General Themes for Classifying Microorganisms
2014
GENERAL METHODS FOR CLASSIFYING MICROORGANISMS
Taxonomy is the science that studies organisms in order to arrange them into groups. It can be
viewed as three separate but interrelated areas:
• Identification; the process of characterizing organisms
• Classification; the process of arranging organisms into similar or related groups,
primarily to provide easy identification and study
• Nomenclature; the system of assigning of names to organisms
To characterize and identify microorganisms, a wide assortment of technologies/ criteria is used
including microscopic examination, culture characteristics, biochemical tests, and nucleic acid
analysis. However, a combination of tests may provide the most accurate identification.
The various methods used to identify bacteria (Prokaryotes) include;
1. Microscopic morphology
This deals with the study of size, shape and staining characteristics of microbes. Main groups of
microorganisms (e.g. bacteria) are classified according the microscopic observation of their
morphology. These include categories such as;
a. Spherical/cocci such as staphylococci, streptococci, diplococci,
b. Rod /Bacilli such as Bacilli, curved rods, coccobacilli, lactobacilli
c. Spiral such as the spirochetes (Treponema pallidum, the cause of syphilis)
d. Gram stain: is used to separate bacteria into two major groups, Gram positive & Gram
negative. The staining characteristics of these groups reflect a fundamental difference in
the chemical structure of their cell walls.
i. Thick layer of peptidoglycan/ retaining of primary gram stains (Gram-positive)
ii. Thin layer of peptidoglycan/ loose the primary stain (Gram-negative)
e. Acid-Alcohol Fast Bacilli (AAFB) stain: This is used to detect members of genus
Mycobacterium in a specimen. Due to the lipid composition of their cell walls (waxy coat
of mycolic acids on top of cell wall), these organisms do not readily take up gram stains.
f. Capsule stains for bacteria such as India ink. Because the viscous capsule does not
readily take up stains, it stands out against a stained background. This is an example of a
negative stain. Cryptococcus neoformans (the cause of cryptococcal
meningoencephalitis) is one of the few types of yeasts (fungi) that produce a capsule.
g. Endospore stains for bacteria such as Schaeffer-Fulton method & Dorner method for
staining members of genera Bacillus (e.g. Bacillus anthracis that causes anthrax, and
Clostridium e.g. Clostridium tetani the causes of tetanus). This stains endospores, a type
of a dormant cell that does not readily take up stains.
h. Flagella stain: the staining agent adheres to and coats the otherwise thin flagella,
enabling them to be seen with the light microscope
2. Biological characteristics
This bases on all kinds of demonstrable or physiological characters of microbes. These include
processes that affect the life of the microbe such as;
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General Themes for Classifying Microorganisms
2014
a. Oxygen tolerance e.g.
i. obligate aerobes, have an absolute requirement for O2 e.g. members of genus
Pseudomonas, a diverse group of Gram negative rods
ii. obligate anaerobes, cant multiply in the presence of oxygen e.g. genus Clostridium
& genus Bacteroides (the major inhabitants of intestines)
iii. facultative anaerobes, grow best if O2 is present, but can also grow without it e.g.
E.coli & yeast (an eukaryotic fungi)
iv. Aerotolerant (obligate fermenter), these are indifferent to oxygen. They can grow
in its presence, but can’t use it to transform energy. They include Lactobacillus
delbrueckii & Streptococcus pyogenes which causes strep. throat
v. Microaerophiles, requires small amount of O2 (2 - 10%), but higher concentrations
are inhibitory e.g. Helicobacter pylori that causes gastric and duodenal ulcers.
b. Optimum temperatures such as:
i. psychrophiles (optimum temperature between -5oC and 15oC)
ii. Mesophiles, (optimum temp between 25oC and 45oC). Most disease causing
bacteria which are adapted to growth in the human body typically have an
optimum temp between 35oC and 40oC
iii. Thermophiles, (optimum temp between 45oC and 70oC)
iv. hyperthermophile microbes (optimum temp between 70oC and 110oC)
c. Optimum pH such as alkalophiles (grows optimally at pH above 8.5), acidophiles (grows
optimally at pH below 5.5), and neutrophile (multiplies in the range of pH 5 to 8)
3. International classification criteria
This is the widely practiced criteria of classification that looks at more than one aspect of the
microorganisms. In here, both biological and morphological characteristics of microbes are used
so as to clearly identify the microbe in the specimen. Examples include;
a. Gram negative Aerobic diplococci e.g. Neisseria gonorrheae & Neisseria meningitidis
b. Gram negative Facultative anaerobic rods e.g. family Enterobacteriaceae with members
like E.coli, Salmonella, Shigella, Klebsiella, Proteus, Yersinia……
c. Gram positive spore-forming rods e.g. Bacillus anthracis, Clostridium tetani,
Clostridium, botulinum, Clostridium perfringens………
d. Gram positive non-spore-forming rods e.g. Lactobacillus, Corynebacterium diphtheriae,
Mycobacterium tuberculosis, Nocardia, Streptomyces, Actinomyces
4. Numerical classification (Andersonian)
This system determines the degrees of relationship between species or strains by a statistical
coefficient which take into account their similarities and differences. The following mathematical
equation is always applied;
S=
Ns
X 100
NS + Nd
Where S = the degree of similarity
Ns = number of shared characteristics or similarities
Nd = number of similarities
The higher the value of S, the closer the organisms are to each other and vice-versa.
