Bacterial Pathogens- CLASSIFICATION

Bacillus anthracis (anthrax)

Neisseria gonorrhoeae (gonorrhea)
Source: CDC

Vibrio cholerae (cholera) Hemophilus influenza (pneumonia, meningitis)

Source: CDC
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More than 16 bacterial Phyla/ Divisions
1) Aquificae 9) Cyanobacteria
2) Xenobacteria 10) Thermomicrobia
3) Fibrobacter 11) Chlorobia
4) Bacteroids 12) Proteobacteria
5) Firmicutes 13) Spirochaetes
6) Actinobacteria 14) Flavobacteria
7) Planctomycetes 15) Fusobacteria
8) Chrysogenetic 16) Verrucomicrobia

...

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TAXONOMY
Taxonomy: "arrangement method is the science of identifying and
naming species, and arranging them into a classification

Taxon- Taxa- Taxonomic unit: collection of related organisms grouped

together for purpose of classification

Binomial System (1740s)

Kingdom/ Domain

Phylum Class Order Family Genus Species

Ernst Haeckel (1866), Whitaker (1969),

Archea (1970s)

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Prokaryote: before nucleus
Eukaryote: true nucleus

All in a phylogeny tree

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Whitakers 5 Kingdom system of classification (1969)

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Kingdom: Monera = 2 Domains - Bacteria+ Archaea- Ancient
Carl Woeses 3 Domain system of classification (1977)

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Microbial Diversity

Prokaryotes
Archea, Bacteria and diseases

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 Domain Bacteria

How to classify Bacteria?

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Criteria for bacteria classification
1. Morphology
2. DNA sequencing
3. Conditions required
4. Biochemical properties

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More than 16 Phyla/ Divisions
1) Aquificae 9) Cyanobacteria
2) Xenobacteria
3) Fibrobacter 10) Thermomicrobia
4) Bacteroids 11) Chlorobia
5) Firmicutes
12) Proteobacteria
6) Actinobacteria
7) Planctomycetes 13) Spirochaetes
8) Chrysogenetic 14) Flavobacteria

15) Fusobacteria

16) Verrucomicrobia

...

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about 23 Phyla/ Divisions

New cultured phyla, new uncultivated phyla

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 Main phyla to study
Some major Phyla related to Medical Microbiology :

1. Proteobacteria: Enteric bacteria like E. coli, Salmonella

typhus, Legionella, Heliobacter pylorii (cause of many ulcers), Neisseria
gonorrhea (cause of gonorrhea). These bacteria are very closely related
to eukaryotic mitochondria.
2. Chlamydias: Parasites: Giardia, Chlamydia (STD)

3. Spirochaetes: Spiral bacteria: cause syphilis, Lyme disease

4. Firmicutes:
Clostridium (tetanus, botulism), Bacillus, Mycoplasma (walking pneumonia).
5. Actinomycetes:
Actinomyces: Streptomyces;
Coryneform bacteria: Corynebacterium, Mycobacterium.

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 Proteobacteria- the biggest phylum

- G- bacteria, majority of known G- bacteria in

Agriculture, Medicine and Industry
- Phylogeny based on 16S rRNA studies
- Extreme metabolic diversity: Common
photosynthetic ancestor, few are still photosynthetic
Mythical Greek god, Proteus: Classes designated by Greek letters

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 5 Subdivisions/Subphyla/ Classes
1. Alpha
2. Beta
3. Gamma About 460 genera and 1600 species
4. Delta
5. Epsilon
In textbook, phenotypic groups:
- Photosynthetic, Nitrifying, Iron-, sulphur- and Hydrogen-oxidizing, Nitrogen-
fixing, Methanotrophic, sulphate- and sulphur-reducing Proteobacteria.

- Enteric, Vibrio, Pseudomonads.

- Stalked and budding (Prosthecea, hypha), Sheathed, Predatory, Spirilla,

Rickettsia, Neisseria.

