Taxonomy and Classification of Microbes (Especially Prokaryotes)
• The Three Domains and What Distinguishes Them
• Review of Characteristics of Prokaryotes, Eukaryotes,
Viruses
• The Taxonomic Hierarchy and Species Definitions
• Characteristics Used to Classify Prokaryotes
• Nine Medically Important Groups of Prokaryotes
• Dichotomous Keys and Microbe Identification
Three Domain System
Eubacteria
Gram positives
Gram negatives
Spirochetes
Cyanobacteria
•Circular DNA chromosome
•Prokaryotic cell type
•Peptidoglycan cell walls
•Straight chain phospholipids
•Antibiotic sensitive
•F-methionine for first aa
Archaea
Methanogens
Halophiles
Thermoacidophiles
•Circular DNA chromosome
•Prokaryotic cell type
•No peptidoglycan in cell walls
•Branched chain phospholipids
•Antibiotic insensitive
•Methionine for first aa
Eucarya
Protista
Animalia
Fungi
Plantae
• Linear DNA chromosomes
• Eukaryotic cell type
• Cell walls variable if present
• Straight chain phospholipids
• Antibiotic insensitive
• Methionine for first aa
The Three-Domain System
Figure 10.1
Taxonomy and Classification of Microbes (Especially Prokaryotes)
• The Three Domains and What Distinguishes Them
• Review of Characteristics of Prokaryotes, Eukaryotes,
& Viruses
• The Taxonomic Hierarchy and Species Definitions
• Characteristics Used to Classify Prokaryotes
• Nine Medically Important Groups of Prokaryotes
• Dichotomous Keys and Microbe Identification
Review Chart of Cell Characteristics
Domain Eukarya
Domain
Bacteria
Cell type
Chromosomes
Cell wall?
Uni/multi
cellular
Energy
source
Example
organism
Domain
Archaea
Protista
Animalia
Plantae
Nonliving
Fungi Viruses
Review Chart of Cell Characteristics
Domain Eukarya
Cell type
Chromosomes
Cell wall?
Uni/multi
cellular
Energy
source
Example
organism
Nonliving
Domain
Domain
Eubacteria Archaea
Protista
Animalia
Plantae
Fungi Viruses
prokaryotic
eukaryotic
eukaryotic
eukaryotic
eukaryotic no cells
prokaryotic
Review Chart of Cell Characteristics
Nonliving
Domain Eukarya
Domain
Domain
Eubacteria Archaea
Protista
Animalia
Plantae
Fungi Viruses
Cell type
prokaryotic
prokaryotic
eukaryotic
eukaryotic
eukaryotic eukaryotic no cells
Chromosomes
1 Circular DNA
1 Circular DNA
Linear DNA
Linear DNA
Linear DNA
in nucleus
in nucleus
in nucleus
Cell wall?
Uni/multicell
ular
Energy
source
Example
organism
in nucleoid
in nucleoid
Linear DNA DNA or
in nucleus
RNA
Review Chart of Cell Characteristics
Nonliving
Domain Eukarya
Cell type
Chromosomes
Cell wall?
Uni/multicell
ular
Energy
source
Example
organism
Domain
Domain
Eubacteria Archaea
Protista
prokaryotic
eukaryotic
prokaryotic
1 Circular DNA 1 Circular DNA Linear DNA
in nucleoid
in nucleoid
in nucleus
yes, most of
none or
murein
pseudomurein
none
Animalia
eukaryotic
Linear DNA
in nucleus
none
Plantae
Fungi Viruses
eukaryotic eukaryotic no cells
Linear DNA Linear DNA DNA or
in nucleus in nucleus RNA
yes, of
cellulose
yes, of
chitin
no
Review Chart of Cell Characteristics
Nonliving
Domain Eukarya
Cell type
Chromosomes
Domain
Domain
Eubacteria Archaea
Protista
prokaryotic
eukaryotic
prokaryotic
1 Circular DNA 1 Circular DNA Linear DNA
in nucleoid
in nucleoid
in nucleus
Cell wall?
