Classification of Microorganisms
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The Study of Phylogenetic Relationships
• Taxonomy is the science of classifying organisms
– Shows degree of similarity among organisms
• Systematics, or phylogeny, is the study of the
evolutionary history of organisms
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The Three Domains
• Developed by Woese in 1978; based on sequences of
nucleotides in rRNA
• Eukarya
– Animals, plants, fungi
• Bacteria
• Archaea
– Methanogens
– Extreme halophiles
– Hyperthermophiles
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Figure 10.1 Three-Domain System
Key Concepts
• All organisms evolved from cells that formed over 3 billion years ago.
• The DNA passed on from ancestors is described as conserved.
• The Domain Eukarya includes the kingdoms Fungi, Plantae, and Animalia,
as well as protists. The Domains Bacteria and Archaea are prokaryotes.
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TABLE 10.1 Some Characteristics of
Archaea, Bacteria, and Eukarya
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TABLE 10.2 Prokaryotic Cells and
Eukaryotic Organelles Compared
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The Three Domains (2 of 2)
• Eukaryotes originated from infoldings of prokaryotic
plasma membranes
• Endosymbiotic bacteria developed into organelles
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Figure 10.2 A Model of the Origin of
Eukaryotes
Early cell Bacteria
Chloroplast
Archaea Mitochondrion
DNA
Eukarya
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Figure 10.3 Cyanophora paradoxa
Bacterium
Eukaryotic host cell
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A Phylogenetic Tree
• Grouping organisms according to common properties
– Fossils
– Genomes
Mutations accumulated in the genomes serve
as a molecular clock
• Groups of organisms evolved from a common
ancestor
• Each species retains some characteristics of its
ancestor
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Figure 10.4a Fossilized Prokaryotes
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Figure 10.4b Fossilized Prokaryotes
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Figure 10.4c Fossilized Prokaryotes
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Scientific Nomenclature
• Common names vary with languages and geography
• Binomial nomenclature is used worldwide to
consistently and accurately name organisms
– Genus
– Specific epithet (species)
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Table 1.1 Making Scientific Names
Familiar
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The Taxonomic Hierarchy
• A series of subdivisions developed by
Carolus Linnaeus to classify plants and animals
• Eukaryotic species: a group of closely related
organisms that breed among themselves
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Figure 10.5 The Taxonomic Hierarchy
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Classification of Prokaryotes
• Prokaryotic species: a population of cells with
similar characteristics
– Culture: bacteria grown in laboratory media
– Clone: population of cells derived from a single
parent cell
– Strain: genetically different cells within a clone
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Figure 10.6 Phylogenetic
Relationships of Prokaryotes
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Classification of Eukaryotes
• Protista: a catchall kingdom for a variety of organisms;
autotrophic and heterotrophic
– Grouped into clades based on rRNA
• Fungi: chemoheterotrophic; unicellular or multicellular;
cell walls of chitin; develop from spores or hyphal
fragments
• Plantae: multicellular; cellulose cell walls; undergo
photosynthesis
• Animalia: multicellular; no cell walls; chemoheterotrophic
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Classification of Viruses
• Not a part of any domain; not composed of cells;
require a host cell
• Viral species: population of viruses with similar
characteristics that occupies a particular ecological
niche
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Methods of Classifying and
Identifying Microorganisms
• Classification: placing organisms in groups of related
species
– Lists of characteristics of known organisms
• Identification: matching characteristics of an
"unknown" organism to lists of known organisms
– Clinical lab identification
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Methods of Classifying and
Identifying Microorganisms
• Bergey's Manual of Determinative Bacteriology
provides identification schemes for identifying bacteria
and archaea
• Approved Lists of Bacterial Names lists species of
known classification
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Methods of Classifying and
Identifying Microorganisms
• In clinical microbiology, lab requisition forms are used
to note types of specimens collected and tests to be
conducted
• Transport media is used to collect and transport
pathogens to a laboratory
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Figure 10.7 A clinical Microbiology
Lab Report Form
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Methods of Classifying and
Identifying Microorganisms
• Morphological characteristics: useful for identifying
eukaryotes; tell little about phylogenetic relationships
• Differential staining: Gram staining, acid-fast staining;
not useful for bacteria without cell walls
• Biochemical tests: determine presence of bacterial
enzymes
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Figure 10.8 The Use of Metabolic
Characteristics to Identify Selected
Genera of Enteric Bacteria
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CLINICAL FOCUS Mass Deaths of
Marine Mammals Spur Veterinary
Microbiology
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Biochemical Tests
• Rapid identification methods perform several
biochemical tests simultaneously
– Results of each test are assigned a number
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Figure 10. 9 One type of Rapid Identification Method for Bacteria: EnteroPluri Test From BD Diagnostics
One tube containing media for 15 biochemical tests
is inoculated with an unknown enteric bacterium.
After incubation, the tube is observed for results.
Phenylalanine
Arabinose
Ornithine
Adonitol
Glucose
Lactose
Sorbitol
Dulcitol
Urease
Citrate
Lysine
Indole
V–P
Gas
H2S
The value for each positive test is circled, and
the numbers from each group of tests are
added to give the code number.
