Download Ch 10 Taxonomy and Classification

Taxonomy and Classification
Classification of Microbes
Taxonomy
• Science of Classification of organisms
• Hopes to show relationships among
organisms
• Is a way to provide universal
identification of an organism
• Why do we care things are related?
Q&A
• Pneumocystis
jirovecii was
thought to be a
protozoan until
DNA analysis
showed it is a
fungus. Why
does it matter
whether an
organism is
classified as a
protozoan or a
fungus?
Phylogeny
or
Systematics
• Shows evolutionary relationships and
history among organisms
• Some obtained from fossil record
• Most bacteria use rRNA sequencing or
some other sequence information
• A goal is to identify all organisms by 2025
Hierarchy
• Evolutionary
relationships
• Species are groups
that interbreed (have
productive sex)
• How this goes
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Species
Genus
Family
Order
Class
Division
Phylum
Kingdom (1969)
Domain (80’s)
The 5 Kingdoms based on
nutrient procurement
• Plantae
– Multicellular
photoautotrophs
• Animalia
– ingestive
• Fungi
– absorptive
• Protozoa
– Mostly singe celled
• Prokaryotes
• Which of these are
microbes?
The 3 domains
• Eukarya
– Plants, animals fungi and protists
• Bacteria
– (with peptidoglycan)
• Archaea
– With unusual cell walls, and membreanes
The Three-Domain System
Figure 10.1
The Three-Domain System
Table 10.1
Endosymbiotic Theory
Figures 10.2, 10.3
Table 10.2
Scientific Nomenclature
• Binomial genus and specific epithet
(species). Is used world wide
• Is always underlined
• Rules for naming are set by international
committee’s
– International Code of Zoological Momenclature
– International Code of Botanical Nomenclature
– Bacteriological Code and Bergey’s Manual
Scientific Names
Scientific Binomial
Source of Genus Name
Source of
Specific Epithet
Klebsiella pneumoniae
Honors Edwin Klebs
The disease
Pfiesteria piscicida
Honors Lois Pfiester
Disease in fish
Salmonella typhimurium
Honors Daniel Salmon
Stupor (typh-) in mice
(muri-)
Streptococcus pyogenes
Chains of cells (strepto-)
Forms pus (pyo-)
Penicillium chrysogenum
Tuftlike (penicill-)
Produces a yellow
(chryso-) pigment
Trypanosoma cruzi
Corkscrew-like (trypano-,
borer; soma-, body)
Honors Oswaldo Cruz
Species Definition
• Eukaryotic species:
– A group of closely related organisms that breed among
themselves
• Prokaryotic species:
–
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–
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A population of cells with similar characteristics
Clone: Population of cells derived from a single cell
Strain: Genetically different cells within a clone
Culture: grown in the lab
• Viral species:
– Population of viruses with similar characteristics that
occupies a particular ecological niche
Is it as easy to classify Microbes as
it is Macrobes?
• How to classify
• What do we have to look at?
Identifying Bacteria
Applications, p. 283
Phylogenetic Relationships of
Prokaryotes
Figure 10.6
Of more than 2600 species
identified so far
• Only about 250 or
10% are pathogens
Classification and Identification
• 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
Bergey’s Manual of Systematic
Bacteriology
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Morphological characteristics
Presence of various enzymes
Serological tests
Phage typing
Fatty acid profiles
DNA finger printing
Sequence of ribosomal RNA
Is still very difficult
• Morphological
characteristic
s: Useful for
Identification Methods
identifying
eukaryotes
• Differential
staining: Gram
staining, acidfast staining
• Biochemical
tests:
Determines
presence of
bacterial
enzymes
A dichotomous key
Figure 10.8
A clinical microbiology lab report form
Figure 10.7
Identifying a Gram – Negative,
Oxidase – Negative Rod
Figure 10.8
•Unknown enteri
inoculated into tube
•After incubation the
15 tests are observed
•A numerical score is
assigned
•The species is
assigned
•This may be of is the
strain has changed
somehow. More tests
are required
• Design a rapid test for a Staphylococcus
aureus. 10-14
Figure 6.10
Serology study of serum and its immune responce
• Combine known
antiserum +
unknown
bacterium
• Slide agglutination
• ELISAp288, 514
• Western blotp289
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Southern Blot p292
DNA chip p293
Figure 10.10
• Strains with different antigens are called
– Serotypes
– Serovars
– biovars
DNA Hybridization
Phage Typing
Determining a
strains
suceptability to
certain phage or
bacterial viruses
Figure 10.13
The Western Blot
Flow Cytometry
• Uses differences
in electrical
conductivity
between species
• Fluorescence of
some species
• Cells selectively
stained with
antibody plus
fluorescent dye
Figure 18.12
A typical
dichotomous
key See
appendix H in
your lab book
Genetics
• DNA base
composition
– Guanine + cytosine
moles% (GC)
• DNA fingerprinting
– Electrophoresis of
restriction enzyme
digests
• rRNA sequencing
• Polymerase Chain
Reaction (PCR)p251
Figure 10.14
Nucleic Acid Hybridization:
DNA Chip
DNA chip
Technolog
y
Figure 10.17
Differentiate between
classificaiton and
identification
Figure 10.5
FISH
• Fluorescent
in situ
hybridization
• Add DNA
probe for S.
aureus
Figure 10.18
Differentiate between strain and
species?
Classification of viruses?
• Not currently placed in Domains or
Kingdoms
• Why?
• Species are usually a population of viruses
with similar characteristics that occupies a
particular ecological niche.
Dichotomous keys are used for
identification of organisms
Cladograms show phylogenetic
relationships among organisms
Differential staining
• Name examples
The gram stain
Using Bergies manual
• Used to Identify bacteria not classify
• Features that are used to differentiate
various organism often have little to do
with arranging the orgs in taxonomic
groups
4 major groups
• Domain Bacteria
– Gram-negative Eubacteria that have cell
walls. Proteobacteria
– Non proteobacteria Gram negative bacteria
– Gram positive Eubacteria that have cell walls
• Domain archaeobacteria
Some groups by identificaiton
• Spirochetes
– Genus Borrelia, Leptospira, Treponema
• Aerobic/microaerophilic, motikle, helical/vibroid gram negative
bacteria
– Geneus Camphylobacter
• Gram negative aerobic/microaerophilic rods and cocci
– Genus Agrobacterium, Alcaligenes, Pseudomonas
• Facultatively anaerobic gram negative rods
– Genus Enterobater, Escherichia, Klebsiella, Serratia, Shigella, Yersinia, Eikenella
• Gram positive Cocci
– Genus lactococcus, streptococcus, Staphylococcus
• Endospore forming gram positive rods and cocci
– Genus bacillus, clostridium
• Regular, nonsporing gram positive rods
– Genus Lactobacillus, listeria