yes, most of
none or
murein
pseudomurein
Uni/multicell
ular
unicellular
Energy
source
Example
organism
unicellular
multicell
none
unicellular
Animalia
eukaryotic
Linear DNA
in nucleus
none
Plantae
Fungi Viruses
eukaryotic eukaryotic
no cells
Linear DNA Linear DNA
in nucleus in nucleus
DNA or
RNA
yes, of
cellulose
yes, of
chitin
no
multicellular multicellular uni & multi no cells
Review Chart of Cell Characteristics
Nonliving
Domain Eukarya
Domain
Domain
Eubacteria Archaea
Protista
Cell type
prokaryotic
Chromosomes
1 Circular DNA
in nucleoid
Cell wall?
yes, most of
murein
none or
none
pseudomurein
Uni/multi
cellular
unicellular
unicellular
Energy
source
Example
organism
prokaryotic eukaryotic
1 Circular DNA
in nucleoid
Linear DNA
in nucleus
unicellular
Animalia
Fungi Viruses
eukaryotic eukaryotic eukaryotic
Linear DNA
in nucleus
none
no cells
Linear DNA Linear DNA
in nucleus
in nucleus
yes, of
cellulose
yes, of
chitin
multicellular multicellular uni & multi
heterotrophic hetero, chemo heterotrophic heterotrophic
chemotrophic
autotrophic
Plantae
DNA or
RNA
no
no cells
autotrophic heterotrophic none
Review Chart of Cell Characteristics
Nonliving
Domain Eukarya
Domain
Domain
Eubacteria Archaea
Cell type
Chromosomes
Cell wall?
prokaryotic
1 Circular DNA
in nucleoid
yes, most of
murein
Protista
Animalia
Plantae
Fungi Viruses
prokaryotic
eukaryotic
eukaryotic
eukaryotic
eukaryotic
no cells
1 Circular DNA
in nucleoid
Linear DNA
in nucleus
Linear DNA
in nucleus
Linear DNA
in nucleus
Linear DNA
in nucleus
DNA or
RNA
none or
pseudomurein
Uni/multi
cellular
unicellular
Energy
source
hetero, chemo,
autotrophic
hetero, chemo
autotrophic
Example
organism
Staphylococcus
aureus
Sulfolobus
unicellular
none
unicellular
none
yes, of
cellulose
yes, of
chitin
multicellular
multicellular
uni & multi
heterotrophic
heterotrophic
autotrophic
heterotrophic
(autotrophic)
Entamoeba
histolytica
Canis
domestica
Tsuga
Saccharomyces
heterophylla
cerevesiae
no
no cells
none
HIV
Taxonomy and Classification of Microbes (Especially Prokaryotes)
• The Three Domains and What Distinguishes Them
• Review of Characteristics of Prokaryotes, Eukaryotes,
Viruses
• The Taxonomic Hierarchy and Species Definitions
• Characteristics Used to Classify Prokaryotes
• Nine Medically Important Groups of Prokaryotes
• Dichotomous Keys and Microbe Identification
Taxonomic Hierarchy
Figure 10.5
Classification of a Particular Bacterium
Domain Eubacteria
Kingdom Prokaryotae (?)
Phylum Gram Positive
Class Scotobacteria
Order Spirochaetales
Family Spirochaetaceae
Genus Treponema
Species pallidum
Scientific name: Treponema pallidum
or Treponema pallidum
No common name except “syphilis bacteria”
The “Species Definition” Varies By Microbial Type
• A eukaryotic species is:
– A group of closely related organisms that breed among
themselves
• A prokaryotic species is:
– A population of cells with similar characteristics
 A clone is a population of cells derived from a single cell
•  A strain is composed of cells of a species with minor identifiable differences
•  A serovar is a strain identified by serological (antibody-identified) means
• A viral species is:
– A population of viruses with similar characteristics that
occupies a particular ecological niche
Taxonomy and Classification of Microbes (Especially Prokaryotes)
• The Three Domains and What Distinguishes Them
• Review of Characteristics of Prokaryotes, Eukaryotes,
Viruses
• The Taxonomic Hierarchy and Species Definitions
• Characteristics Used to Classify Prokaryotes
• Nine Medically Important Groups of Prokaryotes
• Dichotomous Keys and Microbe Identification
Characteristics Used to Classify Prokaryotes
• Morphology
Cell shape
Cell wall anatomy (staining characteristics)
Characteristics Used to Classify Prokaryotes
• Morphology
Cell shape
Cell wall anatomy (staining characteristics)
• Physiology
Spore-forming ability
Motility (how many flagella and where attached)
Fruiting or budding ability
Ability to live with or without oxygen
Characteristics Used to Classify Prokaryotes
• Morphology
Cell shape
Cell wall anatomy (staining characteristics)
• Physiology
Spore-forming ability
Motility (how many flagella and where attached)
Fruiting or budding ability
Ability to live with or without oxygen
• Metabolic abilities
Use of carbohydrates, proteins, lipids
Characteristics Used to Classify Prokaryotes
• Morphology
Cell shape
Cell wall anatomy (staining characteristics)
• Physiology
Spore-forming ability
Motility (how many flagella and where attached, gliding)
Fruiting or budding ability
Ability to live with or without oxygen
• Metabolic abilities
Use of carbohydrates, proteins, lipids
• Serology (recognition by blood antibodies)
• Phage Typing (recognition by specific viruses)
• DNA sequencing (similarities in gene sequences)
Groups of Prokaryotes
Mitochondria in
eukaryotes
Escherichia coli
Haemophilus influenzae
Pseudomonas aeruginosa
Staphylococcus aureus
Streptococcus pneumoniae
Clostridium tetani
Mycobacterium teuberculosis
Corynebacterium diptheriae
    
Chloroplasts in
eukaryotes
References
•• Bergey’s Manual of Determinative
Bacteriology
•Provides identification schemes for
identifying bacteria and archaea
•Morphology, differential
staining, biochemical tests
•• Bergey’s Manual of Systematic
Bacteriology
•Provides phylogenetic information
on bacteria and archaea
•Based on rRNA sequencing
•• Approved Lists of Bacterial Names
•Lists species of known prokaryotes
•Based on published articles
Taxonomy and Classification of Microbes (Especially Prokaryotes)
• The Three Domains and What Distinguishes Them
• Review of Characteristics of Prokaryotes, Eukaryotes,
Viruses
• The Taxonomic Hierarchy and Species Definitions
• Characteristics Used to Classify Prokaryotes
• Nine Medically Important Groups of Prokaryotes
• Dichotomous Keys and Microbe Identification
Important Bacterial G roups in Microbiology
Bacterial Group
Spirochetes
Charac teristics
Long, thin, heli cal cell s.
Movement by spinning axial fi laments.
Gram negative rods,
facult atively anae robic
Can live wit hout oxygen , otherwis e grows with
oxygen (aerobically). Enteric and Vibrio bacteria
in hu man intestinal t ract.
Gram negative a erobic rods Rod and coccu s shapes , li ves in soil , water, and
and cocci
are parasit es of anim als . Lives only in the
presence of oxygen.
Rickettsias and chlamydias Obli gate intracellula r parasit es. Rickettsia s
trans mitt ed by inse cts and ticks. Chlamydias t by
human contact. Rod shap ed or coccoid in form
Mycoplasmas
No cell walls , cell me mbrane wit h un ique sterols ,
very small (1/10 other bacteria), intracell ular
parasit e
Gram posit ive cocci
Gram posit ive, some resistant to penic illi n. Some
Streptococci are he molytic (can break red blood
cells )
Exampl e bacteria in this group
Leptospira interrogans (leptospirosis)
Borrelia burgdo rferi (Lyme Disease)
Treponema pallidum (syph ili s)
Escherichia (in hum an colon, urinary tract infections)
Salmonella (food po is oning, typho id fever)
Shigella (shigellosis diarrhe a)
Vibrio cholerae (cho lera diahrrea)
Hemoph ilus influenzae (ear infe ction s, meningiti s)
Serratia (urinary and respir atory tract infections )
Pseudomona s aeruginosa (var ie ty of infections )
Neisseria gono rrhoeae (gono rrhea)
Bordatella pertussis (pertussis or whoop ing cough )
Rickettsia prowazekii (typhu s)
Chlamydia trachomatis (ure thriti s STD)
Mycoplasma pneumon iae (walking pneu monia)
Staphylococcus aureu s (surg . infections , food poisoning) ;
Streptococcus pneumon iae (pneu monia)
Streptococcus pyogen es (sore thro at/pharyng iti s)
Streptococcus mu tans (dental caries)
Endospo re forming bacteria All gram positi ve rods and cocc i. Forms
Bacillus anthracis (anthrax)
hea t/chemic al resist ant endo spores (hard to kill by Clostridium perfringens (ga s gang rene)
disinfection/hea ting). Clostridia are obli gate
Clostridium tetani (tetanu s)
ana erobes.
Clostridium botulinum (botuli sm)
Mycobacteria
Thick, waxy li pids ancho red to cell wall , retains
Mycobac terium leprae (leprosy)
carbofusion dye in staining reaction call ed the
Mycobac terium tuberculosis (tuber culo sis)
“acid fast” stain.
Archae a
Unu sual cell wall s of NAG suga r units. Oft en
Halobacterium (li ves in salt marshes or salty lakes)
found in extreme env ir onments.Includ es
Sulfolobus (li ves in ho tsprings and hyd rother mal ven ts)
thermophiles, ha lophil es, acidophil es, and
methane produce rs. Ther mophil es ha rd to kill by
hea ting.
Spirochetes
Long, helical bacteria which swim by spinning like corkscrews
Treponema pallidum
causes syphilis
Borrelia burgdorferi
causes Lyme disease
Leptospira interrogans
causes leptospirosis
Gram negative, facultatively anaerobic rods
Escherichia coli
(urinary tract infections)
Vibrio cholerae
(cholera diarrhea)
Salmonella (typhoid
fever, food poisoning)
Shigella sonnei
(shigellosis diarrhea)
Haemophilus influenzae
Serratia marcescens
(ear infections, meningitis) (urinary, resp tract infections)
Gram negative aerobic rods and cocci
Pseudomonas aeruginosa
(burn, wound, & other infections)
Neisseria gonorrhoeae
(gonorrhea)
Bordatella pertussis
(pertussis/whooping cough)
Rickettsias and Chlamydias
obligate intracellular parasites
Rickettsia prowazekii
(typhus)
Chlamydia trachomatis
(urethritis - most common STD)
Mycoplasmas
No cell wall, intracellular parasite, small size,
unusual sterols in cell membrane
Mycoplasma pneumoniae
(“walking pneumonia”)
Gram positive cocci
Staphylococcus
aureus
Streptococcus
pneumoniae
Streptococcus
pyogenes
Endospore forming bacteria
Clostridium
tetani
Bacillus
anthracis
Clostridium
botulinum
Mycobacteria
Thick waxy lipids in cell wall (acid fast)
Mycobacterium tuberculosis
Mycobacterium leprae
Groups of Prokaryotes
Mitochondria in
eukaryotes
Escherichia coli
Haemophilus influenzae
Pseudomonas aeruginosa
Staphylococcus aureus
Streptococcus pneumoniae
Clostridium tetani
Mycobacterium teuberculosis
Corynebacterium diptheriae
    
Chloroplasts in
eukaryotes
Archaea (Archaebacteria)
Many are morphologically part of the Gram-negative Aerobic Rods and
Cocci group
Halobacterium in
salt lake
Sulfulobus in
Yellowstone
hot springs
Taxonomy and Classification of Microbes (Especially Prokaryotes)
• The Three Domains and What Distinguishes Them
• Review of Characteristics of Prokaryotes, Eukaryotes,
Viruses
• The Taxonomic Hierarchy and Species Definitions
• Characteristics Used to Classify Prokaryotes
• Nine Medically Important Groups of Prokaryotes
• Dichotomous Keys and Microbe Identification
Dichotomous Key