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Chapter 1—The Microbial World And You
I.
II.
III.
Microbes in Our Lives.
a. Microorganisms are organisms that are too small to be seen with the unaided eye.
b. “Germ” refers to a rapidly growing cell.
c. Pathogenic microbes cause disease.
d. Most microorganisms do not cause disease.
e. Infectious vs. inherited diseases.
i. [Name some infectious diseases, and the pathogens that cause them.]
Microorganisms:
a. Decompose organic waste.
i. In sewage treatment plants, nutrients in sewage are used by microorganisms, which grow
to huge numbers. They are then killed down before the water flows out of the sewage
treatment plant into a river. As a result, the water that is flushed from our house is
cleaned up before it reaches our rivers. Pathogenic microbes that might otherwise feed
on the nutrients and reproduce in large numbers are instead kept rare.
b. Are producers in the ecosystem via photosynthesis.
i. Phytoplankton are involved in the carbon and oxygen cycles, via oxygenic
photosynthesis. In this process, they use up carbon dioxide (helps control global
warming) and release oxygen.
c. Are involved in nitrogen fixation.
i. Anabaena species and Rhizobium species convert atmospheric nitrogen (N2) into usable
forms: nitrates, ammonia, etc. [Atmosphere ~ 78% N2].
d. Produce industrial chemicals such as ethyl alcohol and acetone.
e. Produce insecticides.
i. Bacillus thuringiensis (Bt) is a bacterium that produces a chemical that is toxic to
caterpillars but not to humans. We spray Bt toxin on plants to minimize damage by
caterpillar pests.
f. Produce fermented foods such as vinegar, cheese, and bread.
i. Yeast (unicellular fungi) ferment sugars, producing ethanol (the alcohol in wine, beer,
and other alcoholic beverages) and carbon dioxide (which forms bubbles in bread causing
it to rise, and bubbles in beer and champagne).
ii. Acetobacteria ferment ethanol to produce acetic acid (vinegars).
iii. Some bacteria metabolize various components of milk to make yogurts and cheeses.
1. Casein (milk protein) is hydrolyzed to produce milk solids and lactose (milk
sugar) which is fermented to produce the acids that give yogurt and cheese their
sour tastes.
iv. Coffee and cocoa fruits are fermented by a series of microbes to soften the husks and
make the beans harvestable.
g. Produce products used in manufacturing (e.g., cellulase) and medical treatments (e.g., insulin).
h. Many antibiotics are produced by or are themselves microorganisms.
i. Alexander Fleming, trying to grow bacteria, noticed that contamination by Penicillium (a
fungus) caused his bacteria to not grow. This led to the discovery of the first antibiotic,
penicillin.
ii. Streptomyces bacteria are common soil microorganisms. Many antibiotics, including
streptomycin, have been isolated from Streptomyces.
i. Only a few are pathogenic, or disease-causing.
Knowledge of microorganisms:
a. Allows humans to:
i. Prevent food spoilage.
ii. Prevent disease occurrence.
1. Vaccines, antibiotics…
IV.
V.
b. Led to aseptic techniques to prevent contamination in medical and microbiology labs.
Naming Microorganisms.
a. Linnaeus established the system of scientific nomenclature in 1735.
b. Each organism has two names: the genus name and the specific epithet.
c. Scientific names:
i. Are italicized or underlined. The genus is capitalized and the specific epithet is lower
case.
ii. Are “Latinized” and used worldwide.
iii. May be descriptive or honor a scientist.
iv. Staphylococcus aureus
1. Describes the clustered arrangement of the cells (staphylo-) and the golden color
of the colonies.
v. Escherichia coli
1. Honors the discoverer, Theodor Eshcerich, and describes the bacterium’s habitat,
the large intestine or colon.
vi. After the first use, scientific names may be abbreviated with the first letter of the genus
followed by the specific epithet:
1. Staphylococcus aureus and Escherichia coli are found in the human body. S.
aureus is found on skin and E. coli is found in the large intestine.
