1. Second Lecture Bacterial Taxonomy and Classification

2. Taxonomy : The science of classification of living organisms. It consists of THREE areas: 1. Classification 2. Nomenclature 3. Identification

3. Classification Arrangement into taxonomic groups (taxa): Kingdoms or domains, divisions or phyla, classes, orders, families, genera and species. Nomenclature : Giving international names to taxa Identification : Known or unidentified species? ( to speciate). The process is called phenotyping.

5. Microbial Classification - Binomial system of nomenclature (18 th century): First: Genus (pl. genera), first letter capital, underline or italicize, e.g., Shigella, or Shigella; genus named also by a single letter ( Shigella = S) Second: Specific epithet; first letter small, underline or italicize (e.g. Shigella dysenteriae, or Shigella dysenteriae; if a single species: “sp.”, more than one species: “spp.” e.g. Shigella spp.

6. Other information about nomenclature - First name + second name = species - Sub-specific epithet = ssp., e.g., H. influenza ssp. aegyptius - Nickname: e.g. Staphylococcus = Staph. -- Bacterial names are named for the disease, e.g. Vibrio cholerae = cholera

8. Classifications of living organisms 1. FIVE Kingdoms (see names) 2. Three-Domain System- based on rRNA differences (by Carl Woese, 1970s): A. TWO domains prokaryotes (Archaea and Bacteria) B. ONE domain Eucarya or Eukarya

9. Ribosomal RNA (rRNA) - rRNA sequencing - rRNA has 2 subunits: 1. Small subunit rRNS (SSUrRNA), ONE RNA: a. Bacteria : 16S; coding gene contains 1500 DNA nucleotides (16S rDNA sequence)* b. Eukaryotes: 18S; coding gene contains 2000 nucleotides (18S rDNA sequences)* * Similarities & differences based on rDNA sequences 2. Large subunit rRNA (LSUrRNA)

10. NOTE: ANSWER ALL THE 10 MCQ QUESTIONS IN YOUR BOOK (BURTON’S MICROBIOLOGY for the HEALTH SCIENCES, Tenth Edition) - Good Luck -

11. Microscopes

12. Learning objective 1. Learn and understand the interrelationship between the different of measures of the METRIC system. 2. Learn the sizes of different organisms. 3. Compare the characteristics and capabilities of the different types of microscopes. 4. Answer correctly (exercise) the 10 MCQ about microscopy of your Burton’s textbook

13. Types of Microscopes 1. Simple 2. Compound light (Bright-field) 3. Dark-field 4. Phase contrast 5. Fluorescence 6. TEM 7. SEM 8. Atomic Force Microscope (AFM)

15. Microscopes 1. Simple microscope: - Anton van Leeuwenhoek - ONE lens - Magnification X 3-20 2. Compound microscope (objective lens): - Hans Jansen & Son Zakarias - Low power X4 X10 (eye piece) = 40 - Medium X10 X 10 = 100 - High X40 X 10 = 400 - Oil-immersion X100 X 10 = 1000

20. Cont./… Microscopes 2. Compound microscope (objective lens): - Hans Jansen & Son Zakarias

22. Microbes * Very tiny (small) * Require microscope to see them * Size & volume: Metric - Micrometer “µm” (10 -6 meter) = Micron (µ) - Nanometer “nm” (10 -9 meter) = Millimicron (mµ) * Microbes : - Coccus (spherical) = 1 µm - Bacillus (rod) = 3 µm long - Viruses = 0.01-0.3 µm - Fungi = 2 - 30 µm - Parasites = 5- 2000 µm

27. Electron Microscopes (EM): 1. Transmission (TEM) - X 1 Million - Internal microbial features’ examination - Killed microbes 2. Scanning (SEM) - Less magnification than TEM - Surface examination of microbes - Killed microbes Atomic Force Microscopes: - Living organisms

33. Microscopy 1. Sizes (see Table 2-1): bacteria: Micrometers (µm) Viruses : Nanometers 2. Total magnification= Objective X Ocular 3. Background of microscopy bright or dark in bright-field and dark-field microscopes respectively cont./…

34. Cont./microscopy 4. Images’ (photographs’) names: - Compound light: Photomicrograph - TEM: Transmission electron micrographs - SEM: Scanning electron micrographs 5. Ocular lens (eye piece) - X10 - Monocular - Binocular - Multi-Head (Teaching) ± Screen

36. Resolving (resolution ) power Is the ability of an optical instrument to distinguish between two adjacent objects. Examples: - Human eye = 0.2 mm - Compound light microscope = 0.2 µm - TEM = 0.2 nm - SEM = 20 nm (X100-200 < TEM)