What is Microbiology?

Micro - too small to be seen with the naked eye Bio - life ology - study of

What is Microbiology?

Microbiology is the Science that studies Microorganisms. Microorganisms, roughly, are those living things that are too small to be seen with the naked eye. Microorganisms cannot be distinguished Phylogenetically from Macroorganisms For example, many fungi are microorganisms, as well as all bacteria, all viruses, and most protists. Microbiology is more a collection of techniques: Aseptic technique Pure culture technique Microscopic observation of whole organisms A microbiologist usually first isolates a specific microorganism from a population and then cultures it.

Microbiology b. >3 billion BC

It is generally believed that microorganisms have existed on earth for several billion years, and over time, plants and animals have evolved from microorganisms.

Above is a fossil cyanobacterium that is 950 million years old. Microorganisms are very diverse in all their aspects: appearance, metabolism, physiology, and genetics. They are far more diverse [in these terms] than plants and animals.

Brief History Microbiology

Anton van Leeuwenhoek (1670s) = microscopy Edward Jenner (1796) = vaccination against smallpox Ignaz Semmelweis (1840s) = hand washing before surgery Louis Pasteur (1860s) = repudiation spontaneous generation Joseph Lister (1860) = father aseptic surgery Robert Koch (1870s) = Kochs postulates Dmitri Iwanowski (1990s) = Inference of viruses Alexander Fleming (1920s) = Penicillin Stephen T. Abedon (2000s) = not one heck of a lot.

History of the Study of Microorganisms

1665 Robert Hooke

little boxes

- cells Cell Theory - all living things are made up of cells

Hookes Microscope

Anton van Leeuwenhoek 1674

- 1st person to actually see living microorganisms

wee animalcules

Leeuwenhoeks Microscope

RBCs

Spontaneous Generation

Theory that life just spontaneously developed from non-living matter Example:
toads, snakes and mice - moist soil flies and maggots - manure and decaying

flesh

Origin of Microbes: Spontaneous Generation Myths

Snakes from horse hairs in stagnant water

Mice from grain and cheese wrapped in a sweater

Maggots from rotting meat Fleas from hair

Flies from fresh and rotting fruit

Mosquitoes from stagnant pondwater Eels from slimy mud at the bottom of the ocean

Locusts from green leaves

Raccoons from hollow tree trunks Termites are generated from rotting wood

Experiments to disprove Spontaneous Generation

Francesco Redi Rudolph Virchow

1668 1858

Theory of Biogenesis Cells can only arise from preexisting cells

Louis Pasteur

1861

Origin of Microbes: Redis Experiment

Pastuer (1861) Refuted Spontaneous Generation

Pasteur filtered air through cotton plug showing that filterable particles cause contamination of sterile broths. Swan-necked flask experiments

Pasteur designed special swan-necked flasks with a boiled meat infusion

Shape of flask allowed air in (vital force) but trapped dust particles which may contain microbes

Origin of Microbes: Pasteurs SwanNecked Flasks

Origin of Microbes: Pasteurs SwanNecked Flasks

Remains sterile.

Contamination of culture

Heat to sterilize (doesnt always work).

Bacteria, fungal spores, and dust adhere to glass.

Broth turbidity indicates bacterial growth.

Germ Theory of Disease

Hard for people to believe that diseases were caused by tiny invisible wee animalcules Diseases, they thought, were caused by:

demons
witchcraft bad luck the wrath of God curses evil spirits

Robert Koch - 1st to prove that

bacteria actually caused diseases
1876 Microbial Etiology of Infectious Disease

etiology - the cause of a disease

Established scientific rules to show a cause and effect relationship between a microbe and a disease
Kochs Postulates

Kochs Postulates
1. The same organisms must be found in all cases of a given disease. 2. The organism must be isolated and grown in pure culture. 3. The isolated organism must reproduce the same disease when inoculated into a healthy susceptible animal. 4. The original organism must again be isolated from the experimentally infected animal.

