Ch 10 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 • Species
relationships • Genus
• Species are groups • Family
that interbreed (have • Order
productive sex)
• Class
• How this goes
• Division
• Phylum
• Kingdom (1969)
• Domain (80’s)
 The 5 Kingdoms based on
nutrient procurement
• Plantae • Which of these are
– Multicellular microbes?
photoautotrophs
• Animalia
– ingestive
• Fungi
– absorptive
• Protozoa
– Mostly singe celled
• Prokaryotes
 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 Source of Genus Source of
Binomial Name Specific Epithet
Klebsiella Honors Edwin The disease
pneumoniae Klebs
Pfiesteria piscicida Honors Lois Disease in fish
Pfiester
Salmonella Honors Daniel Stupor (typh-) in
typhimurium Salmon mice (muri-)
Streptococcus Chains of cells Forms pus (pyo-)
pyogenes (strepto-)
Penicillium Tuftlike (penicill-) Produces a
chrysogenum yellow (chryso-)
pigment
Trypanosoma cruzi Corkscrew-like Honors Oswaldo
(trypano-, borer; Cruz
 Species Definition
• Eukaryotic species:
– A group of closely related organisms that breed among
themselves
• Prokaryotic species:
– 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
• 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 Identification Methods
s: Useful for
identifying
eukaryotes
• Differential
staining: Gram
staining, acid-
fast 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
• 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