In the Name of GOD

What is a Microbe? What is a Microbe?

They are the oldest form of life on earth. They are the oldest form of life on earth. Microbe fossils date back more than 3.5 Microbe fossils date back more than 3.5 billion years to a time when the Earth was billion years to a time when the Earth was covered with oceans that regularly reached covered with oceans that regularly reached the boiling point, hundreds of millions of the boiling point, hundreds of millions of years before dinosaurs roamed the earth.years before dinosaurs roamed the earth.

Without microbes, we couldn’t eat or breathe.Without microbes, we couldn’t eat or breathe.

Without us, they’d probably be just fine.Without us, they’d probably be just fine.

Understanding microbes is vital to Understanding microbes is vital to understanding the past and the future of understanding the past and the future of ourselves and our planet.ourselves and our planet.

MicrobiologyMicrobiology

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

Pure microbiologyPure microbiology Applied microbiologyApplied microbiology

Medical Microbiology Medical Microbiology

The study of The study of relationships relationships between humans between humans and microbes, and microbes, including:including:

- Infection - Infection

- Infective disease - Infective disease

- Colonisation - Colonisation

- Transmission of - Transmission of infective agents infective agents

Development of Development of microscopymicroscopy

1590: 1590: Hans and Zacharias Janssen (Dutch (Dutch

lens grinders) mounted two lenses in a lens grinders) mounted two lenses in a tube to produce the first compound tube to produce the first compound microscope.microscope.

1660: 1660: Robert Hooke (1635-1703) (1635-1703)

published "Micrographia", containing published "Micrographia", containing drawings and detailed observations of drawings and detailed observations of biological materials made with the best biological materials made with the best compound microscope and illumination compound microscope and illumination system of the time. system of the time.

Development of Development of microscopymicroscopy

1676: Anton van Leeuwenhoek (1632-1723) 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.

The History of MicrobiologyThe History of Microbiology

1677 1677 Observed "little animals"Observed "little animals"

(Antony Leeuwenhoek) 17961796 First scientific Small pox First scientific Small pox

vaccinationvaccination (Edward Jenner) 18501850 Advocated washing hands to Advocated washing hands to

stop the spread of diseasestop the spread of disease (Ignaz Semmelweis)

18611861 Disproved spontaneous Disproved spontaneous

generation generation (Louis Pasteur) 18621862 Supported Germ Theory of Supported Germ Theory of

Disease Disease (Louis Pasteur)

TimelineTimeline

____1600_______1700_______ 1800_________ ____1600_______1700_______ 1800_________ 1900_______2000 ____1900_______2000 ____

The History of MicrobiologyThe History of Microbiology

18671867 Practiced antiseptic surgery Practiced antiseptic surgery

(Joseph Lister) 18761876 First proof of Germ Theory First proof of Germ Theory

of Disease with of Disease with B. B. anthracisanthracis discovery discovery (Robert Koch)

18811881 Growth of Bacteria on solid Growth of Bacteria on solid

media media (Robert Koch) 18821882 Outlined Kochs postulates Outlined Kochs postulates

(Robert Koch) 18821882 Developed acid-fast Stain Developed acid-fast Stain

(Paul Ehrlich) 18841884 Developed Gram StainDeveloped Gram Stain

(Christian Gram)

The History of MicrobiologyThe History of Microbiology

18851885 First Rabies vaccination First Rabies vaccination

(Louis Pasteur) 18871887 Invented Petri Dish Invented Petri Dish

(R.J. Petri) 18921892 Discovered viruses Discovered viruses

(Dmitri Iosifovich Ivanovski)

18991899 Recognized viral Recognized viral

dependence on cells for dependence on cells for reproduction reproduction (Martinus Beijerinck)

19001900 Proved mosquitoes Proved mosquitoes

carried the yellow fever carried the yellow fever agentagent (Walter Reed)

The History of MicrobiologyThe History of Microbiology 19101910 Discovered cure for syphilisDiscovered cure for syphilis

