MicrobialTaxonomy

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MICROBIAL TAXONOMY
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Microbes in Practice 2014 Bisen Prakash S, IK International, New Delhi pp 196-259
Chapter 8
MICROBIAL TAXONOMY
8.1 INTRODUCTION
Taxonomy is an area of biological science which comprises three distinct, but highly interrelated
disciplines that include classification, nomenclature and identification. 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 they study
within their particular disciplines. The common language that taxonomy provides minimizes the
confusion about names and allows attention to center on more important scientific issues and
phenomena. In diagnostic microbiology, classification, nomenclature and identification of
microbes play a central role in providing accurate and timely diagnosis of infection.
Classification is the organization of organisms that share similar morphologic,
physiologic and genetic traits into specific groups or taxa. Nomenclature, the naming of
microorganisms according to established rules and guidelines provide the accepted labels by
which organisms are universally recognized. The classification of microbes is based on how they
look and what they can do. The correct identification of micro organisms is of fundamental
importance to microbial systematists as well as to scientists involved in many other areas of
applied research and industry (e.g. agriculture, clinical microbiology and food production).
Increased use of automation and user-friendly software makes these technologies more widely
available. In all, the detection of infectious agents at the nucleic acid level represents a true
synthesis of clinical chemistry and clinical microbiology techniques. Accurate identification
requires a sound classification or system of ordering organisms into groups, as well as an
unequivocal nomenclature for naming them.
Molecular techniques for characterizing microbial genotypes provide a possible basis of
defining a microbial species. Nucleic acid amplification technology has opened new avenues of
microbial detection and characterization, such that growth is no longer required for microbial
identification. Methods of microbial identification can be broadly delimited into genotypic
techniques based on profiling an organism's genetic material (primarily its DNA) and phenotypic
techniques based on profiling either an organism's metabolic attributes or some aspect of its
chemical composition. Classification of microbes can be made on the basis of phenotypic
characteristics and on genotypic characteristics.
8.2 CLASSIFICATION
Classification is one of the fundamental concerns of biology. Facts and objects must be arranged
in an orderly fashion before their unifying principles can be discovered and used as the basis for

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prediction. The development of high speed electronic computers has had a profound impact on
the methods of classification in biological fields. The rapidity of the computer’s operation has
made it possible for the first time to consider large numbers of characteristics in classifying
microbes. Most approaches to the problems of microbial taxonomy have arisen from either of the
two viewpoints, one derived from phylogenetic and other from practical consideration. The
former viewpoint too frequently arises from some major premise, which has little practical
connotation. The latter view point often leads to the submergence of large groups of organisms
not known to be of economic importance, because of an attitude of impatience towards any
system which does not reflect the methods used in the specialized laboratory where steps in the
identification of an unknown organisms must be measured in terms of utility and speed. It must,
therefore, be realized that the precise delineation of species cannot be the primary aim of the
microbial taxonomy at present. It is seldom possible and often it may not even be desirable to
compromise by recognizing the necessity for the organization within a taxonomic system of a
selected body of knowledge of important differential characters which may be applied when
practical consideration that demands that phylogenetically related organisms be distinguished
one from the other. This implies that taxonomic systems must undergo periodic revision with the
advent of new knowledge.
Classification means the act of arranging a number of objects (of any sort) into groups (or
taxa) in relation to attributes possessed by those objects. The word classification is also applied
to the result of any such arrangement. Taxonomy is concerned, inter alia, with definition of the
aims of classification, the design of rules by which arrangements may be achieved, and with the
evaluation of the end results. In biological classifications, the primary objects (microorganisms,
plants, animals) are usually arranged in groups which are themselves members of larger groups
(and so on) in such a way that any item or any group appears as a member of only one larger
grouping, i.e., the groups are non-overlapping. This method of classification is the familiar
hierarchical system which can be conveniently represented by a 'family tree' or dendrogram.
The units at each level (taxonomic rank) of a hierarchical system are given distinctive names or
label a branch of taxonomy known as nomenclature. In biology, the system of nomenclature is
normally used for living organisms, which is derived from that used by the great eighteenth-
century taxonomist Linnaeus (Carl von Linne). In this system, the basic unit (the species) is
given two names one denoting its membership of a taxon at the rank that we label genus (generic
name) followed by a second denoting the particular species (specific name). These names are
written in a latinized form and constitute a so called latinized binomial (e.g., Aspergillus niger,
Bacillus subtilis, Clostridium tetani). Taxa of higher rank (families, orders, etc.) are given single
latinized names with characteristic endings (e.g., Pseudomonadaceae, family; Pseudomonadales,
order). The naming of newly discovered organisms or of newly proposed taxa of higher ranks is
governed by rigid rules standardized by international agreement. It is perhaps worth emphasizing
that it is by no means the only possible one. The simplest system would be merely to label the
different types of organism with some sort of catalogue number which referred to a listed
description. A much more useful approach might be similar to one proposed for the naming of
viruses, viz., the virus is given a group name (probably latinized) which is followed by a
descriptive formula akin to that used by botanists in floral diagrams or to the antigenic formula
of a Salmonella species. The naming of the units defined and delineated by the classification.
This latter method is, in fact, reminiscent of that often used by Linnaeus, who sometimes
followed his latinized generic name with up to a dozen descriptive 'specific' epithets. Ideally, the
coining of new names is contrived to convey as much information as possible about the organism

