Classification and Nomenclature of Bacteria
Classification is the arrangement of organisms into groups or taxa (singular‐taxon) based on mutual
similarity or evolutionary relatedness.
Nomenclature is the branch of taxonomy concerning with assigning names to taxonomic groups in
agreement with published rules. It permits ease of communication.
Mumericlature is coding in figures of the organisms and is done by accession numbers, codes or letters
and figures e.g. 13680‐1469:1 = Staphylococcus aureus
Identification is the process of determining a particular isolate which belongs to a recognized taxon. It is
a practical approach to taxonomy which is more useful in clinical microbiology.
Classification, nomenclature and identification all are interrelated and comprise the trinity that
Cowan referred to as Taxonomy.
Bacteriologists adopted the hierarchical system of classification established by Carolus
Linnaeus (Father of taxonomy) for botany and zoology.
Whittacker (1969) formed 5 Kingdoms for all the living organisms:
1. Animalia (Animal, birds, butterflies, snails, earthworms)
2. Plantae (Plants)
3. Fungi (Edible mushrooms, yeasts, moulds)
4. Protista (Algae, protozoa like paramecium, amoeba and Euglena)
5. Monera/ Prokaryotae (mostly unicellular organisms, bacteria, rickettsia etc.)
Some taxonomists have recommended creating a 6th Kingdom for Archaebacteria.
In this system, species are grouped into genera, genera into families, and so on, and the species
are designated by Latin, or Latinized binomials (binomial nomenclature) e.g. Mycoplasma mycoides
subspecies mycoides (cause of CBPP) is classified as follows:
Kingdom Prokaryotae/ Monera
Division (Phylum) Tenericutes (Teneri‐ soft/tender, cutes‐skin)
Class Mollicutes
Order Mycoplasmatales
Family Mycoplasmataceae
Tribe ‐‐‐‐‐‐‐‐‐‐
Genus Mycoplasma
Species mycoides
Subspecies mycoides
Other example:
Kingdom Plant
Phylum Thallophyta
Class Schiomycetes
Order Eubacteriales
Family Micrococcaceae
Genus Staphylococcus
Species aureus
Binomials are printed in italics, the genera name having an initial capital letter and species
name begins with small letter. If binomials can not be italicized as in writing they must be underlined
separately for genus and species and family name is also italicized.
Monera/ prokaryotae kingdom include organisms like bacteria (including Gram‐positive, Gram‐
negative bacteria, mycoplasma, cyanobacteria, archaebacteria, spirochetes and rickettsia) which do not
reproduce sexually and reproduce by binary fission. It is divided into four main Divisions depending
upon the presence or absence of cell wall and its composition:
Division I Gracilicutes (Gram‐negative bacteria with thin peptidoglycan in cell wall)
Division II Firmicutes (Gram‐positive bacteria with durable or firm cell wall)
Division III Tenericutes (mycoplasma organisms lacking cell wall and peptidoglycan)
Division IV Mendosicutes (organism with defective/faulty cell wall and these organisms thrive in
extremes of environmental conditions called extremophiles and are:
9 Methanogens which produce methane from carbon.
9 Thermoacidophiles which survive in hot acidic volcanic temperature.
9 Halophiles which can survive in salty environment.
Biological classifications are information‐storage systems, and economy in storage is achieved
through the non‐ovelapping hierarchical arrangement. The classification enables the allocation of fresh
isolates to known species (the identification system) or if they can not be so allocated leads to the
recognition of new species.
The only classification of bacteria that has persisted through the years is that contained in the
successive editions of Bergey’s Manual of Determinative Bacteriology and subsequently in the Bergey’s
Manual of Systematic Bacteriology
Criteria for classification of bacteria are
1. Morphology (of individual bacteria) (discussed in first lectures)
2. Staining (Gram‐positive/ Gram‐negative, acid fast) e.g. a Gram staining smear would
reveal that whether a bacteria is gram positive or gram negative. Staining can also
reveal shape, size of bacteria and presence or absence of spores and capsule. Some acid
fast bacteria like mycobacteria can be stained by zeihl nelson method.
3. Growth (colony, pigment, morphology) shape and sie of the colonies on solid media,
The colonies may be flat, umbonate, convex or nodular. They may produce certain
pigments or not. They may be clear transparent or opaque. Some may produce changes
in media like haemolysis on blood agar.
4. Nutrition (autotrophs, heterotrophs, fermentative) it depicts growth requirements of
bacteria.
5. Physiology (discussed in previous lecture)
i. Temperature (mesophiles, psychrophiles, thermophiles)
ii. pH
iii. O2 requirement (aerobic, anaerobic, facaultively anaerobic, microaerophilic)
iv. Salt requirement (halophiles)
v. Osmotic tolerance
vi. Antibiotic sensitivity: the degree of sensitivity of microorganisms to varying
concentrations of antibiotics and chemotherapeutic agents is an important criteria
for classification of bacteria. Zone of inhibition to bacterial growth produced
antibiotic disc is indicative of degree of sensitivity to that antibiotic.
6. Biochemistry
i. Nature of the cell wall
ii. RNA molecules (16S rRNA is used to study evolutionary relationship because it is
universally distributed in all bacteria, constant in function, slow to change, and easy
to isolate)
iii. Ribosomes
iv. Storage inclusions
v. Pigments: some bacteria may produce pigments in media like Pseudomonas
produce pyocyine.
vi. Protein profile by Polyacrylamide gel electrophoresis (PAGE) and amino acid
sequencing.
7. Genetics
It is the most important criteria for classification of bacteria
i. Percentages of bases (G+C%)
ii. DNA (hybridization, genome size, base composition/sequence, Restriction fragment
length polymorphism by restriction endonucleases.)
iii. Phage typing: it is applicable to identification of those bacteria which are sensitive
to the lysis of certain set of bacteriophages. Phage type of the organism is identified
based on the lysis by bacteriophages.
8. Antigenic characterization:
The antigenic composition of bacteria is of great value. The antibodies produced by the
organisms by their inoculation into naturally infected or artificially infected host react
specifically with their counterpart antigen. The antigen antibody reactions are basis f various
serological tests like agglutination, agar gel precipitation, complement fixation test.
9. Typing of bacteria: typing of bacteria is important in epidemiological investigations of disease
where point of origin of infection is not known. Typing can be done by biochemical tests,
serological tests, genome sequencing, bacteriophage typing and bacteriocin typing.
Some definitions:
Strain is a line or population of bacteria that descends from a single ancestral bacterium, as found in
natural habitat and in primary cultures from that habitat and subcultures from the primary cultures.
Type strain is one strain of species. It is usually one of the first strains studied and often is more fully
characterized. It does not have to be the most representative member.
Species is a collection of strains that share many stable characters and differ significantly from other
groups of strains.
Genus is a well defined group of one/ more species and is clearly separate from other genera.
Clones are young colonies that consist exclusively of the progeny of a single cell and not to include any
demonstrable mutant cell.
Isolate is each primary culture isolated from a natural source.