(Paul Ehrlich) 19281928 Discovered Penicillin Discovered Penicillin

(Alexander Fleming) 19771977 Developed a method to sequence Developed a method to sequence

DNA DNA (W. Gilbert & F. Sanger) 19831983 Polymerase Chain Reaction Polymerase Chain Reaction

invented invented (Kary Mullis) 19951995 First microbial genomic sequence First microbial genomic sequence

published published (H. influenzae) (TIGR) 20032003 Complete sequence of human Complete sequence of human

genome was publishedgenome was published

Spontaneous generation controversy:

Aristotle (384-322) and others believed that living (384-322) and others believed that living organisms could develop from non-living organisms could develop from non-living materials.materials.

1688: Francesco Redi (1626-1697) was an Italian 1688: Francesco Redi (1626-1697) was an Italian physician who refuted the idea of physician who refuted the idea of spontaneous spontaneous generationgeneration by showing that rotting meat by showing that rotting meat carefully kept from flies will not spontaneously carefully kept from flies will not spontaneously produce maggots. produce maggots.

1836: Theodor Schwann (1810-1882) passed air 1836: Theodor Schwann (1810-1882) passed air through red hot tubes and observed no growth , through red hot tubes and observed no growth , and helped develop the cell theory of living and helped develop the cell theory of living organisms, namely that all living organisms are organisms, namely that all living organisms are composed of one or more cells and that the cell is composed of one or more cells and that the cell is the basic functional unit of living organisms. the basic functional unit of living organisms.

Spontaneous generation Spontaneous generation controversy:controversy:

1861: Louis Pasteur's 1861: Louis Pasteur's (1822-1895) famous (1822-1895) famous experiments with experiments with swan-necked flasks swan-necked flasks finally finally proved that proved that microorganisms do microorganisms do not arise by not arise by spontaneous spontaneous generation.generation.

John Tyndall (1820-John Tyndall (1820-1893) 1893) proved that proved that dust carried germs.dust carried germs.

Proof that microbes cause Proof that microbes cause diseasedisease

1546: Hieronymus Fracastorius (Girolamo 1546: Hieronymus Fracastorius (Girolamo Fracastoro) wrote "On Contagion" ("De contagione et Fracastoro) wrote "On Contagion" ("De contagione et contagiosis morbis et curatione"), the first known contagiosis morbis et curatione"), the first known discussion of the phenomenon of contagious discussion of the phenomenon of contagious infection. infection.

1835 Agostino Bassi de Lodi showed that a disease 1835 Agostino Bassi de Lodi showed that a disease affecting silkworms was caused by a fungus - the affecting silkworms was caused by a fungus - the first microorganism to be recognized as a contagious first microorganism to be recognized as a contagious agent of animal disease.agent of animal disease.

1847: Ignaz Semmelweiss (1818-1865), a Hungarian 1847: Ignaz Semmelweiss (1818-1865), a Hungarian physician who decided that doctors in Vienna physician who decided that doctors in Vienna hospitals were spreading childbed fever while hospitals were spreading childbed fever while delivering babies. He started forcing doctors under delivering babies. He started forcing doctors under his supervision to wash their hands before touching his supervision to wash their hands before touching patients. patients.

Proof that microbes cause Proof that microbes cause diseasedisease

Friedrich HenleFriedrich Henle proposed criteria for providing proposed criteria for providing that microorganisms were responsible for causing that microorganisms were responsible for causing human disease (the germ theory of disease) in human disease (the germ theory of disease) in 1840.1840.

1857: Louis Pasteur proposed the "germ theory" of 1857: Louis Pasteur proposed the "germ theory" of disease.disease.

1867: Joseph Lister (1827-1912) introduced 1867: Joseph Lister (1827-1912) introduced antiseptics in surgery. By spraying carbolic acid on antiseptics in surgery. By spraying carbolic acid on surgical instruments, wounds and dressings, he surgical instruments, wounds and dressings, he reduced surgical mortality due to bacterial infection reduced surgical mortality due to bacterial infection considerably.considerably.

