Introduction to microbiology. Classification and nomenclature of microorganisms. 09.02.2011

Introduction to microbiology.Introduction to microbiology.

Classification and Classification and nomenclaturenomenclature of of microorganisms.microorganisms.

09.02.2011

Course IntroductionCourse Introduction

Instructor: Instructor:

Dr Elena RomancencoDr Elena Romancenco Department of MicrobiologyDepartment of Microbiology, ,

Virology and ImmunologyVirology and Immunology E-mail: E-mail:

eromancenco@yahoo.comeromancenco@yahoo.com WEBSITE:WEBSITE:www.microbio.ukoz.comwww.microbio.ukoz.com

Course objectivesCourse objectives

List major groups of microorganisms and List major groups of microorganisms and their habitats.their habitats.

Overview and history of Microbiology.Overview and history of Microbiology.

Describe the system of scientific Describe the system of scientific nomenclature used to name nomenclature used to name microorganisms.microorganisms.

DefinitionDefinition

MicrobiologyMicrobiology ((mikros bios logosmikros bios logos – – small, live, study) study small, live, study) study microorganisms and their activities.microorganisms and their activities.

MicrobiologyMicrobiology is the study of is the study of microorganisms usually less than microorganisms usually less than 1mm in diameter which requires 1mm in diameter which requires some form of magnification to be some form of magnification to be seen clearly.seen clearly.

MicrobiologyMicrobiology - - study study the the organisms organisms that can exist as single cells, contain that can exist as single cells, contain a nucleic acid genome for at least a nucleic acid genome for at least some part of their life cycle, and are some part of their life cycle, and are capable of replicating that genome capable of replicating that genome themselves or getting replicated with themselves or getting replicated with the help of host cellsthe help of host cells

Branches of MicrobiologyBranches of Microbiology

Bacteriology:Bacteriology: study of bacteria study of bacteria Mycology:Mycology: study of fungi study of fungi Virology:Virology: study of viruses study of viruses

Beijerinck, NEBeijerinck, NE: discovered intracellular : discovered intracellular reproduction of TMV; coined the term reproduction of TMV; coined the term “virus” (1899)“virus” (1899)

Parasitology:Parasitology: study of protozoa and study of protozoa and parasitic wormsparasitic worms

Branches of MicrobiologyBranches of Microbiology

Immunology:Immunology: study of immunity study of immunity Edward Jenner, UKEdward Jenner, UK: developed vaccination (1798): developed vaccination (1798) Metchnikoff, RUMetchnikoff, RU: discovered : discovered phagocytesphagocytes (1884) (1884) Paul Ehrlich, DEPaul Ehrlich, DE: : theory of immunitytheory of immunity (1890) (1890)

ChemotherapyChemotherapy Treatment of disease by using chemical meansTreatment of disease by using chemical means Antibiotics produced naturally Antibiotics produced naturally Synthetic drugsSynthetic drugs Paul EhrlichPaul Ehrlich (1878) – used arsenic compounds (1878) – used arsenic compounds

to fight disease to fight disease

Branches of MicrobiologyBranches of Microbiology

ChemotherapyChemotherapy Alexander Fleming, Scotland (1928) discovered Alexander Fleming, Scotland (1928) discovered

penicillinpenicillin Selman Waksman, Ukraine (1944) discovered Selman Waksman, Ukraine (1944) discovered

streptomycinstreptomycin ProblemsProblems

Toxicity of drugs => Selective toxicityToxicity of drugs => Selective toxicity Resistance of bacteria to drugsResistance of bacteria to drugs

Microorganisms are Microorganisms are everywhere, but why is so everywhere, but why is so important to learn aboutimportant to learn about

them?them?

Affect our lives in many Affect our lives in many different waysdifferent ways..

Microbes are capable of growing in a wide Microbes are capable of growing in a wide variety of environments.variety of environments.

Bacteria will grow in frigid glaciers to Bacteria will grow in frigid glaciers to boiling volcanic springs, dry sands to the boiling volcanic springs, dry sands to the open ocean. open ocean.

IMPORTANIMPORTANCE OF CE OF MICROORGANISMSMICROORGANISMS

Microorganisms are the oldest forms of life.Microorganisms are the oldest forms of life. Nutrient production & energy flowNutrient production & energy flow Production of foodsProduction of foods Decomposition (bioremediation)Decomposition (bioremediation) Without certain microorganism life could not exist; Without certain microorganism life could not exist;

produce Oproduce O2 2 and Nand N2 2 Production of drugs & vaccinesProduction of drugs & vaccines Genetic engineeringGenetic engineering Causing disease Causing disease

Microorganisms have killed more people than have ever Microorganisms have killed more people than have ever been killed in war.been killed in war.