Exceptions to Kochs Postulates

1. Some organisms have never been grown in pure culture on artificial media Treponema pallidum - Syphilis

Exceptions to Kochs Postulates

Mycobacterium leprae
Leprosy

Never been grown in pure culture on artificial media

Exceptions to Kochs Postulates

In exclusively human diseases, it is not morally acceptable to inoculate a deadly pathogen into a human guinea pig

HIV

Koch established the Microbial Etiology of 3 important diseases of his day

1. Cholera (fecal-oral disease)

Vibrio cholerae

2. Tuberculosis (pulmonary infection)

Mycobacterium tuberculosis

3. Anthrax (sheep and cattle)

Bacillus anthracis

Anthrax

Bacillus anthracis
Gram (+), non-motile, aerobic, spore forming rod Streptobacilli with central spores Livestock
Sheep, cattle, goats

Humans
Handle hides, wool, goat hair, handicrafts from the Middle

East made from animal products

3 Forms of Human Anthrax

1. Cutaneous Anthrax
Enters thru cut or

abrasion Results in painless ulcer (1-3 cm) with black (necrotic) center About 20% mortality rate in untreated cases

2. Gastrointestinal Anthrax
Contaminated meat

Abdominal pain, fever,

vomiting blood, severe diarrhea 25% to 60% mortality rate

3. Inhalation Anthrax
Initial symptoms

resemble common cold Progress to severe breathing problems and shock Usually results in death 1-2 days after onset of acute symptoms Mortality rate 99% in untreated cases Treatment usually not effective after symptoms are present

Anthrax as a Biological Weapon

Deadly if not treated early Spores can be produced in large quantities using basic knowledge of biology Spores may remain viable for years (60 at least) Spores can be spread
Missiles, rockets, bombs, mail, crop dusters ?

No cloud or color No smell No taste Antibiotics only effective if administered early (within 24 48 hours)

Golden Age of Microbiology

1914 Pasteur Pasteurization Fermentation

1857 -

Joseph Lister
Phenol to treat surgical wounds 1st attempt to control

infections caused by microoganisms First one to use antiseptics

Robert Koch
Kochs Postulates

Edward Jenner
Small pox vaccination

Paul Erlich
1st synthetic drug used to treat infections Salvarsan - arsenic-based chemical to treat Syphilis salvation from Syphilis

Edward Jenner Smallpox Vaccine (1796)

Organisms included in the study of Microbiology

1. Bacteria 2. Protozoans 3. Algae 4. Parasites 5. Yeasts and Molds

Fungi

Bacteriology Protozoology Phycology Parasitology Mycology Virology

6. Viruses

Microorganisms - Microbes - Germs

Types of Microorganisms

Bacteria a.k.a., eubacteria (true bacteria) a.k.a., domain Bacteria Archaeabacteria a.k.a., domain Archaea Single-celled members of domain Eukarya. Protozoa Microscopic Algae Microscopic Fungi Viruses and other Agents

Relationship of Microbes

Comparing Domains

Scale of Microbes

Scale of Microbes

5 Kingdoms of Living Organisms

1. Animalia 2. Plantae 3. Fungi 4. Protista 5. Monera - Bacteria and Cyanobacteria

Eukaryotic vs. Prokaryotic

 Prokaryotes

lack a true nucleus and other membrane-bound structure in cells such as the ER and mitochondrion. Eukaryotes have a true nucleus, with chromosomes and a double membrane, and membranebound, cellular structures.

Table 1.1 The differences between prokaryotes and eukaryotes.

Prokaryotes 1. Size- Less than 5 micron micron 2. Nucleus- Primitive type Nuclear membrane- Absent Nucleolus- Absent Dioxyribonucleoprotein- Absent Chromosome- single(circular) Mitotic division- Absent 3. Cytoplasm Mitochondria-Absent Golgi bodies- Absent Endoplasmic reticulum-Absent Ribosome- 70 S Lysosome- Absent

Eukaryotes Greater than 5

Well developed Present Present Present One or more (linear) Present

Present Present Present 80 S Present

4.Chemical Composition Sterols in plasma membrane-Absent Cell wall complex, peptidoglycan -Present Muramic acid- Present 5. Other Respiration is part of plasma, membrane (mesosomes) 6. E.g., Bacteria, blue green algae protzoa

Present Simplepeptidoglycan -Absent Absent

Mitochondria

Algae, fungi,

Types: Bacteria
Description: eubacteria, archaeabacteria, Gram-negative, Grampositive, acid fast, cyanobacteria Types: prokaryotes, absorbers, wet conditions, animal decomposers, cell walls, unicellular Nutrient Type: chemoheterotrophs, photoheterotrophs, chemoautotrophs, photoautotrophs

Types: Bacteria

Durable state: endospores (some) Diseases: tetanus, botulism, gonorrhea, chlamydia, tuberculosis, etc., etc., etc.