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or taxon. Unfortunately, both the restriction to latinized binomials and, often, the rules of
precedence make this aim difficult to achieve.
8.3 IDENTIFICATION
It can be done through various methods either by physical methods or by methods based on
phylogeny. Identification simply involves the comparison of an 'unknown' object (e.g., a newly
isolated bacterium, a collected microorganisms, plant or animal) with all similar objects that are
already known. If the 'unknown' object matches up with a 'known' then the former has been
identified; if not, it may be considered to be a 'new' species, variety, or strain and, when
adequately described, is added to the list of known objects. In practice this act of comparison is
normally carried out not between two actual objects but between the 'unknown' isolate and a
recorded description of previously discovered micro-organisms, plants, animals, etc. The
inadequacy of recorded descriptions of many microbial species can sometimes make accurate
identification very difficult, if not impossible. It is not always appreciated that neither
identification nor nomenclature need necessarily be connected with classification.
These three facets, or the trinity that is taxonomy, are to some extent interdependent, but
in an orthodox scheme they are considered in the order given above, It is arguable whether the
hen or the egg came first, but since the end of the nineteenth century microbiological ethics have
demanded that we should not name a microbe before allotted it to a unit in an orderly
classificatory system (Figure 8.1).
Genotypic and phenotypic criteria are based on observable physical or metabolic
characteristics of microorganisms, that is, identification is through analysis of gene products. The
phenotypic approaches are the classic approach of identification, and most identification
strategies are still based on phenotype. The most commonly used phenotypic criteria include:
 Microscopic evaluation of microbial cellular morphology
 Macroscopic (colony) morphology includes colony size, shape, colour (pigment) surface
appearance, and any changes in the colony growth produced in the surrounding agar
medium.
 Environmental conditions required for growth can be used to supplement other
identification criteria.

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 The enzyme-based tests are designed to measure the presence of one specific enzyme or a
complete metabolic pathway that may contain several different enzymes.
 Molecular methods like Multiplex-PCR, Nested-PCR, RAPD -PCR, ARDRA, different
hybridization techniques, micro arrays, protein-profiling, zymographic analysis,
multilocus enzyme electrophoresis, pulsed field gel electrophoresis, N- terminal
sequencing, riboprinter technique and chromatographic technique have revolutionarized
the area of identification and characterization.
The correct identification of micro organisms is of fundamental importance to microbial
systematists as well as to scientists involved in many other areas of applied research and industry
(e.g. agriculture, clinical microbiology and food production). Increased use of automation and
user-friendly software makes these technologies more widely available. In all, the detection of
infectious agents at the nucleic acid level represents a true synthesis of clinical chemistry and
clinical microbiology techniques. Accurate identification requires a sound classification or
system of ordering organisms into groups, as well as an unequivocal nomenclature for naming
them .
Microbial taxonomy can create much order from the plethora of microorganisms. For
example, the American Type Culture Collection maintains the following, which are based on
taxonomic characterization (the numbers in brackets indicate the number of individual organisms
in the particular category): algae (120), bacteria (14400), fungi (20200), yeast (4300), protozoa
(1090), animal viruses (1350), plant viruses(590), and bacterial viruses (400). The actual number
of microorganisms in each category will continue to change as new microbes are isolated and
classified. The general structure, however, of this classical, so-called phenetic system will remain
the same.
8.4 PRINCIPLES OF TAXONOMY
Taxonomy has 2 functions: the first is to describe as completely as possible the basic taxonomic
units, or species; the second, to devise an appropriate way of arranging and cataloguing these
units. The notion of species consists of assemblage of individuals that share a high degree of
phenotypic similarity, coupled with an appreciable dissimilarity from other assemblage of the
same general kind.
Every assemblage of individuals shows some degree of internal phenotypic diversity
because of genetic variation. Ideally, species should be characterized by complete description of
their phenotypes and genotypes The influence of evolutionary criteria (phyletic classifications)
on taxonomy during the post-Darwinian period is often thought to be the sole aim of the
taxonomist. It is therefore necessary to consider whether other possible aims are valid and,
indeed, whether any other approach might lead to classifications of greater value than the purely
phyletic. To do so we must first make the distinction between special (or artificial)
classifications and natural classifications. A special classification is one made for a single,
defined purpose: it assists in finding the answer to a specific question. A well-known example is
the classification of enteric bacteria according to the biochemical differential tests, as used by the
water bacteriologists. The purpose of this classification is to group together those organisms
which may indicate recent faecal pollution of a water supply and to separate these from other
similar bacteria which do not have this significance. When a bacterial isolate is identified as
falling within a particular group of this system an answer to the question of possible faecal