1. KLASIFIKASI BAKTERI

2. CLASSIFICATION OBSERVATION: Many kinds of organisms:
Some similar to each other.
wood frog,
leopard frog,
bull frog
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Classification.ppt 2

3. CLASSIFICATION Others less similar fish, frogs, snakes 08 June 2009
Classification.ppt 3

4. CLASSIFICATION Others very dissimilar people, pine trees, protozoans
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Classification.ppt 4

5. CLASSIFICATION Why are some kinds similar and others NOT similar?
Question to be answered later?
How can we make sense of (explain) this diversity?
How can we organize what we know about these organisms?
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6. Answer: CLASSIFY
Similar “types” (species) grouped together, separated from other species.
Then, group similar groups together,
etc.
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7. CLASSIFICATION Species = kind of organism
fundamental unit in evolution and ecology
more precise definition soon
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Classification.ppt 7

8. CLASSIFICATION Necessary? YES !!
~ 1 million species of plants,
5-10 million species of animals
+ fungi, protists, bacteria
no good estimates of numbers of species
Human mind needs to organize information.
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Classification.ppt 8

9. CLASSIFICATION Classification system organizes biological knowledge.
Classification itself is HYPOTHESIS about relationships, similarity because of common ancestry.
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10. HYPOTHESIS of relationship
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Classification.ppt 10

11. CLASSIFICATION = Sequence of levels
CLASSIFICATION = Sequence of levels. Linnaean system, from Carolus Linnaeus, 1740's
Kingdom
Phylum
Class
Order
Family
Genus
Species
King Phil called old fat George stupid.
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Classification.ppt 11

12. CLASSIFICATION = Linnaean system
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Classification.ppt 12

13. CLASSIFICATION Whittaker’s Five Kingdoms, 1965
Kingdom Monera (Bacteria)
Kingdom Protista
Kingdom Fungi
Kingdom Plantae
Kingdom Animalia
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Classification.ppt 13

14. CLASSIFICATION Woese, 1985
Prokaryotic organisms are far more diverse than thought previously.
Domain Eubacteria (prokaryotic “true bacteria”)
Domain Archaea (prokaryotic “archaeans”)
Domain Eukarya (eukaryotic organisms)
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Classification.ppt 14

15. CLASSIFICATION Woese, 1985
Prokaryotic organisms are far more diverse than thought previously.
Domain Eubacteria (prokaryotic “true bacteria”)
Kingdom Gram-positive bacteria
Kingdom Gram-negative bacteria
Kingdom Mycoplasmas
Kingdom Rickettsias
Kingdom purple-sulfur bacteria
and more
Domain Archaea (prokaryotic “archaeans”)
Domain Eukarya (eukaryotic organisms)
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Classification.ppt 15

16. CLASSIFICATION Woese, 1985
Prokaryotic organisms are far more diverse than thought previously.
Domain Eubacteria (prokaryotic “true bacteria”)
Domain Archaea (prokaryotic “archaeans”)
Kingdom Thermophiles
Kingdom Halophiles
Kingdom Methanogens
Kingdom ARMANS
(“Archeal Richmond Mine Acidophilic Nanoorganism” Science vol 314, 22 Dec )
Domain Eukarya (eukaryotic organisms)
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Classification.ppt 16

17. CLASSIFICATION Woese, 1985
Prokaryotic organisms are far more diverse than thought previously.
Domain Eubacteria (prokaryotic “true bacteria”)
Domain Archaea (prokaryotic “archaeans”)
Domain Eukarya (eukaryotic organisms)
Kingdom Protista
Kingdom Fungi
Kingdom Plantae
Kingdom Animalia
08 June 2009
Classification.ppt 17

18. CLASSIFICATION Woese, 1985
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Classification.ppt 18

19. CLASSIFICATION Woese, 1985 Domain Kingdom Phylum Class Order Family
Genus
Species
Did King Phil call old fat George stupid ?
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Classification.ppt 19

20. Tree of Life

21. Eukaryote origins:

22. Scientific Nomenclature:
Binomial nomenclature
Genus species
Bacteria-
Journal of Systematic Bacteriology
____________ Manual
Latinized names commemorate microbiologists or describe features of the organism

23. Scientific nomenclature: a hierarchical system

24. Classification of Bacteria:
Bergey’s manual of systematic bacteriology, 2nd edition is being published
(What’s in our lab????????)
Bacterial species are defined as a population of cells with similar characteristics
Strains exist within species

25. Classification of Bacteria: Fig. 10-6

26. Methods of Classification and Identification of Microorganisms:
Necessary to identify microorganism
Bacteria are small and many are similar in shapes so must
Test metabolic reactions
Identify specific characters to identify

27. Bergey’s Manual of Determinative Bacteriology
Not evolutionary relatedness, but provides identification (determinative) schemes based upon
Cell wall composition
Differential staining
Oxygen requirements
Biochemical testing