1878: Joseph Lister developed the first pure culture 1878: Joseph Lister developed the first pure culture techniques. He made serial dilutions in liquid media techniques. He made serial dilutions in liquid media to obtain Bacterium ( Lactobacillus) lactis.to obtain Bacterium ( Lactobacillus) lactis.

Proof that microbes cause Proof that microbes cause diseasedisease

1876: Robert Koch (1843-1910). 1876: Robert Koch (1843-1910). German bacteriologist was the German bacteriologist was the first to cultivate anthrax first to cultivate anthrax bacteria outside the body using bacteria outside the body using blood serum at body blood serum at body temperature. Building on temperature. Building on pasteur's "germ theory", he pasteur's "germ theory", he subsequently published subsequently published ""Koch's Koch's postulatespostulates"" (1884), the critical (1884), the critical test for the involvement of a test for the involvement of a microorganism in a disease: microorganism in a disease:

1-The agent must be present 1-The agent must be present in every case of the disease. in every case of the disease.

2-The agent must be isolated 2-The agent must be isolated and cultured in vitro. and cultured in vitro.

3-The disease must be 3-The disease must be reproduced when a pure culture reproduced when a pure culture of the agent is inoculated into a of the agent is inoculated into a susceptible host. susceptible host.

4-The agent must be 4-The agent must be recoverable from the recoverable from the experimentally-infected hostexperimentally-infected host

Procaryote: primitive nucleusProcaryotes include the Eubacteria (true bacteria) and archaebacteria (ancient bacteria)

Phylogenetic tree of lifePhylogenetic tree of life

Prokaryotes and Prokaryotes and eukaryoteseukaryotes

Strain:Strain: progeny and subcultures of a single progeny and subcultures of a single colony isolate in pure culture.colony isolate in pure culture.

Species:Species: a collection of strains that share many a collection of strains that share many features in common and differ considerably features in common and differ considerably from other strains.from other strains.

1- structural traits of shape, size mode of 1- structural traits of shape, size mode of movement, resting stage, Gram strain reaction, movement, resting stage, Gram strain reaction, macroscopic growthmacroscopic growth

2- biochemical and nutritional traits, end 2- biochemical and nutritional traits, end products,products,

3- physiologic traits relative to oxygen, 3- physiologic traits relative to oxygen, temperature, pH, response to antimicrobial temperature, pH, response to antimicrobial agentsagents

4- ecologic traits4- ecologic traits 5- DNA base composition, homology, genetic 5- DNA base composition, homology, genetic

traitstraits

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

Taxonomy and nomenclature Taxonomy and nomenclature of bacteriaof bacteria

Microbes observed earlier by van Microbes observed earlier by van Leeuwenhoek, were assigned to 6 Leeuwenhoek, were assigned to 6 species in the class chaos by species in the class chaos by Linnaeus.Linnaeus.

Otto MullerOtto Muller organized bacteria in to organized bacteria in to genera and species according to genera and species according to classification methods of Carolus classification methods of Carolus Linnaeus in 1770s. ( beginning of Linnaeus in 1770s. ( beginning of the taxonomic classification of the taxonomic classification of microbes)microbes)

Cohn classified bacteria. (1872) Cohn classified bacteria. (1872)

Taxonomy and nomenclature Taxonomy and nomenclature of bacteriaof bacteria

Important landmarks in the advance of Important landmarks in the advance of bacterial taxonomy were classification of bacterial taxonomy were classification of Chester (1901),Orha-Jensen(1919) and Chester (1901),Orha-Jensen(1919) and Buchanan(1919-1925)Buchanan(1919-1925)

Committee of bacterial and viral taxonomy Committee of bacterial and viral taxonomy (Murphy -1995)(Murphy -1995)