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 1. The (alpha) Proteobacteria
-Some grow at low nutrient
levels
-Some have unusual
morphology

-Many are agriculturally important

-Several medically important genera

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 1. The (alpha) Proteobacteria
Have prosthecae:
Caulobacter
Stalked bacteria found in low
nutrient aquatic environment
Stalks increase surface area for
nutrient uptake
Hyphomicrobium
Budding bacteria found in low
nutrient environment

Produce acetic acid from ethyl alcohol:

Acetobacter
Gluconobacter

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 1.The (alpha) Proteobacteria
Nitrogen-fixing bacteria:
Azospirillum
Grows in association with tropical
grasses and sugar cane
- Rhizobia
Rhizobium, Bradyrhizobium
Infects roots of legumes forming
root nodules
Nitrifying bacteria :
Oxidize nitrogen for energy
Fix CO2 for carbon source
Nitrobacter. NH4+ NO2
(ammonium to nitrite)
Nitrosomonas. NO2 NO3 (nitrite
to nitrate) Nitrosomonas
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 1.The (alpha) Proteobacteria
Plant pathogen:
Agrobacterium
Inserts plasmid into plant cells,
inducing tumors
Crown gall

Human pathogens:
Bartonella - bacillus
Cat-scratch disease
Brucella non-motile coccobacilli
Brucellosis

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 1.The (alpha) Proteobacteria
Obligate intracellular parasite:
Rickettsia bacillus or coccobacilli
Arthropod-borne cause spotted fevers
R. prowazekii - Epidemic typhus (lice)
R. typhi - Endemic murine typhus (fleas)
R. rickettsii - Rocky Mountain Spotted Fever (ticks)

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 2. The (beta) Proteobacteria

Utilize nutrients diffusing from areas of

decomposition of organic matter
Hydrogen gas, ammonia, and methane

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 2. The (beta) Proteobacteria
Thiobacillus
Chemoautotroph,
oxidize sulfur: H2S SO42
Zoogloea
aerobic sewage-treatment
Sphaerotilus
- hollow/ tubular sheath
- polar flagella
- in flowing water or sewage

Zoogloea ramigera

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 2. The (beta) Proteobacteria
Spirillum
Large, aerobic freshwater
bacterium
Neisseria
N. meningitidis
Meningococcal meningitis
N. gonorrhoeae

Burkholderia
Normal lung Infected lung
Aerobic rods; Polar flagella
Some species fix nitrogen
B. cepacia
Nosocomial infections
Grow in disinfectant solutions
Metabolize respiratory secretions

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 3. The (gamma) Proteobacteria

Largest subgroup

Great variety of physiological types

Includes the Enterics

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 3. The (gamma) Proteobacteria
Beggiatoa
Chemoautotroph, oxidize H2S to S0
Gliding motility
Beggiatoa alba is only species

Azotobacter and Azomonas

Nitrogen fixing, free-living soil bacteria
Large ovoid cell with heavy capsule

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 3. The (gamma) Proteobacteria
Francisella
Pleomorphic
Francisella tularensis tularemia (rabbit fever)
Resistant to many antibiotics
Pseudomonas
Aerobic rods; Polar flagella
Extra-cellular and/or florescent pigments
Opportunistic pathogen
Metabolize wide variety of substrates
Resistant to many anti-microbials
Denitrification

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 3. The (gamma) Proteobacteria
Moraxella
Aerobic coccobacilli
Moraxella lucunata
Conjunctivitis

Legionella
Found in streams, warm-water
pipes, cooling towers
L. pneumophilia
Causes a form of pneumonia
called legionellosis
Survive inside aquatic amoeba

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 3. The (gamma) Proteobacteria
Coxiella
Coxiella burnetii
Q fever
Obligate intracellular pathogen
(similar to Rickettsia species)
transmitted via aerosols or milk
Resistant sporelike body
Vibrio
Facultative anaerobic vibrio
Vibrio cholerae
Cholera
Dysentery
V. parahaemolyticus
Less severe gastroenteritis
Undercooked shellfish
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3. The (gamma) Proteobacteria: Enterics
Enterobacteriales (enterics):
Facultatively anaerobic, rods
Peritrichous flagella
Most ferment glucose and other sugars
Inhabit intestinal tract of animals (humans)

Escherichia
Coliforms fecal contamination
UTI and Travelers Diarrhea
Food poisoning E. coli 0157:H7
Salmonella
S. enterica 2400 servors
S. enterica servor typhi
typhoid fever

