This document discusses the classification of bacteria using taxonomy and Carl Woese's three domain system. It covers the main characteristics of different bacterial phyla including Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Spirochaetes, and Archaea. Key details are provided on pathogenic bacteria such as Staphylococcus aureus, Streptococcus pyogenes, Clostridium tetani, Salmonella typhi, and Mycobacterium tuberculosis. The principles of bacterial identification, nomenclature, and Bergey's Manual are also summarized.

1. Classification of Bacteria

2. Taxonomy
The science of classification

3. Carl Woese’s 3 Domains
Based on rRNA nucleotide sequences
Why use this as a basis for classification?

4. Organisms in the 3 Domains
• Eukarya - kingdoms: plantae, animalia, fungi,
protists
• Archaea - prokaryotes
• Bacteria - prokaryotes

5. 2 Types of Prokaryotic Cells
• Eubacteria
– cell walls contain
peptidoglycan
– different nucleotide
sequences in rRNA
– different membrane
lipids
• Archaebacteria
– no peptidoglycan
– rRNA
– lipids
– live in extreme
environments
ex. Thermoacidophiles
Extreme halophiles
Methanogens
http://www.ucmp.berkeley.edu/archaea/archaea.html

6. Comparison of Archaea, Bacteria & Eukarya

7. Naming organisms (nomenclature)
Binomial system uses 2 names
Genus species
ex. Bacillus subtilis
ex. Clostridium tetani
ex. Staphylococcus aureus
Is tubercle bacillus the scientific name of an
organism or a common name?

8. 3. Phylogenetic Classification
• An evolutionary arrangement of species.
• Sharing a recent ancestor as in plants and animals
(fossil records)
• In bacteria?
• Possible by Molecular Methods
– Genetic Homology:
• Base composition (GC ratio)
• Nucleic acid hybridisation.
• Ribosomal RNA (rRNA) sequence analysis
• Protein profiles and amino acid sequences

9. • PURE CULTURE:
• Populations of individuals all derived from the
same single organism.
• STRAIN:
• A Group of Pure Cultures Derived from a
Common Source and Thought to be the Same.
• SPECIES:
• A Group of Closely Similar Strains.

10. INTRASPECIES CLASSIFICATION
• Biotypes
– Biochemical properties.
• Serotypes
– Antigenic features.
• Phage Types
– Bacteriophage susceptibility.
• Colicin Types
– Production of bacteriocins.

11. Species of bacteria - “population of cells
with similar characteristics”
Strain of bacteria - “group of cells
derived from a single cell”
ex. Staphylococcus aureus 13578

12. • Naming of microorganisms.
• Governed by international rules
• Rules published in the International Code of
Nomenclature of Bacteria.
• The International Journal of Systematic
Bacteriology

13. Rules for the Nomenclature of Microorganisms
• There is only one correct name for an organism.
• Names that cause error or confusion should be rejected.
• All names in Latin or are latinized.
– The first word (genus) is always capitalized.
– The second word (species or specific epithet) is not
capitalized.
– Both genus and species name, together referred to as species,
are either underlined or italicized when appearing in print.
– The correct name of a species or higher taxonomic
designations is determined by valid publication, legitimacy
of the name with regard to the rules of nomenclature, and
priority of publication.

14. Nomenclature
• Casual or Common Name:
– e.g. "typhoid bacillus"
• Scientific or International Name:
– Salmonella typhi
– Salmonella london
– Staphylococcus aureus
– Clostridium tetani
– Mycobacterium bovis
– Borrelia burgdorferi

15. Classification vs. Identification
Techniques
Bergey’s Manual of Determinative Bacteriology uses:
• microscopic appearance
• biochemical reactions
• growth requirements
• serology
• phage typing
Classification or identification??

16. Biochemical Tests

17. Serology
Slide Agglutination Test

18. Phage Typing

19. Bergey’s Manual of Systematic Bacteriology
establishes phylogenetic relationships by:
• amino acid sequencing
• protein analysis
• rRNA sequencing – ribotyping
• nucleic acid hybridization

20. DNA Hybridization

21. Identification vs. Classification

22. Spirochetes
Axial filaments for motility
Examples:
Treponema pallidum - syphillis
Borrelia burgdorferi - Lyme
disease
Leptospira interrogans -
leptospirosis

23. Axial Filaments
Movement of spirochetes
Bundles of fibrils that arise at the end of the cell beneath the
outer sheath & spiral around the cell
Ex. Treponema
pallidum
Structure
Filament
Hook
Basal body