ICSB regularly providing lists of resent validly ICSB regularly providing lists of resent validly published species names and proposed changes published species names and proposed changes in nomenclature first in the “in nomenclature first in the “international international journal of systematic and evolutionary journal of systematic and evolutionary microbiologymicrobiology” (IJSEM)” (IJSEM)

Taxonomy and nomenclature Taxonomy and nomenclature of bacteriaof bacteria

The status of microbial scheme is The status of microbial scheme is reviewed about every 10 years in reviewed about every 10 years in successive editions of “successive editions of “Bergey`s Bergey`s manual of systematic bacteriologymanual of systematic bacteriology “ “

Recent advice on characterization Recent advice on characterization methodologies and the definition of methodologies and the definition of the species level is presented by the species level is presented by Stackebrandt et al.(2002) “ species Stackebrandt et al.(2002) “ species should be based on the description should be based on the description of more than one and preferably at of more than one and preferably at least to 10 strains. least to 10 strains.

Classification of bacteriaClassification of bacteria(Bergey`s manual of systematic (Bergey`s manual of systematic

bacteriology)bacteriology) Kingdom procaryotae :Kingdom procaryotae :

1- Gracillicutes (Gram- bacteria)1- Gracillicutes (Gram- bacteria)

2- Firmicutes (Gram+ bacteria)2- Firmicutes (Gram+ bacteria)

3- Tenericutes (cell wall-less bacteria: 3- Tenericutes (cell wall-less bacteria: Mycoplasma / Mollicutes) Mycoplasma / Mollicutes)

4- Mendosicutes (Archaebacteria) 4- Mendosicutes (Archaebacteria)

Numerical identificationNumerical identification

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

Bacterial classificationBacterial classification

1- Phenotypic 1- Phenotypic classification of classification of bacteriabacteria

Microscopic Microscopic morphologymorphology

Colonial morphologyColonial morphology Biochemical testsBiochemical tests

BiotypingBiotyping SerotypingSerotyping

Antibiogram patternsAntibiogram patterns Phage typingPhage typing

Bacterial classificationBacterial classification

2-2- Analytic classification of bacteriaAnalytic classification of bacteria Cell wall fatty-acid analysisCell wall fatty-acid analysis Whole cell analysisWhole cell analysis SDS-PAGESDS-PAGE** analysis of proteins analysis of proteins

(fingerprinting)(fingerprinting) Multifocus locus enzyme Multifocus locus enzyme

electrophoresiselectrophoresis

**sodium doddecyl sulfate polyacrylamide gel electrophoresissodium doddecyl sulfate polyacrylamide gel electrophoresis

Bacterial classificationBacterial classification 3- Genotypic classification of bacteria3- Genotypic classification of bacteria Guanine - cytosine ratio to adenine-thymidine in DNA Guanine - cytosine ratio to adenine-thymidine in DNA

(detect heterogeneity at genus level-25%-75%). S.aureus: (detect heterogeneity at genus level-25%-75%). S.aureus: %32-%36; E.coli, shigella,salmonell:48%-%32-%36; E.coli, shigella,salmonell:48%-53%;M.tubeculosis :62%-70%53%;M.tubeculosis :62%-70%

DNA-DNA hybridization techniques (comparison of base DNA-DNA hybridization techniques (comparison of base sequence compatibility between strains)- > 70% binding sequence compatibility between strains)- > 70% binding and <5% difference = in same species; E.coli100%; and <5% difference = in same species; E.coli100%; B.subtilis1%; p.aeruginosa : %1-3%B.subtilis1%; p.aeruginosa : %1-3%

Nucleic acid sequence analysis (i.e. rRNA sequencing) Nucleic acid sequence analysis (i.e. rRNA sequencing)

E.coli:100%; B.fragilis: 72%E.coli:100%; B.fragilis: 72%

Plasmid analysisPlasmid analysis

RibotypingRibotyping

Chromosomal DNA fragment analysisChromosomal DNA fragment analysis