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In the Name of GOD. 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.

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Presentation on theme: "In the Name of GOD. 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."— Presentation transcript:

1 In the Name of GOD

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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. 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. 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 Pure microbiology Applied microbiology Applied microbiology

5 Medical Microbiology The study of relationships between humans and microbes, including: 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. 1590: Hans and Zacharias Janssen (Dutch lens grinders) mounted two lenses in a tube to produce the first compound microscope.Hans and Zacharias JanssenHans and Zacharias Janssen 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. 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.Robert HookeRobert Hooke

7 Development of microscopy 1676: Anton van Leeuwenhoek ( ) was the first person to observe microorganisms.Anton van Leeuwenhoek 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.Carl Zeiss and Ernst Abbe 1931: Ernst Ruska constructed the first electron microscope.Ernst Ruska

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

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

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

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

12 Spontaneous generation controversy: Spontaneous generation controversy: Aristotle ( ) and others believed that living organisms could develop from non-living materials. Aristotle ( ) and others believed that living organisms could develop from non-living materials. Aristotle 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. 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.Francesco RediFrancesco Redi 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. 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.Theodor SchwannTheodor Schwann

13 Spontaneous generation controversy: Spontaneous generation controversy: 1861: Louis Pasteur's ( ) famous experiments with swan-necked flasks finally proved that microorganisms do not arise by spontaneous generation. 1861: Louis Pasteur's ( ) famous experiments with swan-necked flasks finally proved that microorganisms do not arise by spontaneous generation.Louis Pasteur'sLouis Pasteur's John Tyndall ( ) proved that dust carried germs. 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. 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.Hieronymus FracastoriusHieronymus Fracastorius 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 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.Agostino Bassi de LodiAgostino Bassi de Lodi 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. 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.Ignaz SemmelweissIgnaz Semmelweiss

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 : Louis Pasteur proposed the "germ theory" of disease.Louis Pasteur 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.Joseph Lister 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: 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:Robert KochRobert Koch 1-The agent must be present in every case of the disease. 1-The agent must be present in every case of the disease. 2-The agent must be isolated and cultured in vitro. 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. 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 4-The agent must be recoverable from the experimentally-infected host

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

19 Phylogenetic tree of life

20 Prokaryotes and eukaryotes

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24 Strain: progeny and subcultures of a single colony isolate in pure culture. 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. 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 1- structural traits of shape, size mode of movement, resting stage, Gram strain reaction, macroscopic growth 2- biochemical and nutritional traits, end products, 2- biochemical and nutritional traits, end products, 3- physiologic traits relative to oxygen, temperature, pH, response to antimicrobial agents 3- physiologic traits relative to oxygen, temperature, pH, response to antimicrobial agents 4- ecologic traits 4- ecologic traits 5- DNA base composition, homology, genetic 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. 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) 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) 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( ) 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 ) 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) 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 “ 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. 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 : Kingdom procaryotae : 1- Gracillicutes (Gram- bacteria) 2- Firmicutes (Gram+ bacteria) 3- Tenericutes (cell wall-less bacteria: Mycoplasma / Mollicutes) 4- Mendosicutes (Archaebacteria)

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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. 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 Microscopic morphology Colonial morphology Colonial morphology Biochemical tests Biochemical tests Biotyping Biotyping Serotyping Serotyping Antibiogram patterns Antibiogram patterns Phage typing Phage typing

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

35 Bacterial classification 3- Genotypic classification of bacteria 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% 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 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% Nucleic acid sequence analysis (i.e. rRNA sequencing) E.coli:100%; B.fragilis: 72% Plasmid analysis Plasmid analysis Ribotyping Ribotyping Chromosomal DNA fragment analysis Chromosomal DNA fragment analysis

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