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General Themes for Classifying Microorganisms
2014
5. Biochemical characters (metabolic differences)
This relies on the analysis of the metabolic capabilities of microbes such as the sugars utilized or
the end products and enzymes. In some cases, these characteristics are revealed by the growth &
colony morphology on cultivation media, but most often are demonstrated using biochemical
tests. The following are examples
a. β-hemolytic bacteria such as Staphylococcus aureus & Streptococcus pyogenes
b. α-hemolysis of bacteria such as Streptococcus pneumoniae, Strep. gordonni
c. Catalase enzyme; used to differentiate Streptococcus (-) from Staphylococcus (+), and
Bacillus (+) from Clostridium (-)
d. Coagulase enzyme is important in differentiating Staphylococcus aureus (+) from
Staphylococcus epidermidis (-)
e. Oxidase enzyme is important in distinguishing Neisseria spp & Morexella (+) from
Acinetobacter (-), and all enterics from Pseudomonas spp (+)
f. Lactose fermenters e.g. E.coli & genus Streptococcus, the most common cause of urinary
tract infections forms characteristic pink colonies on MacConkey agar.
g. Urease test (breath test) detects the enzymatic degradation of urea to carbon dioxide and
ammonia by Helicobacter pylori
h. Oxidase test detects the activity of cytochrome c oxidase, a component of the electron
transport chain of specific organisms such as Pseudomonas & Campylobacter.
6. Genotypic Analysis (DNA composition)
It has been established that the sum total of G + C is relatively fixed or falls within a narrow
range for different species and stains of microbes and thus can be used as a basis for genotyping
microorganisms. Slight changes in nucleotide composition of microorganisms could lead to a rise
to new variants.
7. Serological analysis
The serum composition (antibody) can give information about the identity of the microorganism.
Proteins and polysaccharides making up the microbe are characteristic enough to be detected
using specific antibodies. Therefore such tests base on the antibody-antigen specificity.
8. Antibiotic sensitivity: Some microorganisms are sensitive to certain antibiotics while others are
resistant, Bacitracin sensitivity useful in identification of Streptococcus pyogenes while Optochin
sensitivity is used to identify pneumococcus.
Classification of Common Disease-producing Bacteria (Shapes, Arrangements & Gram reaction)
Shape
Cocci (spherical)
Gram positive
”
Gram negative
Bacilli (rod)
Gram negative
facultative rods
Gram negative
aerobic rods
Gram negative
Cell arrangement
Staphylococcus
(cluster of spherical bacteria)
Streptococcus
(chain of spherical bacteria)
Diplococcus (pairs)
micrococcus
bacilli
bacilli
Curved rods
(comma- shaped)
coccobacilli
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Examples
Staphylococcus aureus, Staphylococcus epidermidis,
Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus mutans
Neisseria gonorrhoeae, Neisseria meningitidis
Escherichia coli, Salmonella typhi. Shigella dysenteriae. Klebsiella
pneumoniae. Proteus vulgaris, Yersinia pestis, etc.
Pseudomonas aeruginosa, Brucella abortus, Bordetella pertussis.
Vibrio cholerae, Campylobacter jejuni, Helicobacter pyroli
Moraxella, Acinetobacter
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General Themes for Classifying Microorganisms
Gram positive
Spore-forming rods
Gram positive
Non-spore-forming rods
Filamentous or branched
bacteria
Spirochete
(more flexible)
Spirillum (rigid helix)
Spiral
2014
Bacillus anthracis, Clostridium tetani, Clostridium botulinum, Clostridium
perfringens
Corynebacterium diphtheriae, Listeria monocytogenes
Streptomyces, Actinomyces, Nocardia spp.
Treponema pallidum (cause of syphilis)
Borrelia recurrentis (Lyme disease/ relapsing fever
Spirillum minor
NB: READING ASSIGNMENT
Read and make notes about Bergey’s manual of systematic bacteriology
Classification of eukaryotic Microorganisms
Domain Eukarya contains 4 kingdoms
1. Kingdom Protista: the protozoa are microscopic unicellular organisms that lack the rigid
cellulose cell wall found in plants and algae, lack photosynthetic capability, are usually
motile at least at some stage in life and reproduce most often by asexual fission. The disease
causing protozoa include: Trypanosoma, Giardia, Trichomonas, Leishmania, Entamoeba,
Balantidium, Plasmodium, Toxoplasma, Cryptosporidium, etc.
2. Kingdom fungi: these include both the unicellular (yeasts) and multicellular (molds) forms.
All fungi have chitin in their cell walls, and no flagellated cells at any time during their life
cycle. Classification may be based on the mode of sexual reproduction with groups’
Zygomycetes, Basidiomycetes, & Ascomycetes, while Deuteromycetes (fungi imperfecti)
have not shown any sexual reproduction. Fungal diseases (mycoses) are classified according
to the part of the body that they affect. These include;
a. Superficial mycoses affecting only hair, skin or nails. The skin-invading molds
belong mainly to genera Epidermophyton, Microsporum, and Trichophyton, and are
generally termed dermatophytes. Other fungi include Candida albicans (candidiasis)
and Malassezia (tinea versicolor) affecting the skin. The location of the superficial
mycoses is often Latinized with names such as tinea capitis – scalp, tinea barbae –
beard, tinea axillaris – armpit, tinea corporis – body , tinea cruris – groin, and tinea
pedis – feet.
b. intermediate mycoses which are limited to the respiratory tract or the skin and
subcutaneous tissues
c. systemic mycoses affect tissues deep within the body e.g. histoplasmosis
(Histoplasma capsulatum), blastomycosis (Blastomyces dermatitidis)
3. Kingdom Animalia: these include the multicellular eukaryotic microorganisms commonly
referred to as parasites; they include Helminths such as Schistosomes, liverflukes, etc.
Viruses:
These are not composed of cells thus are acellular. They are classified according to:
a. Nucleic acid type, i.e. DNA virus or RNA virus
b. Availability of envelope, i.e. enveloped or non-enveloped viruses
c. Shape of the capsid i.e. helical, icosahedral or complex.
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