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 3. The (gamma) Proteobacteria: Enterics
Shigella
Shigellosis (bacillary dysentery)
Klebsiella
K. pneumoniae serious form of pneumonia
Some species fix nitrogen
Yersinia
Y. pestis plague
Enterobacter
E. aerogenes and E. cloacae
UTI and nosocomial infections
Pasteurella
mainly pathogens of domestic animals
Cause pneumonia and septicemia
passed to humans from cat and dog bites
P. multocidia - carried by Komodo dragon
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3. The (gamma) Proteobacteria: Enterics
Serratia
S. marcescens
Red pigments, UTIs and respiratory infections
Proteus
Swarmer cells
UTI and wound infections
Haemophilus
- inhabit mucous membranes of upper respiratory
tract, mouth, vagina, and intestinal tract
- require heme fraction (X factor) and NAD cofactor
(V factor)
H. ducreyi
Chancroid (STD)
H. influenzae
meningitis, pneumonia, bronchitis, septic
arthritis, earaches H. ducreyi
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4. The (delta) Proteobacteria
Some species are PREDATOR on other bacteria
Important contributors to the sulfur cycle

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4. The (delta) Proteobacteria
Bdellovibrio
Aerobic, rod with polar
flagella
attack other Gram (-) bacteria
similar to the way a virus
would

Desulfovibrio
Human intestinal tract and anaerobic sediments
obligate anaerobe, sulfur reducing bacteria
Use S for final electron acceptor
Release tons of H2S annually

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4. The (delta) Proteobacteria
Myxococcus
Gliding motility

Feed on bacteria they

encounter

Cells aggregate to form

fruiting body loaded with
myxospores

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 5. The (epsilon) Proteobacteria
Microaerophilic, helical or vibrioid rods
Motile by means of flagella

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5. The (epsilon) Proteobacteria
Campylobacter
C. fetus
causes spontaneous abortion in
domestic animals
C. jejuni
leading cause of bacterial diarrhea

Helicobacter
H. pylori
common cause of stomach ulcers

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And other phyla
G- negative phyla (cont)
Chlamydiae: obligate intracellular bacteria, ovoid in shape, small in
size. Chlamydiae are most successfully isolated while still inside their host
cells.
Eg: Chlamydia trachomatis, which causes the eye-disease trachoma and
the sexually transmitted infection chlamydia; Chlamydophila pneumoniae,
which causes a form of pneumonia; Chlamydophila psittaci, which causes
psittacosis
Spirochaete: distinctive diderm (double-membrane) bacteria,
most of which have long, helically coiled (corkscrew-shaped or spiraled,
hence the name) cells. Spirochaetes stain gram-negative and
are chemoheterotrophic in nature, with lengths between 3 and 500 m and
diameters around 0.09 to at least 3 m.
Eg: Leptospira species, which causes leptospirosis; Borrelia burgdorferi, B.
garinii, and B. afzelii, which cause Lyme disease. Borrelia recurrentis, which
causes relapsing fever. Treponema pallidum subspecies which cause
treponematoses such as syphilis and yaws; Brachyspira pilosicoli and
Brachyspira aalborgi, which cause intestinal spirochaetosis.
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 G+ bacteria: Firmicutes and Actinobacteria
2. Phylum Firmicutes (low GC):
Spore-forming: Bacillus, Clostridium
Non-spore forming: Streptococcus, Staphylococcus
Mycoplasma*: Mycoplasma, Ureaplasma

3.Phylum Actinobacteria (high GC):

Actinomyces: Streptomyces
Coryneform bacteria: Corynebacterium, Mycobacterium*

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2 phyla: Euryarchaeota and Crenarchaeota
1. Euryarchaeota: (Methanogens, Extreme Halophiles )
Methanobacterium

Halobacterium

Thermoplasmata

Thermococci

Halobacterium salinarum

Methanogens: e.g Methanobrevibacter smithii

Strict anaerobes, gut of ruminant mammals

Pyrococcus furiousus
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2 phyla: Euryarchaeota and Crenarchaeota

2. Crenarchaeota (extreme/hyper-thermophiles):
Thermoproteus, Sulfolobus

Many can grow at > 100 C, e.g Pyrolobus fumarii, optimal growth
temperature, 106 C.