Why Study Why Study Medical Medical Microbiology?Microbiology?

The majority of serious diseases in humans (especially those of The majority of serious diseases in humans (especially those of early childhood) are due to microbial infections. early childhood) are due to microbial infections.

Prior to the discovery of antibiotics and vaccines, a large Prior to the discovery of antibiotics and vaccines, a large proportion of children died before adulthood because of proportion of children died before adulthood because of infectious disease. infectious disease.

Till Till 1900, the average life expectancy in the United States was 1900, the average life expectancy in the United States was 40 years of age.40 years of age.

In In 20002000 - - 80 years, largely due to the near eradication of most 80 years, largely due to the near eradication of most serious early childhood diseases.serious early childhood diseases.

This trend is seen in the gap between developed and developing This trend is seen in the gap between developed and developing countries in terms of causes of death (mortality). countries in terms of causes of death (mortality).

MICROBESMICROBES

MICROBESMICROBES includes all those living includes all those living organisms that can not be viewed (seen) organisms that can not be viewed (seen) in any detail by the human eye. in any detail by the human eye.

Alternatively, a Alternatively, a MICROBEMICROBE is any living is any living creature that must be examined with a creature that must be examined with a magnifying lens in order to see its unique magnifying lens in order to see its unique physical characteristics (size, shape, physical characteristics (size, shape, motility, color). motility, color).

MicrobesMicrobes PathogenPathogen or or pathogenicpathogenic -- capable of producing capable of producing

diseasedisease.. Though only a minority of Though only a minority of microorganismsmicroorganisms are are pathogenicpathogenic, ,

practical knowledge of microbes is necessary for their practical knowledge of microbes is necessary for their treatment so is highly relevant to medicine and related health treatment so is highly relevant to medicine and related health sciencessciences..

Normal flora [Normal flora [normal microbiotanormal microbiota]] - - nnot typically-ot typically-disease-causingdisease-causing

microorganisms normally found in and on healthy individuals. microorganisms normally found in and on healthy individuals. • on the skinon the skin, , • in the eyesin the eyes, , • in the nosein the nose,,• in the mouthin the mouth, , • in the upper throatin the upper throat, , • iin the lower urethran the lower urethra,,• in the lower intestine.in the lower intestine.

the the Bacterium Bacterium

Escherichia Escherichia colicoli;;

a a photosynthetiphotosyntheti

c c cyanobacteriucyanobacteriu

mm

a fungusa fungus

Ebola virusEbola virus

the malaria the malaria parasite (a parasite (a protozoanprotozoan

A, Influenza A, Influenza virus; virus; B, West Nile B, West Nile

Virus;Virus;

C, C, Staphylococcus Staphylococcus aureusaureus; ; D, D,

Streptococcus Streptococcus pneumoniaepneumoniae..

Microbial Microbial morphologymorphology Microbial Microbial cytologycytology Microbial Microbial physiologyphysiology Microbial Microbial ecologyecology Microbial Microbial genetics and genetics and

molecular biologymolecular biology Microbial Microbial taxonomytaxonomy

Microbiologists may be Microbiologists may be interested in various interested in various

characteristics or activities ofcharacteristics or activities of micromicrobs and may studybs and may study::

ClassificationClassification of of lifelife

For many years, living organisms were For many years, living organisms were divided into two kingdoms: divided into two kingdoms:

AnimaliaAnimalia (animal) and (animal) and

PlantaePlantae (vegetable). (vegetable).

Classification SchemesClassification Schemes

Plantae

AnimaliaPlantae

Two kingdoms

But afterBut after 1800s, scientists realized 1800s, scientists realized that that these these two kingdoms could not adequately express the two kingdoms could not adequately express the diversity of lidiversity of liffe.e.

Since the 1960s, the most widely used scheme Since the 1960s, the most widely used scheme - - five kingdoms.five kingdoms.

VirusesViruses are are separateseparate group of biological entities, group of biological entities, although not organisms in the same sense as although not organisms in the same sense as Eukaryotes, Archaea and Bacteria. Eukaryotes, Archaea and Bacteria.

