2. Ch 10 Taxonomy and Classification Classification of Microbes

3. 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?

4. 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?

5. 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

6. 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)

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

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

10. Figure 10.1 The Three-Domain System

11. Table 10.1

12. Figures 10.2, 10.3 Endosymbiotic Theory

13. Table 10.2

14. 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 MomenclatureInternational Code of Zoological Momenclature –International Code of Botanical NomenclatureInternational Code of Botanical Nomenclature –Bacteriological Code and Bergey’s ManualBacteriological CodeBergey’s Manual

15. 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 cruziCorkscrew-like (trypano-, borer; soma-, body) Honors Oswaldo Cruz Scientific Names

16. Species Definition Eukaryotic 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

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

18. Applications, p. 283 Identifying Bacteria

20. Figure 10.6 Phylogenetic Relationships of Prokaryotes

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

22. 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

23. 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

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

25. Figure 10.7 A clinical microbiology lab report form

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

27. 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

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

29. Combine known antiserum + unknown bacterium Slide agglutination ELISA p288, 514 Western blot p289 Southern Blot p292 DNA chip p293 Serology study of serum and its immune responce Figure 10.10

30. Strains with different antigens are called –Serotypes –Serovars –biovars

31. DNA Hybridization

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

33. The Western Blot

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

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

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

37. Nucleic Acid Hybridization: DNA chip Figure 10.17 DNA Chip Technolog y

38. Figure 10.5 Differentiate between classificaiton and identification

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

40. Differentiate between strain and species?

41. 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.

42. Dichotomous keys are used for identification of organisms

43. Cladograms show phylogenetic relationships among organisms

44. Differential staining Name examples

45. The gram stain

46. 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

47. 4 major groups Domain Bacteria –Gram-negative Eubacteria that have cell walls. Proteobacteria –Non proteobacteria Gram negative bacteria –Gram positive Eubacteria that have cell walls Domain archaeobacteria

48. 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