Classification of Microorganisms. Fig. 1.
a. Three Domains:
i. Domain Bacteria.
1. Prokaryotes.
2. Peptidoglycan in cell walls.
3. Binary fission.
4. For energy, use organic chemicals, inorganic chemicals, or photosynthesis.
5. Most are free-living decomposers or primary producers. Some are parasitic.
Some are pathogenic.
ii. Domain Archaea.
1. Prokaryotic. Lack peptidoglycan. Live in extreme environments and include:
a. Methanogens.
b. Extreme halophiles.
c. Extreme thermophiles.
iii. Domain Eukarya.
1. Kingdom Protista. Protists.
a. Some species of algae.
i. Some species are multicellular, others are single cell organisms.
ii. Cellulose makes up the cell walls.
iii. Photosynthetic, producing O2 and other organic compounds.
b. Protozoa (amoeba, paramecium, euglena).
i. Single cell organisms.
ii. Some absorb or ingest organic chemicals, some are photosynthetic.
iii. May be motile via pseudopods, cilia, or flagella.
c. Fungus-like protists.
2. Kingdom Fungi (unicellular yeasts, multicellular molds, mushrooms).
a. Fungi use organic chemicals for energy.
b. Chitin is found in the cell walls.
c. Molds and mushrooms are multicellular fungi, consisting of masses of
mycelia, which are composed of filaments called hyphae.
d. Yeasts are unicellular fungi that contain glucans/mannans (carbohydrates)
in their cell walls in addition to chitin.
3. Kingdom Plantae (Plants). Some algae, as well as all mosses, ferns, trees, and
flowering plants.
a. Cell walls are composed of cellulose.
4. Kingdom Animalia (Animals).
a. Helminths. Multicellular animals. Many are parasitic. Some life cycle
stages are microscopic.
i. Phylum Platyhelminthes (flatworms).
1. Class Trematoda (flukes).
2. Class Cestoidea (tapeworms).
ii. Phylum Nematoda (roundworms).
VI.
Viruses.
a. Acellular.
b. Consist of DNA or RNA core.
c. Core is surrounded by a protein coat.
d. Coat may be enclosed in a lipid envelope.
e. Viruses are replicated only when they are in a living host cell.
Three Domains of Cellular Organisms
Bacteria
Cell Type
Prokaryotic
Chromosome One. Circular. No histones or introns.
Ribosomes
Cell Wall
Metabolic
Types
70S
Contains peptidoglycan.
Chemoautotrophs, Chemoheterotrophs,
Photoautotrophs, Photoheterotrophs.
*See table below for definitions.
Archaea
Prokaryotic
One. Circular with
histones and introns.
70S
No peptidoglycan.
Chemoautotrophs,
Chemoheterotrophs,
Photoautotrophs.
Eukarya
Eukaryotic
One to many. Linear with
histones and introns.
80S
No peptidoglycan.
Chemoheterotrophs,
Photoautotrophs.
Definitions for Metabolic Strategies
Get energy from:
Chemoautotrophs
Inorganics such as metals, or reduced molecules like H2S, NH3, H2…
Chemoheterotrophs Organic molecules like glucose, lipids, proteins…
Photoautotrophs
Sunlight, and electrons (e-) taken from H2O that are energized in pigment molecules
(chlorophyll).
Photoheterotrophs
Sunlight, electrons (e-) taken from something other than H2O, like H2S, that are energized
in pigment molecules.
Comparison of Cellular and Acellular Microbes
Cellular (Pro- & Eu-karoytes) Viruses
Cell Type
Cells with plasma membrane, Acellular. Chromosome in
cytoplasm, chromosome(s),
protein sac. No plasma
enzymes. Complex.
membrane, no cytoplasm.
Chromosome Made of DNA.
Either DNA or RNA (but
not both).
Ribosomes
Site of protein synthesis.
None.
Metabolic
Produce ATP as the energetic No ATP production. Very
Types
molecule.
little metabolism.
Prions
Acellular. Single protein
molecules. No genetic material,
no plasma membrane.
None.
None.
