Introduction
Bacteria are ubiquitous single celled microscopic organism and as such, are vital for a balanced ecosystem. Their roles vary from symbiotic to parasitic and have been linked to functions such as nitrogen fixation in the soil, decomposition of dead matter, pathogenesis of several diseases, among others.
It is estimated that fewer than 10% of medically important bacteria have been properly characterized. This means that information on their particular mode(s) of transmission, mechanism of growth and pathology are yet to be properly documented. This is mostly because of the difficulty in growing these organisms under laboratory conditions.
Yet, the diversity of even these identifiable pathogens is so great that it is important to understand the subtle differences associated with each infectious agent. These differences such as their colony morphology, microscopic characteristics, biochemical characteristics and genetic variations serve as the basis for classifying bacteria into various classes.
Bacteria Taxonomy
The science of classifying bacteria is therefore bacterial taxonomy. Classification of bacteria into different taxons (arrangements) serves to indicate the natural relationship between the organisms.
The Linnean system, developed by Carl Von Linne between 1753 and 1758 for both plants and animals, is widely ustised among scholars and classifies bacteria into difeerent kingdom, phylum, class, order, family, genus and specie. The specie level, which is the lowest rank, is the described as a genomically coherent group of individual isolates or strains sharing a high degree of similarity in many independent features when comparably tested under highly standardized conditions.
Bacterial taxonomy consists of three inter-related disciplines including:
- classification
- nomenclature and
- identification.
Classification:
This refers to arrangements of bacteria into groups on basis of their mutual similarity or evolutionary relatedness. It requires experimental and observational techniques necessary in order to place these organisms into different groups. These techniques are developed based on peculiar characteristics of the bacteria including biochemical, physiologic, genetic, and morphologic properties.
Nomenclature:
This refers to the naming of an organism based oninternational rules established by a recognized body. Binomial nomenclature makes use of the genus and specie names assigned to the bacteria, with the first letter of the former written in capital. These names are must be italicized (when written digitally) or underlined (on paper) as the case may be. An example is Escherichia coli, where Escherichia is the genus and coli is the specie.
Identification:
The process of identification consists of a series of tests, designed based on pre-existing knowledge of the characteristics of a particular bacteria. In other words, bacterial specie would have to be properly classified before parameters for its identification can be setup. Identification schemes setup can therefore serve as useful tools in discovering bacteria of medical importance.
Criteria for Classifying Bacteria
Bacteria are classified into taxons based on several characteristics which they possess, including:
- morphology
- growth characteristics
- staining and
- microscopy, among others
1. Morphology
This has to do with study of the structures presented by the bacteria. This may include shapes, arrangement, presence of endospores, flagellum (single or multiple), among others. This can be used to separate bacteria on the genera level (eg. Staphylococci and Streptococci) due to the fact that morphological characteristics are relatively stable among closely related species.
a. Shapes and Arrangements:
Bacteria may present in various shapes and arrangemts. Examples include:
- Cocci – Staphylocci (arranged in clusters eg. Staphylococcus aureus, Staphylococcus epidermidis) and Streptococci (arranged in chains eg. Streptococcus pneumoniae, Streptococccus pyogenes).
- Rods – Bacillus. Clostridium, Enterobacteriaceae (family containing Salmonella, Klebsiella, Escherichia, etc).
- Spiral: these are curved bacteria and include Vibrio (comma-shaped bacteria eg. Vibrio cholerae), Spirilla (rigid spiral structure eg. Camphylobacter jejuni, Helicobacter pylori) and Spirochetes these have helical shape with flexible body eg.
b. Endospore formation
Endospores present in some bacteria serve as means of survival under harsh environmental conditions. Unlike the vegetative cells, they are resistant and can survive for prolonged periods. The bacteria is however unable to replicate in this state and promptly returns to the vegetative state when favourable environment conditions are restored. Examples include Bacillus. Clostridium
c. Cell wall characteristics
The presence of absence of the peptidoglycan layer serves as the basis for the gram staining technique, which divides bacteria into Gram positive (Bacillus. Clostridium, Staphylocci, Streptococci) and Gram negative (Salmonella, Klebsiella, Helicobacter pylori). Other cell wall characteristics such as its absence as seen with Pleomorphic bacteria (Mycoplasma pneumoniae, Mycoplasma genitalium) are also used.
