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Chapter: Microbiology and Immunology: Laboratory Identification of Bacteria and Taxonomy

Bacterial Taxonomy

Bacterial taxonomy comprises: (a) bacterial classification of organism and (b) nomenclature or naming of the microbial isolates.

Bacterial Taxonomy

Bacterial taxonomy comprises: (a) bacterial classification of organism and (b) nomenclature or naming of the microbial isolates.

Bacterial Classification

Bacterial classification may be defined as the arrangement of organisms into taxonomic groups (taxa) on the basis of their phenotypic (observable) and genotypic (genetic) simi-larities and differences. It allows proper and systematic grouping of microorganisms. Organisms are classified into three main kingdoms: Animals, Plants, and Protista. The Protista contains unicellular microorganisms includ-ing eukaryotes and prokaryotes. Although no univer-sally accepted bacterial classification system is available, three main approaches are usually followed. These include (a) phylogenetic, (b) Adansonian, and (c) genetic classifica-tions, which are discussed below:

  Phylogenetic classification

The phylogenetic classification is a type of hierarchical classi-fication that represents a branching tree-like arrangement, one characteristic being employed for divisions at each branch or level. It is called phylogenetic classification, because it denotes an evolutionary arrangement of species.

This classification groups together the types that are related on evolutionary basis where several groups are used, such as Divisions, Classes, Orders, Families, Tribes, Genera, and Species.Some characters of special importance, such as Gram stain-ing properties, lactose fermentation, spore formation, etc., are used to differentiate major groups, whereas less important properties, such as nutritional requirements for growth of bacteria, production of certain enzymes by bacteria, etc., are employed to distinguish minor groups, such as the genera and species.

As per the classification, the full taxonomical position of a bacterium (say, E. coli) can be described as follows:

Division:     Protophyta

Class:                   Schizomycetes

Order:                  Eubacteriales

Family:       Enterobacteriaceae

Tribe:                   Escherichiae

Genus:                 Escherichia

Species:       coli

      Bergey’s Manual of Systematic Bacteriology is an authoritativepublished compilation that describes a phylogenetic classifica-tion of bacteria. The manual is a useful compilation of names and descriptions of bacteria and is the most standard refer-ence book accepted worldwide. The book is extremely useful for identification of newly isolated bacterial types. A minimum number of important characters, such as morphology of the bacteria, staining properties, cultural characteristics, biochemi-cal reactions, antigenic structure, and guanine to cytosine ratio of DNA, etc., are used for identification and classification of bacteria.

  Adansonian classification

The Adansonian classification makes no phylogenetic assump-tion, but considers all the characteristics expressed at the time of the study. Hence it is called a phonetic system. The Adansonian classification was first proposed by Michael Adanson in the eighteenth century. It avoids the use of weighted characteristics. This classification gives equal weight to all measurable features and groups of bacteria on the basis of similarities of several characteristics.

Recently, availability of computer facilities has expanded the scope of phonetic classification by permitting comparison of very large number of properties of several organisms at the same time. The computer analysis of large number of charac-teristics of a bacterium facilitates the identification of several broad subgroups of bacterial strains that are further subdi-vided into species. This type of classification, based on the properties of large number of properties, is known as numeri-cal taxonomy.

  Genetic classification

The genetic or molecular classification is based on homology of the DNA base sequences of the microorganisms. DNA relatedness of the microorganisms is tested first by extract-ing DNA from the organism to be studied, and then study-ing the nucleotide sequence of DNA by DNA hybridization or recombination methods. The degree of hybridization can be assessed by many methods, such as by using labeled DNA preparations.

The study of messenger RNA (mRNA) also provides useful information on genetic relatedness among bacteria. The anal-ysis of ribosomal RNA (rRNA) has proved to be of immense value. Study of the nucleotide sequence of 16S ribosomal RNA from different biologic sources has shown evolution-ary relationships among widely divergent organisms and has contributed to the understanding of new groups of bacte-ria, such as the archaebacteria. Genetic classification is now increasingly used for study of viruses.

  Intraspecies classification

Intraspecies classification makes an attempt to subclassify species of a bacteria based on biochemical properties (bio-types), antigenic properties (serotypes), susceptibility to bacte-riophage (phage types), and production of bacteriocins (colicin types). Recently, molecular methods have increasingly been used for intraspecies classification of microorganisms, espe-cially viruses.

Nomenclature of Microorganisms

Nomenclature refers to the naming of microorganisms. The nomenclature of microorganisms is governed by the International Committee on Systematic Bacteriology and published as Approved List of Bacterial Names in the InternationalJournal of Systematic Bacteriology. This confers and maintainsuniformity for use of names of microorganisms accepted internationally. Similarly, the nomenclature and classification of viruses are governed by the International Committee on Taxonomy of Viruses. Two kinds of names are usually given to bacteria—common name and scientific name: 

·           The common or casual name for a microorganism varies from country to country and is usually known in the local language. For example tubercle bacillus, typhoid bacillus, gonococcus are common names for communication at the local level.

·           The scientific name is the international name that is accepted throughout the world. By accepted taxonomic conventions, the order names end in ales (e.g., the order Eubacteriales), family names end in aceae (e.g., the family Enterobacteriaceae), and the tribe names end in eae (e.g., the tribe Proteae). The order, family, and tribe names begin with capital letters. The genus name also begins with capital let-ter, but species name (e.g., coli) begins with running letter and not capital letter. Both the genus (e.g., Escherichia) and species names are either italicized or underlined when written in the text. The scientific name of the bacterium when written for the first time, is written in full (e.g., Escherichia coli), but later mentioned in an abbreviated form (e.g., Escherichia coli). When bacteria are referred to as a group, their names are neither capitalized nor italicized or underlined (e.g., streptococci).

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