Classification, nomenclature and identification comprise taxonomy of microorganisms. On the basis of common characters or properties, a set of organism is considered into groups. There are no formal rules to define the taxa. On the other hand, nomenclature is the name given for defined taxa as also governed by bacteriological code of nomenclature. The features that are used to differentiate various organisms often have title to do with the fundamental basis for arranging the organisms into taxonomic groups.

The criteria sometimes do not help in characterization of the genera and species which are not characterized by traditional or physiological tests.

Serological tests (agglutination, flurorescent antibody techniques etc.) have limited role in classification but have enormous value in identification. It is important to note that identification may not be based on only a few tests, but rather on the whole battery of test. Genetic tools are the modern one for identification based on the detection of a specific portion of an organism's genetic material.

The Intuitive Method: Since a large array of microbiologists study the characteristics of organisms (morphological, physiological, biochemical, genetical, molecular), sometimes, it is difficult to assign an organism based on all the characters because a character may be important to a particular microbiologist may not be that important to another, hence, different taxonomists may arrive at very different groupings.

Numerical taxonomy: This is based on several characteristics for each strain and each character is given equal weightage. The % similarity of each strain may determine by the following formula:

% S = NS / (NS + ND)
NS = Number of characteristics for each strains which is similar or dissimilar.
ND = Number of characteristics that are dissimilar or different.
On the basis of % S, S = Similarity if it is high to each other , placed into groups larger and so on.

Genetic Relatedness: The classification is based on genetic relatedness (DNA and RNA) between organisms.The % G+C determines the organism whether it is the same or different species. If two organisms have quite different mol % G+C, then the species are different and seem to be not related to each other. Further , characterization is based on the following principles:

DNA-DNA hybridization or DNA- homology: After annealing i.e. separation of two strands and converting them into single strand, the later one is mixed with those obtained from other organism. If the two organisms are similar the pairing will occur in strands of both the organism, and will form heteroduplexes otherwise not.

16S rRNA Sequencing: Ribosomal RNA homology experiments and ribosomal RNA oligonucleotide cataloguing determine the molecular characteristics just to demonstrate degree of relatedness. Due to the highly conserve nature of rRNA genes, the 16S rRNA nucleotide sequence give better informations than DNA molecule. It is important to mention that if there is no DNA-DNA relatedness (homology) between two organisms, still nucleotide sequence of their rRNA cistrons may be studied so as to observe the similarity may be used as a measure of relatedness between organisms, but at a level beyond that of species.

After identification and classification, it is important to assign name to the bacterium. The name should be such so that it is accepted internationally. The bacterial nomenclature is regulated by a committee on systematic nomenclature. List of approved names are published in International Journal of Systematic Bacteriology. It is kept that most of the bacterial names should often be descriptive e.g. Mycobacterium tuberculosis causes tuberculosis. But sometimes, they reflect the microscopic appearance as in the case of Staphylococcus aureus, which is golden (aureus) berry (coccus) that form clusters like, grapes (staphule).

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