Oduduwa University Ipetumodu
Department of Biological Sciences
MMB 201 General Medical Microbiology II
Classification Systems
The classification of bacteria serves a variety of different functions. Because of this variety,
bacteria may be grouped using many different typing schemes. The critical feature for all these
classification systems is that an organism identified by one individual (Scientist, Clinician,
Epidemiologist), is recognized as the same organism by another individual. At present the
typing schemes used by Clinicians and Clinical Microbiologists rely on phenotypic typing
schemes. These schemes utilize the bacterial morphology and staining properties of the
organism, as well as oxygen growth requirements of the species combined with a variety of
biochemical tests. For Clinicians, the environmental reservoir of the organism, the vectors and
means of transmission of the pathogen are also of great importance. Scientists interested in the
evolution of microorganisms are more interested in taxonomic techniques that allow for the
comparison of highly conserved genes among different species. As a result of these
comparisons a phylogenetic tree can be developed that displays the degree of relatedness of
different organisms. A relatively new application of this technology has been the recognition
and characterization of non-culturable pathogens and the diseases that they cause. The new
advances, especially in molecular systematics, led to the view that classifications at all
levels in the taxonomic hierarchy should be based on the integrated use of genotypic and
phenotypic data. This approach, known as polyphasic taxonomy, has become the
lodestone of prokaryotic systematics.
A classification guide that organized bacteria in groups by phenotypic characteristics, is the
Bergey’s Manual of Determinative Bacteriology. The manual is useful for identifying
unknown bacterial cultures, and is intended specially for the identification of those bacteria
that have been described and cultured. The second guide, Bergey’s Manual of Systematic
Bacteriology attempts to organize bacterial species according to known phylogenetic
relationships. The manual does not classify bacteria according to evolutionary relatedness but
provides identification (determining) schemes, based on such criteria as cell wall composition,
morphology, differential staining, oxygen requirement, and biochemical testing. In this
manual, bacteria are assigned 19 parts based primarily on following features like energy and
carbon source, mode of locomotion, morphology (cell shapes and arrangement), gram stain
reaction, gaseous requirement and endospore formation ability.
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The manual includes 35 sections based on characters like general shape, morphology, gram
staining, presence of endospore, motility, oxygen relationships, mode of energy production.
A. Phenotypic classification systems: This is a classification scheme most commonly
used by Clinicians and Clinical Microbiologists. It includes the following:
I. Gram stain and bacterial morphology: Of all the different classification systems, the
Gram stain has withstood the test of time. Discovered by H.C. Gram in 1884 it remains
an important and useful technique to this day. It allows a large proportion of clinically
important bacteria to be classified as either Gram positive or negative based on their
morphology and differential staining properties. Slides are sequentially stained with
crystal violet, iodine, then destained with alcohol and counter-stained with safranin.
Gram positive bacteria stain blue-purple and Gram negative bacteria stain red. The
difference between the two groups is believed to be due to a much larger peptidoglycan
(cell wall) in Gram positives. As a result the iodine and crystal violet precipitate in the
thickened cell wall and are not eluted by alcohol in contrast with the Gram negatives
where the crystal violet is readily eluted from the bacteria.
As a result bacteria can be distinguished based on their morphology and staining properties.
Some bacteria such as mycobacteria (the cause of tuberculosis) are not reliably stained due to
the large lipid content of the peptidoglycan. Alternative staining techniques (Kinyoun or acid
fast stain) are therefore used that take advantage of the resistance to destaining after lengthier
initial staining. Based on the nature of their cell wall and Gram staining characteristics, four
major divisions of Prokaryotes and their respective type of cell wall, can be identified:
Gracilicutes are the Gram negatives, Firmicutes are Gram positive, Tenericutes lack cell wall
and Mendoricutes are prokaryotes which have unusual cell wall. The bacterial morphology
takes into account the different shapes and arrangement of the cells which include, cocci
(spherical), bacilli (rod-shaped), spiral and filamentous forms.
II. Oxygen Growth Requirements: Microorganisms can be grouped on the basis of their
need for oxygen to grow. Facultatively anaerobic bacteria can grow in high oxygen or
low oxygen content and are among the more versatile bacteria. In contrast, strictly
anaerobic bacteria grow only in conditions where there is minimal or no oxygen present
in the environment. Bacteria such as bacteroides found in the large bowel are examples
of anaerobes. Strict aerobes only grow in the presence of significant quantities of
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oxygen. Pseudomonas aeruginosa, an opportunistic pathogen, is an example of a strict
aerobe. Microaerophilic bacteria grow under conditions of reduced oxygen and
sometimes also require increased levels of carbon dioxide. Neisseria sp. (e.g., the cause
of gonorrhea) are examples of micraerophilic bacteria.
Fig. 1 Classification by some phenotypic characteristics
EXERCISE
1. What are the phenotypic classification schemes?