Introduction to Microbiology

Introduction to Microbiology

Bio3124

Lecture 1

A Historical Perspective

Objectives and readingObjectives and reading

• Reading: Ch.1

• What is microbiology?

• History: How it came to be a field of study?

• Modern microbiology: day to day impact on society

The Scope and Relevance of MicrobiologyThe Scope and Relevance of Microbiology

• importance of microorganisms– first living organisms on the planet

• How many bugs are out there?

– live everywhere life is possible– more numerous than any other kind of

organisms– global ecosystem depends on their activities

(possess 50% of earth’s carbon and 90% of nitrogen)

– influence human society in many ways

Microbes and Microbiology?Microbes and Microbiology?

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• Microbes are living organisms– Except for viruses, which are noncellular– Metabolize energy, grow, reproduce• Visualized by a microscope• Unicellular , potentially exist independently• simple in their construction; lack differentiated

cells and distinct tissues• Microbiology: study of organisms too small to

be seen by the unaided eye (i.e., microorganisms)

• How small?

• ~10 nm to 100 μm

• different type of optical system needed to resolve

• Where the bugs stand in the universe? Click here

•Naked eye

Size of Microorganisms

Thiomargarita namibiensis(Pearl of Namibia)

Exceptions to the size rule

• Sulfur Pearl of Namibia was dicovered by Heide Schultz chemolitothrophic G- bacterium

• 1000X larger than bacteria (0.5-1 mm)

Exceptions to the size rule

• Mimivirus: DNA virus

• 1.2 Mbp genome, ds linear

• 400-800 nm in diameter

• Infects amoeba

• Unique genes

• Primitive life form?

MimivirusClick to read more

The Microbial TreeThe Microbial Tree

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• Difficult to classify– Difficult to distinguish by shape– Often reproduce asexually– Pass DNA to each other horizontally

• Use biochemical properties to classify– Gram stain (G- and G+)– Ability to metabolize different substrates (Bergey’s manual determinative

bacteriology)• Use DNA sequence to classify

– Microbial genomes are sequenced (click to link to database)– Bacterial genomes are relatively small– Genome = organism’s total genetic content

• Complete gene sequence known for many species– Over 3000 bacteria, over >100 archaea– thousands of viruses

• Microbes have greatest diversity of genomes– Important for understanding evolution

The Microbial Family TreeThe Microbial Family Tree

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Carl WoeseCarl Woese 16s rRNA gene conserved Divergence reflects

relatedness Phylogenetic tree Microbial world in 3 domains Prokaryotes include 2 domains

Domain of Eubacteria Domain of Archaea

Eukaryotic domain Algea Fungi Protista

MicrobesMicrobes

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• 6 major groups studied by microbiologists• Cellular forms:

– Prokaryotes• Bacteria

– Eukaryotes• Algae

• Acellular:– Viruses

• Archaea

Protists Fungi

History of Microbiology

Old times…Old times…• Humans knew how to deal with germs before even

knowing about their existence۩ Storing food in cooler temperatures۩ Salting, drying, smoking۩ Use of spices۩ Cremation of dead۩ concealing and burying dead beyond a nearest

passing river or in a distant area۩ traditional, mystical and superstitious explanations

Discovery of MicroorganismsDiscovery of MicroorganismsDiscovery of MicroorganismsDiscovery of Microorganisms

Antony van Leeuwenhoek (1632-1723), the father of microbiology

– a hobbyist microscopist Dutchman

– first to observe and describe microorganisms accurately

Leeuwenhoek’s microscopeLeeuwenhoek’s microscope

─ Composed of one lens─ Light shines objects at a

45˚ angle─ Worked like a dark field

microscope─ Magnification: 50-300

fold─ bright microorganisms

could be seen in a dark bkg

PMN

RBC

Original blood smear image by LeeuwenhoekNote the polymorphonuclear cell and RBC Spirillum as seen by Leeuwenhoek’s microscopeTripartite structure of a human sperm

Leeuwenhoek’s ObservationsLeeuwenhoek’s Observations

Reported to the Royal Society of London (1673)

Accurate shape, detailed movement

Subjects were most possibly bacteria and protozoa and called them “animalcules“

also reported spermatozoa, blood cells

Check out a paper by Brian J. Ford about Leeuwenhoek

Where do microorganism originate from? Where do microorganism originate from?

Spontaneous generation??Spontaneous generation??

Few days of beingexposed to air.

The Conflict over Spontaneous GenerationThe Conflict over Spontaneous GenerationThe Conflict over Spontaneous GenerationThe Conflict over Spontaneous Generation

• spontaneous generation

– living organisms can develop from nonliving or

decomposing matter

– publically a common sense vision with social and cultural

roots (almost 2000 years ago)

– Examples:

• flies from rotten meat and animal carcasses

• Mice from fungus infested grain barns

– Scientific methodology was not established

– What was the proof?

Jan Baptista Van Helmont (1577-1644)

Jan Baptista Van Helmont (1577-1644)

• A Flemish noble man, alchemist and

physician

• discovered carbon dioxide, introduced

the term gas in its present scientific

sense

• believed in spontaneous generation

• Paper by Louis Rosenfeld about Van Helmont

Jan Baptista Van HelmontThe Origin of life

(17th Centuray)

Jan Baptista Van HelmontThe Origin of life

(17th Centuray)

Adult mice

1579-1644

Spontaneous Generation Spontaneous Generation

Could spontaneous Could spontaneous generation be true for generation be true for

microorganisms?microorganisms?

Could spontaneous Could spontaneous generation be true for generation be true for

microorganisms?microorganisms?

Francesco Redi(1626-1697)

Francesco Redi(1626-1697)

• First blow to spontaneous generation• Laying eggs is required for maggots and flies to come to

existence • Supporters of SG: Life is necessary in order to bring about life

in certain cases!

John Needham (1713-1781)

John Needham (1713-1781)

• Conclusion: Organic matter had vital force that confers properties of life to non-living matter

• BUT: he had left the flasks unsealed after bioling

Lazzaro Spallanzani (1729-1799)

Lazzaro Spallanzani (1729-1799)

• Air carries germs to broth and boiling kills the existing ones• Supporters of SG: • Compounds essential for generation of life were destroyed

by heating!!• sealing prevents air that is necessary for spontaneous

generation

MicroorganismsKilled

Time

MicroorganismsKilled

Time

Louis Pasteur (1822-1895)

Louis Pasteur (1822-1895)

Observations:Observations:

• John Tyndall: Organisms retained on cotton filters resemble microorganisms in contaminated foods

– Microorganisms are found in the air

– Microorganism in air settle on the surfaces

Pateur’s Swan neck flasks could supply air but could also trap ambient germs from entering broth

Pasteur Refutes the Spontaneous Generation Pasteur Refutes the Spontaneous Generation

Pasteur Refutes the Spontaneous Generation Pasteur Refutes the Spontaneous Generation

• ambient germs are necessary for promoting growth• principle of sterility and aseptic work is important

Germ theory: Microorganisms Cause DiseaseGerm theory: Microorganisms Cause Disease

• For over 17 centuries the Galenism (Greek

physician 129-199 B.C.) was predominant

view for diseases according to which,

– Diseases are due to imbalances in 4

humors: blood, phlegm, yellow bile and

black bile

Relationship between Microorganisms and DiseaseRelationship between Microorganisms and DiseaseRelationship between Microorganisms and DiseaseRelationship between Microorganisms and Disease

• Agostino Bassi (1773-1856)– showed that a disease of silkworms was caused by a

fungus

• M. J. Berkeley (~1845-1852)– demonstrated that the great Potato Blight of Ireland

was caused by a water mold

• Louis Pasteur (1822-1895)– showed that the pébrine disease of silkworms was

caused by a protozoan Nosema bombycis

Other evidence…Other evidence…

• Joseph Lister (1827-1912)– provided indirect evidence

– used diluted carbolic acid (phenol) to wash surgical devices and wash wounds

– developed the principles of aseptic surgery

– his patients had fewer postoperative infections

– Disease frequency dropped in his hospital

Final proof…Final proof…

• Robert Koch (1843-1910)

– established the relationship

between Bacillus anthracis and

anthrax

– used criteria developed by his

mentor Jacob Henle (1809-1895)

– these criteria now known as

Koch’s postulates

Read more about R. Koch. Check literature section

Microorganisms and Diseases Robert Koch 

Microorganisms and Diseases Robert Koch 

ObservationsObservations  ::• The microorganism (Bacillus anthracisBacillus anthracis) is

found only in the infected animals and not in healthy animals.

• Infected animals pass the disease to healthy ones

• The microorganism found outside of the animal could infect healthy animals

Germ theory: Koch’s postulatesGerm theory: Koch’s postulates

Questions:Questions:1.Can Koch’s Postulates be applied to all

microorganisms that cause disease?

2.How can you apply Koch’s postulates to viruses and viral diseases?

3.How can one apply Koch’s postulates to non-cultivable microorganisms?

The Development of Techniques for Studying Microbial Pathogens

The Development of Techniques for Studying Microbial Pathogens

• Koch’s work led to discovery or development of:– agar– Petri dish– nutrient broth and nutrient agar– methods for isolating microorganisms in pure

culture

The Pure Cultures and Isolation of Single ColoniesThe Pure Cultures and Isolation of Single ColoniesThe Pure Cultures and Isolation of Single ColoniesThe Pure Cultures and Isolation of Single Colonies

KochKoch  ::

Observation: Slices of potato when

exposed to air, will generate large

number of bacteria (colonies) of

different sizes, colours and forms

ColoniesColonies

Problem: Not all bacteria could grow on potatoes!Problem: Not all bacteria could grow on potatoes!

Solution :Solution : Koch used gelatin as a means for solidification of rich culture media.

He formulated various culture media

Disadvantages of GelatinDisadvantages of Gelatin

• Gelatin liquefaction: It is digested by various microorganisms eg. gelatinase positive enterococci and streptomyces

• Low melting temperature: It is in the liquid state above the temperature of 28oC.

AgarAgar

• Polysaccharide derived from the cell walls of a red algae (Rhodophyta)

• A polysaccharide polymer that contains 3,6-anhydrogalactose, 2-O-methyl-α-l-galactopyranose and 6-O-methyl agarobiose

• Solid at >37oC.• Melts at 100oC.• Not digested by most bacteria

Gracilaria (red seaweeds)

Corollary to Germ TheoryCorollary to Germ Theory

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• Stop germ transmission, stop disease spread– Kill germ, prevent disease

• Antiseptics– 1865: Aseptic surgery

» Joseph Lister

• Antibiotics– 1929–1941: Penicillin

» Alexander Fleming– Many newer antibiotics– Bacteria become resistant

Corollary to Germ TheoryCorollary to Germ Theory

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• Stop germ transmission, stop disease spread– Stop spread of germs

• Epidemiology, public health measures

– Resistant individuals prevent spread of germs• 1798: Vaccination with cowpox prevents smallpox

– Turkish physicians, Lady Montagu, Edward Jenner

Other developments…Other developments…

• Pasteur and Roux– discovered that incubation of cultures for

long intervals between transfers caused pathogens to lose their ability to cause disease (attenuation)

• Pasteur and his coworkers– developed vaccines for chicken cholera,

anthrax, and rabies

Modern microbiology: day to day impact on society

Modern microbiology: day to day impact on society

Microbes Shape Human HistoryMicrobes Shape Human History

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• Food & Pharmaceuticals• Bread, wine, cheese, Chocolate

– Can also destroy crops• Hormones, antibiotics etc

• Microbial diseases change history– 14th century: Bubonic plague (Black death)

caused by Yersinia pestis in Europe– 19th century: Tuberculosis caused by

Mycobacterium tuberculosis – today: AIDS by the human

immunodeficiency virus (HIV)

The golden age of microbiology (1857-1914)The golden age of microbiology (1857-1914)

• Many pathogens discovered

• Microbial metabolism studies undertaken

• Microbiological techniques refined

• A better understanding of the role of immunity

and ways to control and prevent infection by

microbes

Genetics and DNA RevolutionGenetics and DNA Revolution

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• Molecular genetics depends on bacteria– Concept of “gene” proposed for bacteria– DNA structure– Genetic code– Transcription, translation– Restriction enzymes– Recombinant DNA– Cloning– PCR reaction (watch the interview with Kery Mullis)– E. coli has best understood genome

The Future of MicrobiologyThe Future of Microbiology

Challenges and opportunities for future microbiologists

• infectious disease

• new and improved industrial processes

• microbial diversity and microbial ecology

– less than 1% of earth’s microbial population has been

cultured

More challenges and opportunities…More challenges and opportunities…

• biofilms

• genome analysis

• microbes as model systems

• assessment of implications of new discoveries and technologies

• Stephen Jay Gould (1941-2002): “This is truly the "age of bacteria" - as it was in the beginning, is now and ever shall be.”