Classification of Microorganisms

Describe the classification of micro-organisms, including viruses, bacteria, protozoa and fungi

Microorganisms can be classified as prokaryotes (bacteria), viruses, or eukaryotes (which include fungi, helminths, and protozoa).


  • Bacteria are prokaryotic organisms
  • Most clinically relevant bacteria can be classified by Gram stain and shape1
    • Gram stain separates bacteria according to their cell wall composition
      It cannot be used on organisms that lack a cell wall, such as mycoplasma.
      • A crystal violet followed by an iodine solution is applied to the slide, which is then washed with a solvent
        • Gram +ve organisms will retain the stain due to their thick peptidoglycan cell wall, whilst gram negative organisms become colourless
      • A safranin pink stain is then applied, which stains the gram -ve bacteria pink
    • Bacteria can also be classified by shape into:
      • Cocci
        Appear round on microscopy.
      • Rods

Combining of these two systems classifies a large proportion of microbes:

Examples: Gram Positive Gram Negative
Cocci Staphylococcus Aureus, Streptococcus Pneumoniae N. Meningitidis, N. Gonorrhoea
Rods Listeria, Clostridium difficile Escherichia Coli, Pseudomonas aeruginosa

Bacterial Subclassification

Additional testing can be done to further classify bacteria:

  • Catalase testing is performed on Gram positive cocci
    Hydrogen peroxide is added to a bacterial sample, and in the presence of catalase will produce oxygen.
    • Catalase positive indicates Staphylococci
    • Catalase negative indicates Streptococci (and enterococci)
  • Coagulase testing is performed on Staphylococcal species
    Coagulase is an enzyme which cleaves fibrinogen to fibrin. The staphylococcal colony is added to rabbit plasma and incubated. In the presence of coagulase, fibrin is formed.
    • Coagulase positive strongly suggests S. Aureus
    • Coagulase negative examples include S. epidermidis or S. saprophyticus
  • Haemolytic testing is performed on Streptococcal species
    Bacterial colonies are added to blood agar, and the colour change (due to haemolysis) is noted.
    • α haemolytic organisms produce dark green agar, as methaemoglobin is produced by hydrogen peroxide produced by these organisms. Examples include:
      • Strep. pneumoniae
      • Strep. viridans
    • β-haemolytic organisms produce yellow agar from complete haemolysis. Examples include:
      • Strep. pyogenes
      • Strep. agalactiae
    • γ-haemolytic organisms leave the agar unchanged. Examples include:
      • E. faecalis
      • E. faecium
  • Additionally, gram negative rods should be further classified into pseudomonal and non-pseudomonal organisms


Viruses consist of molecules of either DNA or RNA shielded in a protein coat. They require the use of host cell structures for reproduction and are therefore obligate intracellular parasites. They can be classified by five properties:

  1. DNA/RNA
    DNA viruses replicate in the cell nucleus using a host polymerase.
  2. Double-stranded or single-stranded
    1. Most DNA viruses are double-stranded (dsDNA)
    2. Most RNA viruses are single-stranded (ssRNA)
  3. Negative-sense or positive-sense (single-stranded viruses only)
    1. Positive-sense genomes may be translated directly into mRNA
    2. Negative-sense genomes require an RNA-dependent RNA polymerase to translate them to a positive-sense strand prior to translation.
  4. Capsid Symmetry
    The protein coat may be either icosahedral or helical
  5. Enveloped or non-enveloped
    In addition to a protein coat, viruses may have a lipid membrane (acquired from the host cell) around their protein coat.

Eukaryotic Organisms

Eukaryotic organisms include fungi, protozoa, and helminths, as well as plants and animals. They differ from prokaryotic organisms in a number of ways:

Property Prokaryotes Eukaryotes
Chromosomes Single, circular Multiple
Nucleus and Organelles None Membrane bound nucleus and organelles
Cell wall Usually In plants
Ribosome 70S 80S in cell, 70S in organelles
Size 0.2-2mm 10-100mmm
  • Fungi typically feed on dead/decomposing/the immunocompromised and produce spores. They are subclassified into:
    • Yeasts
      Yeasts are unicellular. They are divided into:
      • Candida
        • Albicans
        • Non-albicans More difficult to treat.
      • Cryptococcus
    • Moulds
      Moulds are filamentous.
      • Aspergillus
      • Penicillium
    • Dimorphous Have characteristics of both yeasts and moulds.
      • Histoplasma
  • Protozoa are parasitic single-celled eukaryotes. They can be intracellular or extracellular.

  • Helminths are parasitic multi-celled eukaryotes. They can be intracellular or extracellular. They are subdivided into tapeworms (cestodes), flukes (trematodes), and roundworms (nematodes).


1. This classification does not capture spirochetes, mycoplasmas, chlamydias, and other less commonly encountered organisms. A more complete classification uses six properties:
  1. Cell Wall Structure
    1. Flexible (e.g. Spirochetes)
    2. Rigid
    3. Non-existent (e.g. Mycoplasma spp.)
  2. Morphology
    1. Unicellular
    2. Filamentous
  3. Growth Location
    1. Extracellular
    2. Obligate intracellular parasites (e.g. Chlamydia spp.)
  4. Gram Stain
    1. Gram positive
    2. Gram negative
  5. Shape
    1. Cocci
    2. Rods
  6. O2 tolerance
    1. Aerobes
    2. Anaerobes (e.g. Clostridium spp.)


  1. Harvey RA, Cornelissen CN, Fisher BD. Lippincott Illustrated Reviews: Microbiology (Lippincott Illustrated Reviews Series). 3rd Ed. LWW.
  2. CICM September/November 2008
Last updated 2020-06-11

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