Several staining techniques (gram staining, acid fast staining, spore staining etc) have developed by targeting some of the characteristics listed above and serve as an efficient tool for classifying and identifying these organisms under the microscope.
2) Colony/Growth Characteristics:
Bacteria can be grown in the laboratory using a media. These can either be:
a. Selective:
These are used to restrict the growth of unwanted bacteria and is used in cases where the sample to be inoculated is gotten from an unsterile site. Selecting for a particular subset of bacteria requires the use of inhibitory agents such as sodium azide (inhibits growth of Gram negative bacteria)
b. Non-Selective:
This is designed to allow optimum growth of most bacteria. They include the nutrient agar, muller-hinton agar, among others.
c. Differential:
These media are designed so that specific organisms react characteristically. Such characteristic can be used to identify the bacteria and/or the members of the genera.
For example, lactose fermenting members of the Enterobacteriaceae such as Escherichia coli appear pink on a MacConkey agar while non-lactose fermenting members (Salmonella and Shigella species) appear as white colonies. Other differential media include the blood agar, chromocult agar, among others.
The colony characteristics of bacteria are invaluable in classifying and identifying such bacteria in order to avoid redundancies while isolating. This is because different bacteria have different appearance(s) depending on the media used. Colony characteristics usually taken note of include colony shape, edge, colour, elevation, surface, etc. Some colony characteristics are depicted in the figure below:
3. Biochemical Tests
These tests vary and are used to identify traits common to a bacteria or genera. They include, but are not limited to:
a. Carbohydrate Breakdown
The ability to produce acidic metabolic products (lactic acid, acetic acid, formic acid), fermentatively or oxidatively, from a range of carbohydrates (eg, glucose, sucrose, and lactose) has been applied to the identification of most groups of bacteria. For example, all Enterobacteriaceae are glucose fermenters; While both Neisseria gonorrhoeae and Neisseria meningitides are glucose fermenters, the latter alone can ferment maltose.
b. Catalase production.
The enzyme catalase catalyzes the conversion of hydrogen peroxide to water and oxygen. When a colony is placed in hydrogen peroxide, liberation of oxygen as gas bubbles can be seen. The test is particularly useful in differentiation of staphylococci (positive) from streptococci (negative),
c. Coagulase.
The enzyme coagulase acts with a plasma factor to convert fibrinogen to a fibrin clot. It is used to differentiate Staphylococcus aureus from other, less pathogenic staphylococci
d. Indole
The indole reaction tests the ability of the organism to produce indole, a benzopyrrole, from tryptophan. Indole is detected by the formation of a red dye after addition of a benzaldehyde reagent.
NB: There are other criteria for classifying bacteria which include, but are not limited to the following:
- Oxygen Requirement
- Temperature requirement
- Nutrional Relationships.
Steps in Identifying an Unknown Bacteria
1. Cultivation:
Here the specimen/sample is cultured into a basal medium (peptone water or nutrient broth) and incubated for 18-24 hr.
2. Isolation
After incubation, the broth cultures are streaked on selective media specific for the suspected or choice organism. Then incubated appropriately.
3. Purification
A colony is picked from the cultured plates and further streaked again on a new selective agar/nutrient agar and incubated appropriately.
4. Microscopy:
A pure colony growing on the agar plate is used to make a smear, stained and examined under the oil immersion lens.
5. Biochemical tests
These are confirmatory test specific for a bacterium that further identifies the isolated organism.
6. Molecular approach
Involves isolation amplification of the DNA then the bases are sequenced and compared to known sequences held in the reference library (GeneBANK) using the BLAST tool/platform.
Importance of Bacterial Taxonomy
- Taxonomy helps classifying and arranging bewildering diversity of bacteria into groups or taxa on the basis of their mutual similarity or evolutionary relatedness.
- Bacterial taxonomy helps bacteriologists to make predictions and frame hypotheses for further research based on knowledge of identical bacteria.
- Contribution of bacterial taxonomy in accurately identifying bacteria is of practical significance.