Comparing the resultant code number with a Code Number Microorganism Atypical Test Results
computerized listing shows that the organism in
the tube is Citrobacter freundii. 62352 Citrobacter freundii Citrate
62353 Citrobacter freundii None
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Biochemical Tests
• Automated rapid identification system is available for
medically important bacteria and yeast
– The data from a mass spectrophotometer are
compared to a database
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Figure 10.10 Cellular Proteins Detected by
Mass Spectrophotometry Create a Spectrum
That Can Be Compared to a Database
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Serology
• The science that studies serum and immune
responses in serum
• Microorganisms are antigenic—they stimulate the
body to form antibodies in the serum
• In an antiserum, a solution of antibodies is tested
against an unknown bacterium
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Serology
• In the slide agglutination test, bacteria agglutinate
when mixed with antibodies produced in response to
the bacteria
• Serological testing can differentiate between species
and strains within species
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Figure 10.11 A Slide Agglutination
Test
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Serology
• Enzyme-linked immunosorbent assay (ELISA)
– Known antibodies and an unknown type of
bacterium are added to a well; a reaction identifies
the bacteria
• Western blotting
– Identifies antibodies in a patient's serum; confirms
HIV infection, and Lyme disease
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Figure 10.12 An ELISA Test
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Figure 18.14a The ELISA Method
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If Lyme disease is suspected in a patient:
Electrophoresis is used to separate Borrelia
burgdorferi proteins. Proteins move at Lysed
Polyacrylamide
different rates based on their charge and size bacteria
gel
Figure 10.13 when the gel is exposed to an electric current.
Proteins
The Western Larger
Blot Smaller
The bands are transferred to a nitrocellulose Paper towels
filter by blotting. Each band consists of many Salt solution Sponge
molecules of a particular protein (antigen). The
bands are not visible at this point.
Gel
Nitrocellulose
filter
The proteins (antigens) are positioned on the filter
exactly as they were on the gel. The filter is then
washed with patient’s serum followed by antihuman
antibodies tagged with an enzyme. The patient
antibodies that combine with their specific antigen
are visible (shown here in red) when the enzyme’s
substrate is added.
The test is read. If the tagged antibodies stick to
the filter, evidence of the presence of the
microorganism in question—in this case, B.
burgdorferi—has been found in the patient’s
serum.
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Phage Typing
• Test for determining which phages a bacterium is
susceptible to
• On a plate, clearings called plaques appear where
phages infect and lyse bacterial cells
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Figure 10.14 Phage Typing of a Strain
of Salmonella Enterica
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DNA Sequencing
• DNA base composition
– Guanine + cytosine %
– GC + AT = 100%
– Two organisms that are closely related have
similar amounts of various bases
– Online databases (NCBI Genome Database)
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DNA Fingerprinting
• DNA fingerprint
– Electrophoresis of restriction enzyme digests of an
organism's DNA
– Comparing fragments from different organisms
provides information on genetic similarities and
differences
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Figure 10.15 DNA fingerprints
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Nucleic Acid Hybridization
• Nucleic acid hybridization measures the ability of
DNA strands from one organism to hybridize with
DNA strands of another organism
– Greater degree of hybridization, greater degree
of relatedness
– Hybridization of >70% indicates same species
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Figure 10.16 DNA-DNA Hybridization
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Nucleic Acid Hybridization
• Nucleic Acid Amplification Tests (NAATs) use PCR
to amplify DNA of an unknown microorganism that
cannot be cultured
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Nucleic Acid Hybridization
• Southern blotting uses nucleic acid hybridization to
identify unknown microorganisms using DNA probes
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Figure 10.17 A Plasmid
DNA Probe Used Salmonella
DNA
to Identify fragment
Bacteria
Unknown bacteria
A Salmonella DNA are collected
fragment is cloned in on a filter.
E. coli.
The cells are lysed,
and the DNA
is released.
Cloned DNA fragments are marked
with fluorescent dye and separated
into single strands, forming
DNA probes. The DNA is separated into
single strands.
DNA probes are added
to the DNA from the Fluorescent probe
unknown bacteria.
Salmonella DNA
DNA probes hybridize with
Salmonella DNA from sample.
Then excess probe is washed DNA from
off. Fluorescence indicates
other bacteria
presence of Salmonella.
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Nucleic Acid Hybridization
• A DNA chip (also known as a microarray) contains
DNA probes and detects pathogens by hybridization
between the probe and DNA in the sample
– Detected by fluorescence
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Figure 10.18a-b DNA Chip
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Figure 10.18c-d DNA Chip
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Nucleic Acid Hybridization
• Ribotyping
– rRNA sequencing
• Fluorescent in situ hybridization (FISH)
– Fluorescent DNA or RNA probes stain the
microorganisms being targeted
– Determines the identity, abundance, and relative
activity of microorganisms in an environment
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Figure 10.19 FISH, or Fluorescent in
Situ Hybridization
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Putting Classification Methods
Together
• Dichotomous keys
– Identification keys based on successive questions
• Cladograms
– Maps that show evolutionary relationships among
organisms; based on rRNA sequences
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Figure 10.20 Building a Cladogram
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Animation: Dichotomous Keys:
Sample with Flowchart
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Animation: Dichotomous Keys:
Practice
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