The Microbial World. Microbiology , Microbes, infections

Microbiology

1. The Microbial World Spring 2019

2. A Glimpse of History The Origin of Microorganisms 2

3. 3 Antony van Leeuwenhoek – Microbiology as a science – 1674 – lake water through a glass lens – carefully ground Robert Hooke – Observed first microorganism in 1665 – microfungus , which he called microscopic mushroom He also described how to make the kind of microscope that van Leeuwenhoek made almost 10 years later

4. The Origin of Microorganisms 4

5. Microorganisms have existed on earth for about 3.5 billion years – may be over this time. Where did these microscopic forms originate ? Spontaneous? Non-spontaneous? Some Famous Experiments Francesco Redi – worms originated from the eggs of flies John Needham – 1749 (boiled infusions + sealed with cork) Father Spallanzani – 1776 (boiled for longer time + melted necks) Destruction of “Vital Force” by heating

6. 6 Louis Pasteur-1861 Giant in Science Father of modern microbiology Air is filled with microorganisms Air filtration through a cotton plug Examination under microscope Growth in infusions Specially constructed Swan necked flasks

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8. 8 John Tyndall English physicist-1876 Different infusions required different boiling times to be sterilized 5 minutes to 5 hours in the case of hay infusions Hay in the lab can enhance the sterilization time. Why? How? Two forms: A cell that is readily killed by boiling, and one that is heat resistant

9. Ferdinand Cohn – 1876 – A botanist – Also found the heat resistant forms – endospore Anthrax – Bacillus anthracis – resistant spores

10. Microbiology – A Human Prospective Life can not exist without microbes Pathogens…? Beneficial Impacts…? Bacteria Archaea Protozoa Algae Fungi Multicellular parasites Non-living agents i.e. viruses, viroids , and prions 12

11. Diversity among microorganisms Far different from one another –than plants and animals Microbes –the most abundant form of life on earth as well as the oldest 500-1000 species live on a healthy human True contribution and biological role –underestimated (1% cultivated) Important Roles Nitrogen fixation Carbon recycling Supplying the O 2

12. Cellulose breakdown – cellulase –in environment as well as in digestive tracts of cattle, sheep, deer, and other ruminants Degradation of materials in sewage water Applications of Microbiology Food Production Bioremediation Useful Products Medical Microbiology

13. Food Production Egyptian Bakers (2100BC) –Yeast Beer production in Egypt –Fermentation Milk fermentation – Yogurt cheeses, and buttermilk Probiotics Bioremediation Polychlorinated biphenyls (PCBs ) Dichloro diphenyl trichloro ethane ( DDT) Trichloro ethylene Degrade oil Radioactive wastes A bacterium was discovered that can live on trinitrotoluene (TNT )

14. Other Useful Products Cellulose –used in stereo headsets Hydroxybutyric acid used in the manufacture of disposable diapers and plastics Ethanol, as a substitute for gasoline—a “biofuel” Chemicals poisonous to insects Antibiotics used in the treatment of disease Amino acids, used as dietary supplements

15. Medical Microbiology Sinister role –influenza in 1918–1919 Smallpox , bubonic plague, and influenza

16. Microorganisms As Model Organisms Model Organisms –same metabolic and genetic properties All cells are composed of same elements Synthesize their cell structures by the same basic mechanisms Duplicate their DNA by similar processes Degrade food materials to harvest energy via the same metabolic pathways The study of microorganisms has many advantages Results can be obtained quickly –Microbes grow rapidly Can be grown on –simple inexpensive media Understanding of life have come through the study of microorganisms 18

17. Members of The Microbial World Three domains of the life; Bacteria (Eubacteria) Archaea ( Archaebacteria –ancient bacteria) Eucarya 19 Microscopically similar Prokaryotic cell Nucleoid Genetically quite different

18. Bacteria They are all single-celled prokaryotes Specific shapes i.e. cylindrical, spherical, spiral. Rigid cell wall –peptidoglycan Binary fission –Identical to the original cells Flagella for movement 20

19. Archaea Same shape and size Also multiply with Binary fission –Identical to the original cells No peptidoglycan in cell wall Can grow in extreme environments Great Salt Lake and the Dead Sea Boiling hot springs at Yellowstone National Park Cold waters of Antarctica and Alaska 21

20. Nomenclature The first word –genus –first letter capitalized The second indicates the species –not capitalized Both words are always italicized or underlined Escherichia coli Specie VS Strain, E . coli strain B 22

21. Viruses, Viroids , and Prions Viruses are; Obligate intracellular parasites All forms of life including members of the Bacteria, Archaea , and Eucarya can be infected by viruses 24

22. Identification and Classification of Microbes 26

23. Grouping Criteria Would you group them according to shape? Or would it make more sense to group them according to their motility? According to their medical significance? But then, how would you classify two apparently identical bacteria that differed in their disease-causing potential? 27

24. Initial efforts Ferdinand Cohn –classification based on shape –too many kinds but too few shapes. 2 nd attempt by Sigurd Orla -Jensen –physiological properties rather than morphology Albert Kluyver and C. B. van Niel –evolutionary relationship –distinguished b/w resemblance and relatedness 1970, Roger Stanier –gene products can be compared –was assumed that all microbes are similar Many features –chemical nature of cell wall/membrane, rRNA Carl Woese – rRNA sequence 28

25. Principles of Taxonomy Identification Classification Nomenclature Strategies used for the Identification Microscopic examination Culture characteristics Biochemical tests Nucleic acid analysis 29

26. Strategies used for the classification Taxonomic Hierarchies Specie –prokaryotes VS eukaryotes, not identical, stains VS specie Genus Family Order Class Phyla Kingdom Domain –characteristics of a cell that makeup an organism

27. Bergey’s Manual of Systematic Bacteriology All known species are described there. The new edition is published based on genetic relatedness Information on; The ecology Methods of enrichment Culture Isolation of the organisms Methods for their maintenance and preservation

28. Representative Genera

29. Representative Genera

30. Representative Genera

31. Nomenclature International Code for the Nomenclature of Bacteria Bacterial names may originate from any language –Latin suffix Lactococcus lactis –Streptococcus – Lactococcus (Streptococcus) lactis 37

32. Principles of Taxonomy Identification Classification Nomenclature Strategies used for the Identification Microscopic examination Culture characteristics Biochemical tests Nucleic acid analysis 38

33. Microscopic examination Size and Shape –wet mount –Bacteria, fungus, protozoa Clinical diagnosis Gram staining Differentiate between Gram + ve and – ve Have limitations i.e. can not identify the Streptococcus pyogenes Can not differentiate between Salmonella and E.coli of stool samples Acid Fast Strain Mycobacterium –Tuberculosis 39

34. Metabolic capabilities Culture characteristics Serratia marcescens – red pigment at 22 o C Pseudomonas auroginosa – green pigment Streptococcus pyogenes –Blood agar – β hemolysis E.coli – UTI –Pink colonies on MacConkey agar –lactose fermentation Biochemical tests –for conclusive identification Catalase –present in all aerobes

35. tetramethyl -p- phenylenediamine

36. Bromcresol purple

37. Other Methods Serology FAME Serology Identification of the molecules that make up the surface structures i.e . c ell wall, capsule, flagella, and pili. This method rely on the specificity of interaction between antibodies and antigens FAME Cellular fatty acid composition can be used for the identification Gram negative – cytoplasmic and outer membrane Cells grown –treated – sodium hydroxide and methanol –fatty acids and volatile methyl esters –GC-MS 51

38. Genotypic Characteristics for the Identification DNA probe and PCR Probe-Single-stranded piece of nucleic acid, usually DNA, Labelled with a dye/radioisotope Complementary to the sequence of interest Fluorescence in situ hybridization (FISH )-16sRNA PCR of specific DNA Sequencing Ribosomal RNA Genes-16s, SSU Using rDNA to identify Uncultivated Organisms-Whipple’s disease- Tropheryma whipplei 52

39. Characterizing Strain Differences Salmonella enterica serotype Enteritidis Biochemical typing - biovar or a biotype Vibrio cholera- Eltor 54 A group of strains that have a characteristic biochemical pattern

40. Classifying the Microbes Stromatolites General Principles – draw backs 60

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