No ATP production. Very little
metabolism.
VII.
A brief history of microbiology, the debate over spontaneous generation, and the “golden age of
microbiology” (1857-1914).
a. The Earth is about 4.6 billion years old.
b. > 3.5 billion years ago: Ancestors of bacteria were the first life on Earth.
c. 4300 B.C.: Babylonian clay tablets have beer recipes.
d. 600 A.D.: Mayans make fermented beverage from cacao (chocolate).
e. 1590: Janssen develops the compound microscope.
f. In the 1600’s, two competing hypotheses sought to explain how life began.
i. The hypothesis that living organisms arise from nonliving matter was called spontaneous
generation. According to spontaneous generation, a “vital force” forms life.
ii. The alternative hypothesis, that the living organisms arise from preexisting life, was
called biogenesis.
g. 1665: Robert Hooke reported that living things were composed of little boxes or cells.
h. 1668: Francisco Redi performs the first documented controlled scientific experiment.
i. He filled six jars with decaying meat, covered three tightly, and left the other three
uncovered.
ii. The uncovered meat, exposed to flies, developed maggots. The covered meat did not.
iii. Redi concluded that adult flies are necessary for the production of maggots. This is the
first major blow to spontaneous generation in favor of biogenesis.
iv. Proponents of spontaneous generation countered that life cannot spontaneously generate
without fresh air.
v. Redi performs the experiment again, this time using gauze to cover some of the jars. The
results were the same.
i. 1673: The first microbes were observed by Antoni van Leeuwenhoek who described live
microorganisms (animalcules) that he observed in teeth scrapings, rainwater, and peppercorn
infusions. This marked the beginning of microbiology. Fig. 2.
j. 1745: John Needham shows that boiled broth, transferred to covered flasks and left overnight,
becomes richly contaminated with microorganisms. He forcefully argues the microbes must be
born from the broth. He publishes a formal presentation of the Theory of Spontaneous
Generation.
k. 1765: Lazzaro Spallanzani performs experiments with boiled and unboiled gravy. He shows that
boiled gravy will only spoil if exposed to air. He concludes that spontaneous generation cannot
be correct.
l. Fermentation and Pasteurization.
i. In 1857, Pasteur showed that microbes (yeasts) are responsible for fermentation of wine.
1. Fermentation is the conversation of sugar to alcohol to make beer and wine.
2. Bacteria that use alcohol and produce acetic acid spoil wine by turning it to
vinegar (acetic acid).
3. Microbial growth is also responsible for spoilage of food.
ii. 1857: Pasteur developed the process of pasteurization that saves the French wine
industry. Pasteur demonstrated that these spoilage bacteria could be killed by heat that
was not hot enough to evaporate the alcohol in wine. This application of a high heat for a
short time is called pasteurization, which is now used in a wide variety of foods.
iii. Also in the 1850’s, Pasteur developed the basic ideas of aseptic technique.
m. In 1858, Rudolf Virchow develops the Cell Theory. All living things are composed of cells and
come from preexisting cells.
n. 1861: Louis Pasteur demonstrated that microorganisms are present in the air.
o. 1861: Louis Pasteur provides the final disproof of the theory of spontaneous generation in favor
of biogenesis. He maintains boiled broth in a swan-necked flask, open to the air, for many days
without contamination. Fig. 3.
p. In 1881, Koch develops the technique of streaking for isolation on solid media.
VIII.
IX.
X.
XI.
q. In 1882 Hess, working in Koch’s lab, develops nutrient agar (a new solid medium) for microbial
growth.
r. In 1892 Sergei Winogradsky develops the idea of microorganisms being involved in
biogeochemical cycles. [Nitrification, Sulfur cycle].
