bacteria, protozoa, algae, fungi, and Archaea. It is important that these aspects of these organisms are always taken into consideration when microbial taxonomy is to be attempted. Living organisms including microbes are usually named using a binomial system which was developed by the Swedish biologists, Carolus (Carl) Linnaeus (1707 – 1778) in the mid-18th century. Linnaeus classified and named a wide variety of plant and animal species in the early 1700s; and his classification as at the time still stands the basis for the classification of living organisms even till date, even though some recent molecular techniques are now being employed in the taxonomical arrangements of organisms. Carolus Linnaeus’ system of classification is still used till date in part, and with modification in addition to other methods of classification that involves molecular techniques as aforementioned. Linnaeus developed a system of classifying living organisms (inclusive of microorganisms) in a Latinized and italicized approach that gives two names (genus/generic name and species/specific epitaph) to every living organisms.  

Carolus Linnaeus developed the binomial system of (microbial) classification; and this technique is also employed in the characterization of microorganisms and other living systems for easy identification and differentiation. Out of the many system of classification that was developed as at the time, only Linnaeus’ simplified system of classification stood the test of time and survived till date. The binomial nomenclature (which assigns two names to an organism i.e., the generic name and the specific name) is generally used by microbiologists when naming and classifying microorganisms. In the binomial system of classification, each species is assigned two names viz: the generic (genus) name and the specific epitaph (species) name. The genus (plural: genera) name is always capitalized while the species name is not; and they are either italicized or underlined depending on the mode of writing them, whether by hand or with a computer. The reason for italicizing or underlining the scientific names (i.e., the genus and species names) of microorganisms is because these names generally have a Latin or Greek origin. They are not English words and usually, they are derived from the Greek or Latinized versions of the names of persons that discovered them or places they were discovered.

The species name is often the fundamental taxonomic group in microbial taxonomy because while the generic name may change (i.e., if the organism is assigned to another taxon due to new information about it), the species name still remains and is always given priority in microbial cataloguing. For example, Enterococcus faecalis was formerly known as Streptococcus faecalis. But after the genus Streptococcus was later divided into two new genera viz: Lactococcus and Enterococcus; S. faecalis is now known as E. faecalis. Also, once the genus name of an organism has been previously mentioned in a text, it can be abbreviated in subsequent text with the initial of the genus followed by the specific epitaph name in full. For example, Enterococcus faecalis can be shortened and written as E. faecalis once it has been previously mentioned in a text in full. It is improper to write the generic name in a short format. For example, Entero faecalis – is wrong as written. Instead it can be written as: E. faecalis or in full as Enterococcus faecalis. This also applies to the names of other microorganisms in the field of microbiology; and it is important that readers and beginners take this important aspect of microbial taxonomy seriously.  

Genus contains one or more species of organism that is different and entirely separate from species of other genera. Species are collections of strains of an organism that have many stable attributes in common, and which notably differ from other groups of strain. A strain is a population of microorganisms or organisms that differ distinguishably from at least some other population of organisms within a given taxa. Strains are population of organisms that originate from a pure culture isolate or a single microorganism. However, some biologists still believe that the Linnaean (i.e., Carolus Linnaeus’) system of classification is limiting due to some evolutionary differences amongst organisms. Other more recent advanced and high-throughput (molecular) techniques included in the classification of organisms, and which is genetic or molecular-based include:

  • G+C content (i.e., the organism’s guanine and cytosine DNA content),
  • DNA sequencing technique,
  • DNA hybridization,
  • Biotyping,
  • Serotyping,
  • Ribotyping,
  • Metagenomics,
  • PCR characterization,
  • Electrophoresis techniques,
  • Analysis of the ribosomes (especially the 16S ribosomal RNA of an organism), and other chemical characterization systems. Both phenotypic and genotypic differences are often used when characterizing prokaryotes (bacteria). These later and genetic classification systems are important, fast, less-time consuming and reliable.

Further reading

Brooks G.F., Butel J.S and Morse S.A (2004). Medical Microbiology, 23rd edition. McGraw Hill Publishers. USA.

Gilligan P.H, Shapiro D.S and Miller M.B (2014). Cases in Medical Microbiology and Infectious Diseases. Third edition. American Society of Microbiology Press, USA.

Madigan M.T., Martinko J.M., Dunlap P.V and Clark D.P (2009). Brock Biology of Microorganisms, 12th edition. Pearson Benjamin Cummings Inc, USA.

Mahon C. R, Lehman D.C and Manuselis G (2011). Textbook of Diagnostic Microbiology. Fourth edition. Saunders Publishers, USA.

Patrick R. Murray, Ellen Jo Baron, James H. Jorgensen, Marie Louise Landry, Michael A. Pfaller (2007). Manual of Clinical Microbiology, 9th ed.: American Society for Microbiology.

Wilson B. A, Salyers A.A, Whitt D.D and Winkler M.E (2011). Bacterial Pathogenesis: A molecular Approach. Third edition. American Society of Microbiology Press, USA.

Woods GL and Washington JA (1995). The Clinician and the Microbiology Laboratory. Mandell GL, Bennett JE, Dolin R (eds): Principles and Practice of Infectious Diseases. 4th ed. Churchill Livingstone, New York.

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