Classification of Microorganisms
• Evolutionary history- common ancestral relatedness
– All cells use ATP, DNA, cell membranes, etc.
• Prokaryotes about 3.5 billion years ago, eukaryotes
about 1.5 billion years ago.
• Taxonomy – The science of the classifications of organisms.
Taxa = hierarchal categories
• A universal system. Example, International Committee on
Systemic Bacteriology, Journal of Systemic Bacteriology
• Provides a means to identify organisms
•Brief history of Taxonomy
•Originally 2 categories: plants and animals
•1857: bacteria and fungi added to plants
•1959: fungi get their own kingdom
•1968: Kingdom Prokaryote
•1969: 5 kingdoms proposed
•1978: 3 domains established above the kingdoms
Three Domain System
• Studies of rRNA (ribosomal RNA) sequences demonstrate 3
distinctly different cell lineages.
• Proposed by Carl Woese in 1978
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Three Domain System
• 1. Domain Bacteria – “True bacteria” – Peptidoglycan cell
wall. Contains all the pathogenic prokaryotes and most soil and
water bacteria.
• 2. Domain Archaea – Don’t have peptidoglycan. Live in
extreme environments and carry out unusual metabolic
processes.
• A. Anaerobic methanogens produce CH4 methane from CO2
and H2 .
• B. Extreme halophiles require high salt concentrations
• C. Hyptherthermophiles grow in hot environments
• 3. Domain Eukarya (includes the 4 kingdoms of Protista,
Fungi, Plantae, and Animalia)
– A. Protista
– Have flagella sometime during lifecycle
–Include protozoa
– B. Fungi
• Includes unicellular yeast and multicellular fungi
• Absorbs organic matter through plasma membrane
• Cells in multicellular fungi joined to form hyphae
• Most fungi lack flagella
• Fungi develop from spores or other hyphae fragments
– C. Plantae
• Include multicellular algae
• Use photosynthesis for energy
– D. Animalia
• Include worms
• Obtain nutrients and energy by ingesting organic matter
through a mouth of some kind
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Scientific Nomenclature
– 1. Binomial naming: Genus and species
• Always unique
– Name must be italicized or underlined
• Genus species
• Genus species
• Example: Staphylococcus aureus, Escherichia coli
Taxonomic Hierarchy
– Similar species are grouped into a genus; family; order; class;
phylum; kingdom; domain
Methods of Classifying and Identifying Microorganisms
– 1. Definitions
• Classification – List of characteristics and means for
comparison to aid in identification (Bergey’s Manual)
• Identification – Figuring out what organism it is for practical
purposes of treatment of infection. Not necessarily done with
same means or rigor as classification.
– So, once an organism has been classified, a scheme
for identification can be established using some key
characteristics.
2– Morphological characteristics
• a. Can do in a limited manner, e.g. some related bacteria look
the same on a plate.
– Example: Staphs and enteric can be recognized
• b. Differential staining: Gram stain for most.
Acid Fast stain for Mycobacteria
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• c. In clinical microbiology you often start with what you think
you have based on these criteria.
– 3. Differential staining: one of the first steps for identification
• a. Gram stain
• b. Acid fast stain
– 4. Biochemical Tests
• a. The possession of various enzymes as determined by
biochemical tests, e.g. fermentation tests .
• b. Also selective and differential media is used to get an
early preliminary ID, saves time. Ex. Blood agar, MacConkey
agar.
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– 5. Serology
• Use antibodies in a variety of ways to either detect presence
of microorganisms directly or past infections indirectly by
presence of antibodies to an organism.
• Antibodies have a specific reaction to the organism that
provoked their production so a positive reaction can be used
for a specific ID.
– 6. DNA fingerprinting and Polymerase Chain Reaction
(PCR)
• Can tell relatedness of organisms. Improves classification
schemes. DNA fingerprinting is used in epidemiological
studies of source of outbreaks.
• PCR used to detect small amounts of organisms or organisms
not detectable by conventional culture techniques.
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