Session 6

Classification
of
Microorganisms
 Student Learning Outcomes
Define taxonomy, taxon, and phylogeny.
List the characteristics of the Bacteria, Archaea, and Eukarya domains.
Differentiate among eukaryotic, prokaryotic, and viral species.
Explain the scientific naming
Differentiate between culture, clone, and strain.
Compare and contrast classification and identification.
Explain the purpose of Bergey’s Manual.
Describe how staining and biochemical tests are used to identify bacteria.
Explain how serological tests and phage typing can be used to identify an
unknown bacterium.
Describe how a newly discovered microbe can be classified by ribotyping,
DNA fingerprinting, and PCR.
Describe how microorganisms can be identified by nucleic acid
hybridization, DNA chips, and FISH.
Explain and apply a dichotomous key
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 Taxonomy and Phylogeny
Taxonomy: Science of classifying organisms. Provides
universal names for organisms.
 Taxonomic categories: Taxon / Taxa
Phylogeny or Systematics: Evolutionary history of group of
organisms.
 Taxonomic hierarchy shows phylogenetic (evolutionary),
relationships among organisms.
 1969: Living organisms divided into five kingdoms.
 1978: Two types of prokaryotic cells found. Prokaryotic
relationships determined by rRNA sequencing.
 All Species Inventory (2001–2025)
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The Three-Domain System
Foundation Fig 10.1

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Level Above Kindom: The Three-Domain System

Carl
Woese

1978

Eubacteria (virtuosos)
Archaea (weirdoes)
Eukarya (predators and thieves)
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Endosymbiotic Theory: Origin of Eukaryotes
Figs 10.2, 10.3

Cyanophora paradoxa: modern example of

possible
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 Scientific Nomenclature

Common names
 Vary with languages
 Vary with geography
Binomial Nomenclature (genus + specific epithet)
 Used worldwide
 Escherichia coli
 Homo sapiens

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 Scientific Names

Scientific Binomial Source of Genus Source of

Name Specific Epithet
Klebsiella pneumoniae Honors Edwin Klebs The disease

Pfiesteria piscicida Honors Lois Pfiester Disease in fish

Salmonella Honors Daniel Salmon Stupor (typh-) in
typhimurium mice (muri-)
Streptococcus Chains of cells Forms pus (pyo-)
pyogenes (strepto-)
Penicillium Tuftlike (penicill-) Produces a yellow
chrysogenum (chryso-) pigment
Corkscrew-like Honors Oswaldo
Trypanosoma cruzi (trypano-, borer; Cruz
soma-, body)
 Classification: Species Definition
 Eukaryotic species: A group of closely related organisms
that breed among themselves
 Prokaryotic species: A population of cells with similar
characteristics (Bergey’s Manual of Systematic
Bacteriology is standard reference on bacterial
classification).
 Culture: Grown in laboratory media
 Clone: Population of cells derived from a single cell
 Strain: Genetically different cells within a clone
 Viral species: Population of viruses with similar
characteristics occupying a particular ecological niche.
Viruses: not placed in kingdom nor domain – not
composed of cells – cannot grow without a host cell.
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Phylogenetic Relationships of Prokaryotes

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Domain Eukarya
 Animalia: Multicellular; no cell walls;
chemoheterotrophic
 Plantae: Multicellular; cellulose cell walls;
usually photoautotrophic
 Fungi: Chemoheterotrophic;
unicellular or multicellular; cell walls of chitin;
develop from spores or hyphal fragments
 Protista: A catchall kingdom for eukaryotic
organisms that do not fit other kingdoms
 Grouped into clades based on rRNA
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 Fig 10.8

Classification and
Identification

Classification: Placing organisms in

groups of related species. Lists of
characteristics of known organisms.
Identification: Matching characteristics
of an “unknown” to lists of known
organisms.
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 Identifying Bacteria

Applications,
p. 283
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 Bergey’s Manual:
Classifying and Identifying Prokaryotes

Bergey’s Manual of
Determinative Bacteriology Morphology, differential
Provides identification staining, biochemical
schemes for identifying tests
bacteria and archaea

Bergey’s Manual of
Systematic Bacteriology
Based on rRNA
Provides phylogenetic
sequencing
information on bacteria and
archaea
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Clinical Lab Identification
Morphological
characteristics
Useful for identifying Numerical Rapid Identification
eukaryotes
Differential staining
Gram staining, acid-
fast staining
Biochemical tests
Determines presence
of bacterial enzymes

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 Serology
 Involves reactions of
microorganisms with Fig 10.10: Slide Agglutination
specific antibodies:
Combine known anti-
serum with unknown
bacterium
 Useful in determining the
identity of strains and
species, as well as
relationships among
organisms.

 Examples:
 Slide agglutination
 ELISA (see lab)
 Western blot (no details)
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Phage Typing Fig 10.13

Identification of
bacterial species
and strains by
determining their
susceptibility to
various phages.
More details on
bacteriophages
in Ch 13

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 Genetics
 DNA fingerprinting:
Number and sizes of DNA
fragments (fingerprints)
produced by RE digests are
used to determine genetic
similarities.
 Ribotyping: rRNA sequencing
 Polymerase chain reaction
(PCR) can be used to amplify
a small amount of microbial
DNA in a sample. The
presence or identification of Fig 10.14: Electrophoresis of
an organism is indicated by RE digest of plasmid DNA
amplified DNA. (see lab)
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Nucleic Acid Hybridization

Single strands of DNA or RNA, from related organisms

will hydrogen-bond to form a double-stranded molecule;
this bonding is called nucleic acid hybridization.

Examples of Applications:
• Southern blotting,
• DNA chips, and
• FISH

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Nucleic Acid Hybridization: DNA Chip

Fig 10.17
Fluorescent In Situ Hybridization (FISH)

Add DNA or RNA

probe attached to
fluorescent dye
for S. aureus

Fig 10.18a–b
 Thank You.

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