28. Morphological Characteristics:
Cocci, bacilli, spirilla, spirochetes
Position of any flagella
Position of developing endospores with in the cell

29. Differential Staining:
Gram Stain
Acid Fast Stain
Quick and may allow a physician to begin appropriate treatment

30. Biochemical tests: Enzymatic activities
ex.: ability of bacteria to ferment a variety of carbohydrates
Ecological roles: nitrogen fixation for example
Enteric Bacteria: some are pathogens
Escherichia, Enterobacter, Citrobacter ferment glucosa
Shigella and Salmonella (PATHOGENS)

32. Bacteria are identified using a series of physiological, immunological or molecular characteristic

33. Gram-Negative Rods Enteric Bacteria E. coli Salmonella Shigella
Yersinia
Pseudomonas
Proteus
Vibrio cholerae
Klebsiella pneumoniae

34. Gram-Negative Rods
Fastidious GNRs
Bordetella pertussis
Haemophilus influenzae
Campylobacter jejuni
Helicobacter pylori
Legionella pneumophila
Anaerobic GNRs
Bacteroides fragilis
Fusobacterium

35. Gram-Positive Rods
Clostridia
Anaerobes
C.perfringens
C. tetani
C. botulinum
C. difficile
Bacillus cereus
Aerobe
Listeria monocytogenes
Faculative anaerobe

36. Gram-Negative Cocci
Neisseria gonorrhoeae
The Gonococcus
Neisseria meningitidis
The Meningococcus
Both Gram-negative intracellular diplococci

37. Gram-positive Cocci
Staphylococci
Catalase-positive
Gram-positive cocci in clusters
Staphylococcus aureus
coagulase-positive
Staph. epidermidis
and other coagulase negative staphylococci

38. Gram-Positive Cocci
Streptococci
Catalase-negative
Gram-positive cocci in chains or pairs
Strep. pyogenes
Strep. pneumoniae
Viridans-type streps
Enterococcus faecalis

39. Non-Gram-stainable bacteria
Unusual gram-positives
Spirochaetes
Obligate intra-cellular bacteria

40. Unusual Gram-positives
Mycoplasmas
Smallest free-living organisms
No cell wall
M. pneumonia, M. genitalium
Mycobacteria
Acid-fast bacilli, stained by Ziehl-Neelsen stain
M. tuberculosis
M. leprae
M. avium

41. Spirochaetes
Thin spiral bacteria
Viewable by phase-contrast microscopy or silver stain
Treponema pallidum
Borrelia burgdorferi
Leptospira

42. Obligate intracellular bacteria
Rickettsia
Coxiella burneti
Chlamydias
C. trachomatis
C. pneumoniae
C. psittaci

46. Identification of Enteric Pathogens:

47. Enterotube:

48. Fast Identification Techniques:
Serology: antigens on bacteria cause antibodies to be formed, then can be used to id the bacteria, even specific strains!
Slide agglutination
ELISA – enzyme linked immunosorbent assay
Western blotting-Bacterial antigens in serum
Phage typing: uses viruses that infect bacteria to identify bacteria

49. Slide Agglutination:

52. Other methods: Fatty Acid Profiles: bacteria produce a consistent set
Commercial system to separate cellular fatty acids from those of known microorganisms
Flow cytometry
Cells flow-numbers and shapes-laser
Immunoflourescent tags reveal specific organisms

53. Fatty acid analysis
Fatty acid methyl ester (FAME) chromatogram of an unknown species, showing chromatographic column retention times and peak heights. Note: 10:0, 12:0, 16:0, and 19:0 indicate saturated fatty acids with 10, 12, 16, and 19 carbons; 16:1 and 18:1, monounsaturated 16-carbon and 18-carbon fatty acids; omega number, the position of the double bond relative to the omega end—that is the hydrocarbon end (not the carboxyl end)—of the fatty acid chain; cis and trans, the configuration of the double bond. For example, omega 7 cis indicates a cis double bond between the seventh and eighth carbons from the omega end of the fatty acid. Also, 2OH indicates a hydroxyl group at the second carbon from the omega end; cyclo omega 8, a cyclo-carbon at the eighth position from the omega end. The 18:1 omega 7 cis, omega 9 trans, and omega 12 trans peak results from either one fatty acid or a mixture of fatty acids with double bonds at the three positions indicated (the chromatographic column does not separate these three fatty acids). Courtesy of MIDI (Microbial Identification, Incorporated, Delaware).

54. Identification by DNA based methods:
DNA base composition: G-C % ‘ages
DNA fingerprinting- specific id
rRNA sequencing-phylogenic relationship
Polymerase chain reaction(PCR)-increase amount of DNA so it can be studied
Hybridization, Southern blotting, and DNA probes are other DNA based id techniques

55. DNA Chip Technology:

56. Summary of Classification Methods:
Dichotomous keys
Widely used, based upon questions each of which has two possible answers, eventually get to identification
Cladograms are used to show degrees of evolutionary relationship

57. Summary of Classification/Identification: