1. In the Name of GOD

3. What is a Microbe?
They are the oldest form of life on earth. Microbe fossils date back more than 3.5 billion years to a time when the Earth was covered with oceans that regularly reached the boiling point, hundreds of millions of years before dinosaurs roamed the earth. Without microbes, we couldn’t eat or breathe. Without us, they’d probably be just fine. Understanding microbes is vital to understanding the past and the future of ourselves and our planet.

4. Microbiology
Microbiology is the study of living microorganisms (microbes) , simple in structure, and usually small in size, include bacteria, algae, fungi, protozoa, and viruses.
Pure microbiology
Applied microbiology

5. Medical Microbiology
The study of relationships between humans and microbes, including:
- Infection
- Infective disease
- Colonisation
- Transmission of infective agents

6. Development of microscopy
1590: Hans and Zacharias Janssen (Dutch lens grinders) mounted two lenses in a tube to produce the first compound microscope.
1660: Robert Hooke ( ) published "Micrographia", containing drawings and detailed observations of biological materials made with the best compound microscope and illumination system of the time.

7. Development of microscopy
1676: Anton van Leeuwenhoek ( ) was the first person to observe microorganisms.
1883: Carl Zeiss and Ernst Abbe pioneered developments in microscopy (such as immersion lenses and apochromatic lenses which reduce chromatic aberration) which persist until the present day.
1931: Ernst Ruska constructed the first electron microscope.

8. The History of Microbiology
Timeline ____1600_______1700_______ 1800_________ 1900_______2000 ____
1677
Observed "little animals" (Antony Leeuwenhoek)
1796
First scientific Small pox vaccination (Edward Jenner)
1850
Advocated washing hands to stop the spread of disease (Ignaz Semmelweis)
1861
Disproved spontaneous generation (Louis Pasteur)
1862
Supported Germ Theory of Disease (Louis Pasteur)

9. The History of Microbiology
1867
Practiced antiseptic surgery (Joseph Lister)
1876
First proof of Germ Theory of Disease with B. anthracis discovery (Robert Koch)
1881
Growth of Bacteria on solid media (Robert Koch)
1882
Outlined Kochs postulates (Robert Koch)
Developed acid-fast Stain (Paul Ehrlich)
1884
Developed Gram Stain (Christian Gram)

10. The History of Microbiology
1885
First Rabies vaccination (Louis Pasteur)
1887
Invented Petri Dish (R.J. Petri)
1892
Discovered viruses (Dmitri Iosifovich Ivanovski)
1899
Recognized viral dependence on cells for reproduction (Martinus Beijerinck)
1900
Proved mosquitoes carried the yellow fever agent (Walter Reed)

11. The History of Microbiology
1910
Discovered cure for syphilis (Paul Ehrlich)
1928
Discovered Penicillin (Alexander Fleming)
1977
Developed a method to sequence DNA (W. Gilbert & F. Sanger)
1983
Polymerase Chain Reaction invented (Kary Mullis)
1995
First microbial genomic sequence published (H. influenzae) (TIGR)
2003
Complete sequence of human genome was published

12. Spontaneous generation controversy:
Aristotle ( ) and others believed that living organisms could develop from non-living materials.
1688: Francesco Redi ( ) was an Italian physician who refuted the idea of spontaneous generation by showing that rotting meat carefully kept from flies will not spontaneously produce maggots.
1836: Theodor Schwann ( ) passed air through red hot tubes and observed no growth , and helped develop the cell theory of living organisms, namely that all living organisms are composed of one or more cells and that the cell is the basic functional unit of living organisms.

13. Spontaneous generation controversy:
1861: Louis Pasteur's ( ) famous experiments with swan-necked flasks finally proved that microorganisms do not arise by spontaneous generation.
John Tyndall ( ) proved that dust carried germs.

14. Proof that microbes cause disease
1546: Hieronymus Fracastorius (Girolamo Fracastoro) wrote "On Contagion" ("De contagione et contagiosis morbis et curatione"), the first known discussion of the phenomenon of contagious infection.
1835 Agostino Bassi de Lodi showed that a disease affecting silkworms was caused by a fungus - the first microorganism to be recognized as a contagious agent of animal disease.
1847: Ignaz Semmelweiss ( ), a Hungarian physician who decided that doctors in Vienna hospitals were spreading childbed fever while delivering babies. He started forcing doctors under his supervision to wash their hands before touching patients.

15. Proof that microbes cause disease
Friedrich Henle proposed criteria for providing that microorganisms were responsible for causing human disease (the germ theory of disease) in 1840.
1857: Louis Pasteur proposed the "germ theory" of disease.
1867: Joseph Lister ( ) introduced antiseptics in surgery. By spraying carbolic acid on surgical instruments, wounds and dressings, he reduced surgical mortality due to bacterial infection considerably.
1878: Joseph Lister developed the first pure culture techniques. He made serial dilutions in liquid media to obtain Bacterium ( Lactobacillus) lactis.

16. Proof that microbes cause disease
1876: Robert Koch ( ). German bacteriologist was the first to cultivate anthrax bacteria outside the body using blood serum at body temperature. Building on pasteur's "germ theory", he subsequently published "Koch's postulates" (1884), the critical test for the involvement of a microorganism in a disease:
1-The agent must be present in every case of the disease.
2-The agent must be isolated and cultured in vitro.
3-The disease must be reproduced when a pure culture of the agent is inoculated into a susceptible host.
4-The agent must be recoverable from the experimentally-infected host

18. Procaryote: primitive nucleus
Procaryotes include the Eubacteria (true bacteria) and archaebacteria (ancient bacteria)

19. Phylogenetic tree of life

20. Prokaryotes and eukaryotes

24. Strain: progeny and subcultures of a single colony isolate in pure culture.
Species: a collection of strains that share many features in common and differ considerably from other strains.
1- structural traits of shape, size mode of movement, resting stage, Gram strain reaction, macroscopic growth
2- biochemical and nutritional traits, end products,
3- physiologic traits relative to oxygen, temperature, pH, response to antimicrobial agents
4- ecologic traits
5- DNA base composition, homology, genetic traits

25. Species biotype (biovar): within a species collection or cluster, a strain that is chosen arbitrarily to best represent that species . Biotype strains are used as reference strains
Serotype( serovar)
Pathotype (pathovar)
Morphotype (morphovars)
Phage type (phagovar)

26. Taxonomy and nomenclature of bacteria
Microbes observed earlier by van Leeuwenhoek, were assigned to 6 species in the class chaos by Linnaeus.
Otto Muller organized bacteria in to genera and species according to classification methods of Carolus Linnaeus in 1770s. ( beginning of the taxonomic classification of microbes)
Cohn classified bacteria. (1872)

27. Taxonomy and nomenclature of bacteria
Important landmarks in the advance of bacterial taxonomy were classification of Chester (1901),Orha-Jensen(1919) and Buchanan( )
Committee of bacterial and viral taxonomy (Murphy )
ICSB regularly providing lists of resent validly published species names and proposed changes in nomenclature first in the “international journal of systematic and evolutionary microbiology” (IJSEM)

28. Taxonomy and nomenclature of bacteria
The status of microbial scheme is reviewed about every 10 years in successive editions of “Bergey`s manual of systematic bacteriology “
Recent advice on characterization methodologies and the definition of the species level is presented by Stackebrandt et al.(2002) “ species should be based on the description of more than one and preferably at least to 10 strains.

29. Classification of bacteria (Bergey`s manual of systematic bacteriology)
Kingdom procaryotae :
1- Gracillicutes (Gram- bacteria)
2- Firmicutes (Gram+ bacteria)
3- Tenericutes (cell wall-less bacteria: Mycoplasma / Mollicutes)
4- Mendosicutes (Archaebacteria)

31. Numerical identification
Based on surveys that define tables of the expected frequency of positively in a series of tests for each species.” Unknown” isolate compare with this table.

32. Bacterial classification
1- Phenotypic classification of bacteria
Microscopic morphology
Colonial morphology
Biochemical tests
Biotyping
Serotyping
Antibiogram patterns
Phage typing

34. Bacterial classification
2- Analytic classification of bacteria
Cell wall fatty-acid analysis
Whole cell analysis
SDS-PAGE* analysis of proteins (fingerprinting)
Multifocus locus enzyme electrophoresis
*sodium doddecyl sulfate polyacrylamide gel electrophoresis

35. Bacterial classification
3- Genotypic classification of bacteria
Guanine - cytosine ratio to adenine-thymidine in DNA (detect heterogeneity at genus level-25%-75%). S.aureus: %32-%36; E.coli, shigella,salmonell:48%-53%;M.tubeculosis :62%-70%
DNA-DNA hybridization techniques (comparison of base sequence compatibility between strains)- > 70% binding and <5% difference = in same species; E.coli100%; B.subtilis1%; p.aeruginosa : %1-3%
Nucleic acid sequence analysis (i.e. rRNA sequencing) E.coli:100%; B.fragilis: 72%
Plasmid analysis
Ribotyping
Chromosomal DNA fragment analysis