24. Campylobacter jejuni
• microaerophilic
• motile vibrio
• Gram negative
• animals esp poultry & cattle
• grows @ 42oC
• most commonly identified
bacterial cause of diarrhea in
world (CDC)
– unpasteurized milk
– food

25. Pseudomonas aeruginosa
• Gram negative aerobic
rod
• “bacillus of blue-green
pus”
– pyocyanin pigment
• fermented grape smell
• normal flora
– skin & intestine
• unusual carbon sources
• antibiotic resistant
• infections
– wound, ear, urinary,
respiratory, burns

26. Gram negative aerobic cocci
Neisseria gonorrhoeae in pus
Neisseria meningitidis
Branhamella catarrhalis

27. Enterobacteriales
Non-pathogens
• Escherichia
• Klebsiella
• Proteus
• Serratia
• Etc.
Family- enterobacteriaceae
Describe the microscopic appearance of these organisms.

28. Enterobacteriaceae cont’d
Pathogens
• Salmonella (typhi)
– typhoid fever
• Shigella (dysenteriae)
– bacillary dysentery
• Yersinia (pestis)
– bubonic plague

29. Vibrionales
Vibrionaceae
Vibrio cholerae
Shape?
Facultatively
anaerobic

30. Hemophilus influenzae
• Aerobic Gram negative
rod
• Normal flora in intestine
and respiratory tract
• Most common cause of
meningitis in children
– Hib vaccine
• Also causes otitis media,
pneumonia, epiglottitis
Why is the name of this organism misleading?
What can you learn from the name?

31. Bacteroidaceae - Bacteroides fragilis
• Gram negative
anaerobic rods
• Found in the human
intestine & mouth
– 95% of the bacteria in
a stool specimen &
20% of the weight!
– One billion per gram of
feces!
• Most common
anaerobe isolated from
infections
– appendicitis,
peritonitis, complicate
abdominal surgery

32. Rickettsia & Chlamydia
Gram negative obligate intracellular parasites
Rickettsia
transmitted to humans by insects & ticks
Ex. Rickettsia rickettsii - Rocky Mountain spotted fever

33. Chlamydia
Not transmitted by insects
Chlamydia trachomatis
Causes:
1.Trachoma - world’s leading
infectious cause of blindness
Middle East, North Africa, India
2.Non-gonococcal urethritis
common std in U.S.

34. Chlamydia psittaci causes:
1. Psittacosis (“parrot fever”)
2. Ornithosis
Chlamydia pneumoniae - pneumonia

35. Mycoplasmas
• No cell wall
– pleomorphic
– penicillin sensitive or
resistant?
• Smallest free-living
organisms
• Microscopic fried-egg
colonies
• Ex. Mycoplasma
pneumoniae

36. Gram Positive Cocci
Staphylococcus Streptococcus
Micrococcus luteus

37. Staphylococcus aureus
• Gram positive cocci, clusters
• Yellow pigment
• Causes
– common food poisoning
– surgical wound infections
• resistance
– toxic shock syndrome

38. Streptococcus pyogenes
• Gram positive cocci in chains
• Diseases
– pharyngitis (sore throat)
– scarlet fever *
– erysipelas *
* look for a description of this disease

39. Endospore-Forming Gram Positive Rods
• Bacillales - Bacillus
– aerobes or facultative anaerobes
– common in soil
– ex. Bacillus anthracis, Bacillus subtilis
• Clostridiales - Clostridium
– obligate anaerobes
– found in soil
– diseases
• tetanus (Clostridium tetani), botulism (C. botulinum),
gas gangrene (C. perfringens)

40. Spore-Forming Organisms
Bacillus cereus - spore stain Clostridium tetani - Gram stain

41. Corynebacterium
Characteristics of
Corynebacterium sp.:
• pleomorphic Gram positive
rod
• metachromatic granules
• unusual arrangements
– palisades
– Chinese letters
• C.diphtheriae causes
diphtheria

42. Mycobacteria
Characteristics of
Mycobacterium sp.
• Gram positive small rods
• acid-fast
– mycolic acid complexed
with peptidoglycan (waxy)
• diseases:
– tuberculosis
– leprosy (M. leprae)
Acid-fast stain of sputum showing
Mycobacterium tuberculosis

43. Streptomycetes
Characteristics of
Streptomyces:
• mold-like bacteria
– branching, spores
• produce geosmin
– soil smell
• several species
produce antibiotics
– ex. streptomycin