Classification Classification sschemeschemes, , 5 kingdom5 kingdomss

Plantae

AnimaliaPlantaeProtistaMonera Fungi

Domain Bacteria(Eubacteria)

Domain Archaea

(Archaeabacteria)

Prokaryotes

Eukaryotes

Classification of LifeClassification of Life

33 major D major Domains of omains of lifelife Bacteria Bacteria Archaea Archaea Eukaryota (Eukarya)Eukaryota (Eukarya)

TThe first two are he first two are Prokaryotes Prokaryotes ((Bacteria and Archaea)- Bacteria and Archaea)- without truewithout true nucleus, while nucleus, while the Eukaryotes all have a true the Eukaryotes all have a true nucleus in each cell.nucleus in each cell.

The 3 Domains. Source: http://www.ucmp.berkeley.edu/alllife/images/domains_small.gif

Kingdom MoneraKingdom Monera

All organisms in the Kingdom Monera are All organisms in the Kingdom Monera are prokaryotesprokaryotes. . lack nuclei and organelleslack nuclei and organelles most of their cell walls are made of most of their cell walls are made of peptidoglycanpeptidoglycan (the exceptions (the exceptions

are the archaebacteria). are the archaebacteria).

The The archaebacteriaarchaebacteria have cell walls that lack peptidoglycan, cell have cell walls that lack peptidoglycan, cell membranes that utilize different membranes that utilize different lipidslipids, and ribosomes similar to , and ribosomes similar to those found in those found in eukaryoteseukaryotes. .

The The bacteriabacteria (eubacteria-true bacteria)(eubacteria-true bacteria) are characterized by how are characterized by how they metabolize resources, their means of motility, and their they metabolize resources, their means of motility, and their shape. shape.

Most organisms in the Kingdom Monera reproduce through Most organisms in the Kingdom Monera reproduce through binary fissionbinary fission (asexual) or (asexual) or conjugationconjugation ( (sexual). sexual).

BacteriaBacteria

Most utilize Most utilize flagellaflagella for movement. for movement.

Digestion is Digestion is extracellularextracellular (outside the cell) and (outside the cell) and nutrients are absorbed into the cell. nutrients are absorbed into the cell.

Circulation and digestion in Kingdom Monera is Circulation and digestion in Kingdom Monera is accomplished through accomplished through diffusiondiffusion. .

BacterialBacterial ClassificationClassification

byby

Metabolism Metabolism Morphology Morphology (shape)(shape)

StainingStaining, etc, etc

According theAccording the metaboli metabolismsm

AutotrophsAutotrophs manufacture their own organic manufacture their own organic compounds. compounds.

HeterotrophsHeterotrophs obtain their energy by feeding obtain their energy by feeding on other organic substances. on other organic substances.

SaprophytesSaprophytes,, a special kind of heterotroph, a special kind of heterotroph, obtain energy by feeding on decaying matter. obtain energy by feeding on decaying matter.

According the According the symbiotic symbiotic relationshipsrelationships with other organisms with other organisms::

InIn parasitismparasitism, harm is caused to the host., harm is caused to the host.

In In commensalismcommensalism, one organism benefits , one organism benefits while the other is unaffected.while the other is unaffected.

In In mutualismmutualism, both organisms benefit. , both organisms benefit.

According the rAccording the respirationespiration::

In In obligate aerobesobligate aerobes, the prokaryotes must , the prokaryotes must have oxygen to live. have oxygen to live.

In In obligate anaerobesobligate anaerobes, the organisms cannot , the organisms cannot survive in the presence of oxygen. survive in the presence of oxygen.

And in And in facultative anaerobesfacultative anaerobes they can they can survive with or without oxygen. survive with or without oxygen.

According theAccording the shapes shapes:: coccicocci (spherical), (spherical),

bacillusbacillus (rod shaped), and (rod shaped), and

spirillumspirillum (spirals). (spirals).

Classification of bacteriaClassification of bacteria

• CocciCocci Micrococcus Micrococcus StaphylococciStaphylococci

• Irregular clusters of cocciIrregular clusters of cocci DiplococciDiplococci

• Pairs of cocciPairs of cocci StreptococciStreptococci

• Chains of cocciChains of cocci

Classification of bacteriaClassification of bacteria

BacilliBacilli Rod likeRod like DiplobacilliDiplobacilli

• Pairs of bacilliPairs of bacilli StreptobacilliStreptobacilli

• Chains of bacilliChains of bacilli

SpirochetesSpirochetes• Spiral Spiral

SSizeize of bacteriaof bacteria

Unit of microbial Unit of microbial measurementmeasurement

  micrometers (um)micrometers (um)• 1 um being 10-6  m   or 1 um being 10-6  m   or

0.000001 m(1/25,000 0.000001 m(1/25,000 inch)inch)

nanometers  nanometers  • 1 nm being 10-9 or 1 nm being 10-9 or

0.000000001 m. 0.000000001 m.

   Pathogenic bacterial Pathogenic bacterial

species vary from species vary from approximately approximately 0.4 to 2 0.4 to 2 um in sizeum in size

TaxonomyTaxonomy TaxonomyTaxonomy is the classification of organisms. The is the classification of organisms. The

most common system in use today is the most common system in use today is the Five Five KingdomsKingdoms::

MoneraMonera ( (ProkaryotaProkaryota)), , ProtistaProtista, , FungiFungi, , PlantaePlantae, and , and AnimaliaAnimalia..

Organisms in eachOrganisms in each kingdomkingdom are divided into phyla. are divided into phyla. In each In each phylumphylum,, organisms are separated into classes. organisms are separated into classes. In each In each classclass,, organisms are segregated into orders. organisms are segregated into orders. In each In each orderorder, organisms are divided into families. , organisms are divided into families. In each In each familyfamily, organisms are separated by genus. , organisms are separated by genus. And finally, in each And finally, in each genusgenus organisms are divided into organisms are divided into speciesspecies. .

Just remember that Just remember that KKing ing PPhilip hilip CCan an OOrrder der FFor or GGeenialnial SStudents. tudents.

Naming micoorganismsNaming micoorganisms

Binomial (scientific) nomenclature Binomial (scientific) nomenclature

Gives each microbe 2 namesGives each microbe 2 names GenusGenus - noun, always capitalized and may be - noun, always capitalized and may be

abbreviated abbreviated speciesspecies - adjective, lowercase, never abbreviated - adjective, lowercase, never abbreviated A genus name may be used alone to indicate a genus A genus name may be used alone to indicate a genus

group; a species name is never used alonegroup; a species name is never used alone• eg: eg: Bacillus subtilisBacillus subtilis

            B. subtilisB. subtilis

Both italicized or underlinedBoth italicized or underlined Staphylococcus aureus (S. aureus)Staphylococcus aureus (S. aureus) Bacillus subtilisBacillus subtilis (B. subtilis)(B. subtilis) Escherichia coliEscherichia coli (E. coli)(E. coli)

NomenclatureNomenclature

Common or descriptive names Common or descriptive names (trivial names)(trivial names) Names for organisms that may be in Names for organisms that may be in

common usage, but are not taxonomic common usage, but are not taxonomic namesnames

• eg: tubercle bacillus eg: tubercle bacillus         (        (Mycobacterium tuberculosisMycobacterium tuberculosis))

• meningococcus meningococcus ((Neiserria meningitidisNeiserria meningitidis))

• Group A streptococcus Group A streptococcus ((Streptococcus Streptococcus pyogenespyogenes))

EukaryotesEukaryotes

ProkaryotesProkaryotes

KingdomKingdom - - MoneraMonera Domain Domain - Bacteria - Bacteria PhylumPhylum – Proteobacteria – Proteobacteria ClassClass – Gammaproteoba– Gammaproteoba OrderOrder – Enterobacteriale– Enterobacteriale FamilyFamily – Enterobacteriace– Enterobacteriace GenusGenus – Escherichia– Escherichia SpeciesSpecies – – Escherichia coliEscherichia coli

Louis PasteurLouis Pasteur

"The role of the "The role of the infinitely small in infinitely small in nature is infinitely nature is infinitely

large"large"

Historical PerspectivesHistorical Perspectives

HistoricalHistoricalYEARYEAR NAMENAME ACHIEVEMENTACHIEVEMENT11stst century BC century BC VaroVaro Concept of “Animalia Concept of “Animalia

minuta”minuta”

15461546 FracostoriusFracostorius Contagion- Cause of Contagion- Cause of syphilissyphilis

15901590 JensenJensen Hand lensHand lens

16831683 Antony van Antony van LeeuwenhoekLeeuwenhoek

First MicroscopeFirst Microscope

““Animalcules”Animalcules”

16781678 Robert HookRobert Hook Compound microscopeCompound microscope

17451745 Needham (Priest)Needham (Priest) AbiogenesisAbiogenesis

18361836 Schulze & SchwanSchulze & Schwan Air contains microbesAir contains microbes

18401840 Oliver Homes, Poet Oliver Homes, Poet physicianphysician

Contageousness & Contageousness & Puerperal feverPuerperal fever

18461846 Ignaz SemmelweisIgnaz Semmelweis Cause, concept & Cause, concept & prophylaxis of child-bed prophylaxis of child-bed feverfever

18531853 Augustino BassiAugustino Bassi Silk worm disease due to Silk worm disease due to a fungusa fungus

Pioneers of MicrobiologyPioneers of Microbiology

Robert HookeRobert Hooke, UK (1665), UK (1665) Proposed the Cell TheoryProposed the Cell Theory Observed cork with crude microscopeObserved cork with crude microscope All living things are composed of cellsAll living things are composed of cells

Spontaneous generationSpontaneous generation Some forms of life could arise spontaneously from Some forms of life could arise spontaneously from

non-living matternon-living matter

Francesco Redi,Francesco Redi, IT (1668) IT (1668) Redi’s experiments first to dispprove S.G.Redi’s experiments first to dispprove S.G.

Antonie van LeeuwenhoekAntonie van Leeuwenhoek

First to observe living First to observe living microbesmicrobes

his single-lens his single-lens magnified up to 300Xmagnified up to 300X

(1632-1723)

Louis PasteurLouis Pasteur French chemistFrench chemist Father/Founder of Modern Father/Founder of Modern

MicrobiologyMicrobiology Fermentation – a Fermentation – a

microbiological processmicrobiological process Beer/Wine not produced Beer/Wine not produced

without microbeswithout microbes Showed microbes caused Showed microbes caused

fermentation & spoilagefermentation & spoilage Disproved spontaneous Disproved spontaneous

generation of m.o.generation of m.o. Developed aseptic techniques.Developed aseptic techniques. Developed a rabies vaccine.Developed a rabies vaccine.

(1822-1895)

Louis Pasteur 1822-95Louis Pasteur 1822-95

Methods & Techniques of cultivationMethods & Techniques of cultivation Introduced sterilizationIntroduced sterilization Tyndalization (Tyndal-1877)Tyndalization (Tyndal-1877) Studied Silkworm disease, anthrax, Studied Silkworm disease, anthrax,

chicken cholera, hydrophobia.chicken cholera, hydrophobia. Introduced live vaccines – Jenner (Cow-Introduced live vaccines – Jenner (Cow-

pox vaccine)pox vaccine) Antirabic vaccineAntirabic vaccine Pasteur InstitutesPasteur Institutes

Joseph Lister 1867Joseph Lister 1867

Prof of Surgery, Prof of Surgery, Glasgow Royal Glasgow Royal InfirmatoryInfirmatory

Introduced Antiseptic Introduced Antiseptic SurgerySurgery

Called Father of Called Father of Antiseptic SurgeryAntiseptic Surgery

Robert KochRobert Koch German general practitionerGerman general practitioner Perfected bacteriological Perfected bacteriological

techniquestechniques Isolated pure cultures of Isolated pure cultures of

bacteria for the first timebacteria for the first time Discovered Anthrax bacilli, Discovered Anthrax bacilli,

Cholera vibrio, M. tuberculosisCholera vibrio, M. tuberculosis Father of Medical MicrobiologyFather of Medical Microbiology HypersensitivityHypersensitivity Established a sequence of Established a sequence of

experimental steps to show experimental steps to show that a specific m.o. causes a that a specific m.o. causes a particular disease.particular disease.

(1843-1910)

Koch’s postulates

The organism must be present in every case of the infectious disease.It should be possible to isolate the organism in pure culture from the lesion.Inoculation of the pure culture into suitable lab animal should produce a similar disease.It should be possible to re-isolate the organism in pure form from the lesions produced in the experimental animal.Specific antibodies to the organism should be demonstrable in patients suffering from the disease.

Highlights in the History Highlights in the History of Microbiologyof Microbiology

18871887 Invented Petri Dish Invented Petri Dish

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

(Dmitri Iosifovich (Dmitri Iosifovich Ivanovski)Ivanovski)

18991899 Recognized viral Recognized viral

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

19001900 Proved mosquitoes Proved mosquitoes

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

19101910 Discovered cure for Discovered cure for

syphilis (Paul Ehrlich)syphilis (Paul Ehrlich)

19281928 Discovered Penicillin Discovered Penicillin

(Alexander Fleming)(Alexander Fleming)

Highlights in the History Highlights in the History of Microbiologyof Microbiology

19771977Developed a method Developed a method to sequence DNA to sequence DNA (W. Gilbert & F. (W. Gilbert & F. Sanger)Sanger)

19831983Polymerase Chain Polymerase Chain Reaction invented Reaction invented (Kary Mullis)(Kary Mullis)

19951995First microbial First microbial genomic sequence genomic sequence published (published (H. H. influenzaeinfluenzae) (TIGR)) (TIGR)