Rod-Shaped Bacteria

Spherical Bacteria

Spiral-Shaped Bacteria
Spirochete: Borrelia burgdorferi

Naming of Bacteria

Genus and species - Binomial System of Taxonomic Classification Information usually given:
1. Describes an organism 2. Identifies a habitat 3. Honors a scientist or researcher

Binomial Nomenclature (1/3)

Examples: Escherichia coli, E. coli, Escherichia spp., and the genus Escherichia The genus name (Escherichia) is always capitalized The species name (coli) is never capitalized The species name is never used without the genus name (e.g., coli standing alone, by itself, is a mistake!)

Binomial Nomenclature (1/3)

The genus name may be used without the species name (e.g., Escherichia may stand alone, though when doing so it no longer actually describes a species) When both genus and species names are present, the genus name always comes first (e.g., Escherichia coli, not coli Escherichia)

Binomial Nomenclature (2/3)

Both the genus and species names are always italicized (or underlined)always underline if writing binomials by hand The first time a binomial is used in a work, it must be spelled out in its entirety (e.g., E. coli standing alone in a manuscript is not acceptable unless you have already written Escherichia coli in the manuscript)

Binomial Nomenclature (2/3)

The next time a biniomial is used it may be abbreviated (e.g., E. for Escherichia) though this is done typically only when used in combination with the species name (e.g., E. coli) The species name (e.g., coli) is never abbreviated

Binomial Nomenclature (3/3)

It is a good idea to abbreviate unambiguously if there is any potential for confusion (e.g., Enterococcus vs. Escherichia) These rules are to be followed when employing binomial nomenclature even in your speech. It is proper to refer to Escherichia coli as E. coli or even as Escherichia, but it is not proper to call it coli or E.C.!

Types: Cyanobacteria
Description: also called blue-green algae, cyanobacteria are a kind of bacteria (more specifically, a kind of eubacteria) Types: photosynthetic aquatic procaryotes, green lake scum, cell walls Nutrient Type: photoautotrophs

Durable state: ? Diseases: none

Types: Algae
Description: photosynthetic aquatic eukaryotes, cell walls, both unicellular and multicellular types Types: brown, red, green, diatoms, dinoflagellates, euglenoids Nutrient Type: photoautotrophs Durable state:?

Diseases: Some poisonings associated with unicellular types: Alexandrium

causes Paralytic Shellfish Poisoning (PSP), Dinophysis causes Diarrhetic Shellfish Poisoning (DSP), Pseudonitzschia multiseries causes Amnesic Shellfish Poisoning (ASP) [some would describe some as protists]

Types: Fungi
Description: yeasts (unicellular fungi), molds (filamentous fungi) Types: eucaryotes, nutrient absorbers, dry conditions, plant decomposers, cell walls, ~100 human pathogens Nutrient Type: chemoheterotrophs

Durable state: spores (not endospores) Diseases: mycoses: candida, ringworm (pictured), athlete's foot, jock itch, etc.

Types: Helminths
Description: Flatworms (platyhelminths), roundworms (nematodes) Types: metazoan (multicellular animal) parasites, engulfers and absorbers Nutrient Type: chemoheterotrophs

Durable state:? Diseases: trichinosis, hook worm, tape worm (pictured are scolex-heads of), etc.

Types: Protozoa (Protists)

Description: Unicellular and slime molds, flagellates, ciliates

Types: eucaryotes, parasites (most not), engulfers and absorbers, wet conditions, no cell wall, ~30 human pathogens Nutrient Type: chemoheterotrophs (some classifications include some photoautotrophs as well) Durable state: cysts (some) Diseases: malaria, giardiasis, amoebic dysentery, etc. (shown are harmless--to us--protist components of pond water: Amoeba, Blepharisma, Paramecium, Peranema, & Stentor)

Types: Viruses
Description: Viruses are not cells but some viruses do have lipid envelopes Types: acellular, obligate intracellular parasites Nutrient Type: not applicable Durable state: virion particles, some can encase in durable state of host Diseases: common cold, flu, HIV, herpes, chicken pox, etc.