Pyrolobus fumarii Hydrothermal vent

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Summary
Taxonomy

Classification of bacteria

Bacterial diversity and several examples in life, esp. in human

diseases.

Classification of Archea and its diversity

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 Review Questions
1. How Bacteria are classified?
2. How Archeae are classified?
3. Why did not we talk about Archeae and Diseases?

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FYI

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Phenotypic groups of Phylum Proteobacteria
1. Photosynthetic proteobacteria:

purple sulphur/ non-sulphur bacteria, eg. Thiospirilum, Chromatium

anoxygenic photosynthesis- bacteriochlorophyll a and b

Remind Oxygenic photosynthesis:

6CO2 + 12H2O + photons (CH2O)6 + 6O2 + 6H2O

Anoxygenic photosynthesis, eg. Purple sulphur bacteria

6CO2 + 6H2S + photons (CH2O)6 + 6S

Or, ?CO2 + ?S + ?H2O + photons (CH2O)6 + ?H2SO4

Task: Balance the above chemical reaction

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Phenotypic groups of Phylum Proteobacteria
1. Photosynthetic proteobacteria:

purple sulphur/ non-sulphur bacteria, eg. Thiospirilum, Chromatium

anoxygenic photosynthesis- bacteriochlorophyll a and b

Remind Oxygenic photosynthesis:

6CO2 + 12H2O + photons (CH2O)6 + 6O2 + 6H2O

Anoxygenic photosynthesis, eg. Purple sulphur bacteria

6CO2 + 6H2S + photons (CH2O)6 + 6S

Or, 6CO2 + 4S + 10H2O + photons (CH2O)6 + 4H2SO4

Purple non- sulphur bacteria, more complicated: Photo-/ Chemo-heterotrophs

Eg.: Rhodospirillum, Rhodopseudomonas

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Rhodopseudomonas palustris is a rod-shaped gram-negative
purple non-sulfur bacterium, notable for its ability to switch between four
different modes of metabolism: photoautotrophic, photoheterotrophic,
chemoautotrophic and chemoheterotrophic.

R. palustris can grow with or without oxygen, or it can use light, inorganic
or organic compounds for energy. It can also acquire carbon from either
carbon dioxide fixation or green plant-derived compounds.

R. palustris is found extensively in nature and has been isolated from

swine waste lagoons, earthworm droppings, marine coastal sediments and
pond water.

Rhodopseudomonas palustris
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Phenotypic groups of Phylum Proteobacteria
1. Photosynthetic proteobacteria

2. Nitrifying-, Iron-, Sulphur- and Hydrogen-oxidizing, Methanotrophic,

Sulphate- and Sulphur-reducing Proteobacteria (Chemolithotrophs)

3. Nitrogen- fixing Proteobacteria (Nitrogenase), e.g.: Azotobacter,

Rhizobium

Root nodule of Fabaceae Agrobacterium, A. tumefaciens, tumor- forming

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Phenotypic groups of Phylum Proteobacteria
1. Photosynthetic proteobacteria

2. Chemolithotrophs

3. Nitrogen- fixing Proteobacteria

4. Enteric Proteobacteria, Vibrio, Pseudomonads

Vibrio and Photobacterium: marine bioluminescent species (Luciferase)

FMNH2 + O2 + RCHO FMN + RCOOH + H2O + light

Vibrio cholerae, 2 circular chromosomes

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Phenotypic groups of Phylum Proteobacteria
1. Photosynthetic proteobacteria

2. Chemolithotrophs

3. Nitrogen- fixing Proteobacteria

4. Enteric Proteobacteria, Vibrio, Pseudomonads

Pseudomonas: straight or curved rods with polar flagella, Entner-Doudoroff

pathway
e.g: Pseudomonas, Burkholderia

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Identification of enteric bacteria
Biochemical Test Descriptions
Indole Indole Tryptophan
Methyl Red Acid production (low pH indicator, red colour)
Voges- Proskauer Glucose Acetoin
Citrate utilisation Citrate as sole carbon source
Urease Urea NH4+, CO2 (increased pH)
Gas from sugars Gas is collected in a Durham tube
H2S production S-containing aa, SO4 H2S, (Fe) FeS (black)
Ornithine decarboxylase Ornithine pH change
Motility Cellular movement on soft agar
Gelatin liquefaction Gelatine- proteolytic enzymes
% GC Measurement of DNA melting points

