1. Taxonomy and Classification
Classification of Microbes

2. 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?

3. 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?

4. 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

5. Hierarchy Evolutionary relationships
Species are groups that interbreed (have productive sex)
How this goes
Species
Genus
Family
Order
Class
Division
Phylum
Kingdom (1969)
Domain (80’s)

7. The 5 Kingdoms based on nutrient procurement
Plantae
Multicellular photoautotrophs
Animalia
ingestive
Fungi
absorptive
Protozoa
Mostly singe celled
Prokaryotes
Which of these are microbes?

8. The 3 domains Eukarya Bacteria Archaea
Plants, animals fungi and protists
Bacteria
(with peptidoglycan)
Archaea
With unusual cell walls, and membreanes

9. The Three-Domain System
Figure 10.1

10. The Three-Domain System
Table 10.1

11. Endosymbiotic Theory
Figures 10.2, 10.3

12. Table 10.2

13. 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

14. Source of Specific Epithet
Scientific Names
Scientific Binomial
Source of Genus Name
Source of Specific Epithet
Klebsiella pneumoniae
Honors Edwin Klebs
The disease
Pfiesteria piscicida
Honors Lois Pfiester
Disease in fish
Salmonella typhimurium
Honors Daniel Salmon
Stupor (typh-) in mice (muri-)
Streptococcus pyogenes
Chains of cells (strepto-)
Forms pus (pyo-)
Penicillium chrysogenum
Tuftlike (penicill-)
Produces a yellow (chryso-) pigment
Trypanosoma cruzi
Corkscrew-like (trypano-, borer; soma-, body)
Honors Oswaldo Cruz

15. Species Definition Eukaryotic species: Prokaryotic 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
Viruses arose from independently replicating strands of NA like a plasmid or are paracitic cells that lost function to live on their own.

16. Is it as easy to classify Microbes as it is Macrobes?
How to classify
What do we have to look at?

17. Identifying Bacteria
Applications, p. 283

18. Same as fig Showing how a major group of bacteria relate to the classic eukaryotic classification scheem

19. Phylogenetic Relationships of Prokaryotes
Figure 10.6

20. Of more than 2600 species identified so far
Only about 250 or 10% are pathogens

21. 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

22. 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

23. Identification Methods
Morphological characteristics: Useful for identifying eukaryotes
Differential staining: Gram staining, acid-fast staining
Biochemical tests: Determines presence of bacterial enzymes
Identification Methods
A dichotomous key
Figure 10.8

24. A clinical microbiology lab report form
Fig 10.7
Figure 10.7

25. Identifying a Gram – Negative, Oxidase – Negative Rod
Figure 10.8

26. 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

27. Design a rapid test for a Staphylococcus aureus. 10-14
Figure 6.10

28. 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

29. Strains with different antigens are called
Serotypes
Serovars
biovars

30. DNA Hybridization

31. Phage Typing
Determining a strains suceptability to certain phage or bacterial viruses
Figure 10.13

32. The Western Blot

33. Flow Cytometry
Uses differences in electrical conductivity between species
Fluorescence of some species
Cells selectively stained with antibody plus fluorescent dye
Figure 18.12

34. A typical dichotomous key See appendix H in your lab book

35. Genetics DNA base composition DNA fingerprinting rRNA sequencing
Guanine + cytosine moles% (GC)
DNA fingerprinting
Electrophoresis of restriction enzyme digests
rRNA sequencing
Polymerase Chain Reaction (PCR)p251
Figure 10.14

36. Nucleic Acid Hybridization: DNA chip
DNA Chip Technology
Figure 10.17

37. Differentiate between classificaiton and identification
Figure 10.5

38. FISH Fluorescent in situ hybridization Add DNA probe for S. aureus
Figure 10.18

39. Differentiate between strain and species?
A group of bacteria derived from a single cell is called a strain.
Groups of closely related strains constitute a bacterial species.

40. 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.
Not composed of cells and cannot grow without a host cell.

41. Dichotomous keys are used for identification of organisms

42. Cladograms show phylogenetic relationships among organisms

43. Differential staining
Name examples

44. The gram stain

45. 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

46. 4 major groups Domain Bacteria Domain archaeobacteria
Gram-negative Eubacteria that have cell walls. Proteobacteria
Non proteobacteria Gram negative bacteria
Gram positive Eubacteria that have cell walls
Domain archaeobacteria
Check Bergey's for description.

47. 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