Other Agents

Bacteria - what comes to mind?

Diseases Infections Epidemics Food Spoilage Only 1% of all known bacteria cause human diseases About 4% of all known bacteria cause plant diseases 95% of known bacteria are non-pathogens

Microbes Benefit Humans

1.Bacteria are primary decomposers recycle nutrients back into the environment (sewage treatment plants) 2. Microbes produce various food products

cheese, pickles, sauerkraut, green olives yogurt, soy sauce, vinegar, bread

Beer, Wine, Alcohol

3. Microbes are used to produce Antibiotics

Penicillin
Mold
Penicillium notatum

1928 Alexander Fleming

4. Bacteria synthesize chemicals that our body needs, but cannot synthesize

Example: E. coli
B vitamins - for metabolism
Vitamin K - blood clotting

Escherichia coli
Dr. Escherich Colon (intestine)

5. Biochemistry and Metabolism

Very simple structure rapid rate of reproduction provides instant data

6. Microbial Antagonism

Our normal microbial flora prevents potential pathogens from gaining access to our body

7. Insect Pest Control

Using bacteria to control the growth of insects Bacillus thuringiensis

caterpillars bollworms corn borers

8. Bioremediation
Using microbes to clean up pollutants and toxic wastes Exxon Valdez - 1989

2 Genera
Pseudomonas sp. Bacillus sp.

9. Recombinant DNA Technology Gene Therapy Genetic Engineering

Bacteria can be manipulated to produce enzymes and proteins they normally would not produce
Insulin

Human Growth Hormone

Interferon

10. Microbes form the basis of the food chain

Marine and fresh water microorganisms

Microbes do benefit us, but they are also capable of causing many diseases

Pneumonia Whooping Cough Botulism Typhoid Fever Measles Cholera Scarlet Fever Mumps Syphilis Gonorrhea Herpes 1 Chlamydia Tuberculosis Herpes 2 Meningitis Tetanus RMSV Strep Throat Lyme Disease AIDS Black Plague Diarrhea Gangrene

Microbes & Ecology

Microbes are producesthey provide energy to ecosystems, especially aquatic ecosystems Microbes are fixersthey make nutrients available from inorganic sources, e.g., nitrogen Microbes are decomposersthey free up nutrients from no longer living sources Microbes form symbioses (such as mycorrhizal fungi associated with plant rootsthough somewhat macroscopic, the bacteria found in legume root nodules, etc.) Microbes serve as emdosymbionts (e.g., chloroplasts and mitochondria)

Mycorrhizal Fungi

Microbes & Industry

Industry:

Fermentation products (ethanol, acetone, etc.)

Food:

Wine, cheese, yogurt, bread, halfsour pickles, etc.

Recombinant products (e.g., human insulin, vaccines) Bioremediation

Biotech:

Environment:

Each carton of Bugs+Plus provides easy to follow step-by-step instructions, containers of specially-formulated wet and dry nutrients and a container of microbes cultured for their ability to digest oil and other petroleum derivatives.

Microbes & Disease

Microbes both cause and prevent diseases Microbes produce antibiotics used to treat diseases

The single most important achievement of modern medicine is the ability to treat or prevent microbial disease
Most of this course will consider the physiology of microbes and their role in disease

The Germ Theory of Disease = Microbes cause disease!

(yes, it wasnt so long ago that humans didnt know this) Nevertheless, most microorganisms, including most bacteria, do not cause diseases in any organism (including in humans)

Impact of Infectious Disease

Infectious diseases are diseases caused by microbes 200,000 deaths per year in U.S. from infectious diseases ~20 million died from influenza (a disease caused by a virus) in 1918

New infectious diseases still being discovered

Normal Flora
These are the ~harmless microorganisms found on your body. Every part of your body that normally comes in contact with outside world (deep lungs and stomach are exceptions).

Brueghel: The Triumph of Death (1560)