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Identification of some biochemical properties

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Phenotypic groups of Phylum Proteobacteria
1. Photosynthetic proteobacteria

2. Chemolithotrophs

3. Nitrogen- fixing Proteobacteria

4. Enteric, Vibrio, Pseudomonads

5. Acetic acid bacteria:

Acetobacter (+TCA cycle, acetate CO2, H2O; cellulose- synthesizing

ability !),

Gluconobacter (-TCA cycle)

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Phenotypic groups of Phylum Proteobacteria
1. Photosynthetic proteobacteria

2. Chemolithotrophs

3. Nitrogen- fixing Proteobacteria

4. Enteric, Vibrio, Pseudomonads

5. Acetic acid bacteria: Acetobacter, Gluconobacter

6. Stalked and budding Proteobacteria (Aqua, Prosthecea, hypha), e.g.

Caulobacter,
Hyphomicrobium

Sheathed Proteobacteria (chain of cells surrounded by a sheath), e.g.

Sphaerotilus, Leptothrix

Spirilla (Spiral-shaped bacteria with polar flagella),

e.g. Campylobacter, Helicobacter,

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Phenotypic groups of Phylum Proteobacteria
1. Photosynthetic proteobacteria

2. Chemolithotrophs

3. Nitrogen- fixing Proteobacteria

4. Enteric, Vibrio, Pseudomonads

5. Acetic acid bacteria: Acetobacter, Gluconobacter

6. Stalked and budding Proteobacteria, Sheathed Proteobacteria

Spirilla (Spiral-shaped bacteria with polar flagella

7. Predatory Proteobacteria (-lytic enzymes), e.g. Bdellovibrio, Myxococcus

Rickettsia (anthropod-borne intracellular parasites of vetebrates)

Neisseria and related Proteobacteria (aerobic non-motile cocci, in pairs)

And other Gram negative phyla

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And other G- phyla
1. Cyanobacteria (blue-green): oxygenic
photosynthesis,

e.g.: Oscillatoria, Anabaena, Prochlorococcus

Prochlorococcus
Oscillatoria is a
Prochlorococcus is a
genus of
genus of very small (0.6
filamentous
m) marine cyanobacteria
cyanobacterium
with an unusual
which is named for
pigmentation (chlorophyll b)
the oscillation in its
movement

Anabaena

Anabaena planktonica in
Siltcoos Lake (S. Hager)

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 And other G- phyla
1. Cyanobacteria (blue-green): oxygenic photosynthesis

2. Chlorobi (green sulphur, similar to purple sulphur): Chlorosomes, Outer

deposition of S, CO2 assimilation

3. Chloroflexi (green non-sulphur, similar to purple non-sulphur): filamentous

thermophiles

4. Aquificae: highly thermophilic, autotrophs (oxidation of H2 or H2S)

5. Thermotogae: highly thermophilic, anaerobic heterotrophs, surrounded by a

proteinaceous sheath (toga)

6. Deinococcus- Thermus: remarkable physiological properties (thermophile,

PG-cell wall, radioresistance)

7. Planctomycetes, Chlamydiae, Spirochaetes, Bacteroidetes, Verrucomicrobia

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G+ phyla: 2500 species: chemoheterotrophic
1. Phylum Firmicutes (low GC):
Spore-forming: Bacillus, Clostridium

Non-spore forming: Streptococcus, Staphylococcus

Mycoplasma*: Mycoplasma, Ureaplasma

2. Phylum Actinobacteria (high GC):

Actinomyces: Streptomyces

Coryneform bacteria: Corynebacterium, Mycobacterium*

Corynebacterium diphtheriae

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Against the comparison

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 Rickkettsiaceae
Rickkettsiaceae: Cowdria, Coxiella, Erhlichia,
Neorickettsia, Rickettsia, Rickettsiella, Rochali
maea Wobachia