The Germ Theory of Disease.
a. 1840s: Ignaz Semmelweis advocated that doctors should wash their hands to prevent
transmission of puerperal fever from one OB patient to another when they assist in childbirth.
i. This disease was also known as childbed fever. We now know that it was due to a
streptococcus infection which caused septicemia (bacterial growth in the blood).
b. 1867: Joseph Lister used a chemical disinfectant known as carbolic acid (phenol) to prevent
surgical wound infections after looking at Pasteur’s work showing microbes are in the air and
can spoil food, etc. This reduced infection from surgery dramatically and served as proof that
surgical infections are caused by microorganisms.
c. 1876: Robert Koch provided proof that a bacterium causes anthrax. He provided the
experimental steps, Koch’s postulates, used to prove that Bacillus anthracis causes anthrax, and
proved the Germ Theory of Disease.
d. 1884: Koch’s Postulates formalized. They are the set of steps required to identify the causative
agent of a disease.
i. [See Fig. 3, Chapter 14 (Epidemiology)].
Vaccination.
a. 1798: Edward Jenner performs the first vaccinations against smallpox. He collects the pus from
cowpox blisters on the hands of milkmaids. He contaminates a lance with this pus and then cuts
the skin of children.
b. Called vaccination from vacca for cow.
c. The protection is called immunity.
The Birth of Modern Chemotherapy.
a. Treatment with chemicals is chemotherapy.
b. Chemotherapeutic agents used to treat infectious disease can be synthetic drugs or antibiotics.
c. Antibiotics are chemicals produced by bacteria and fungi that inhibit or kill other microbes.
d. Quinine, from the bark of the South American Chinchona tree, was long used to treat malaria.
e. 1910: Paul Ehrlich developed a synthetic arsenic drug, salvarsan, to treat syphilis.
f. 1928: Alexander Fleming discovered the first antibiotic. Fig. 5.
i. He observed that Penicillium notatum (a fungus) made an antibiotic, penicillin, which
killed Staphylococcus aureus.
1. This discovery was an accident. He was searching for antimicrobial chemicals
and used Staphylococcus cultures to test these chemicals. He left some of these
bacterial cultures on the lab bench when he went on vacation. Upon returning, he
saw that some of his cultures were contaminated with Penicillium, and noticed
that no bacteria grew next to the Penicillium.
g. 1930s: Sulfonamides were synthesized.
h. 1940s: Penicillin was tested clinically and mass-produced.
Modern Developments in Microbiology.
a. Note: You will NOT be tested on bacteriology, mycology, parasitology, immunology, or
virology.
b. 1953: Watson and Crick developed the 3D model of the structure of DNA. This molecular
structure immediately caused biologists to understand that DNA is the genetic material. The
publication of these results ignites an explosion in the growth of knowledge and application of
genetic principles.
c. In the 1960s, Paul Berg inserted animal DNA into bacterial DNA and the bacteria produced an
animal protein. This is also known as genetic engineering/recombinant DNA technology.
d. 1961: Francois Jacob and Jacques Monod discovered the role of mRNA in protein synthesis.
They also develop the lac operon model. This is the first determination of a mechanism by
which an environmental cue turns a gene on/off.
XII. Microbes and Human Welfare.
a. Microbial Ecology.
i. Bacteria recycle nutrients, carbon, sulfur, phosphorus, etc., that can be used by plants and
animals.
ii. Bacteria degrade organic matter in sewage.
b. Bioremediation.
i. Bacteria degrade or detoxify pollutants by breaking them down into less harmful
substances. Oil, Mercury.
c. Biological Insecticides.
i. Microbes that are pathogenic to insects are alternatives to chemical pesticides that can be
used to prevent insect damage to agricultural crops and disease transmission.
ii. Bacillus thuringiensis infections are fatal in many insects but harmless to other animals
including humans and plants.
XIII. Modern Biotechnology and Genetic Engineering.
a. Biotechnology, the use of microbes to produce foods and chemicals, is centuries old.
b. Genetic engineering is a new technique for biotechnology. Through genetic engineering, bacteria
and fungi can produce a variety of proteins including vaccines and enzymes.
c. Missing or defective genes in human cells can be replaced in gene therapy.
d. Genetically modified bacteria are used to protect crops from insects, freezing, drought, etc.
XIV. Microbes and Human Disease.
a. Bacteria were once classified as plants, which gave rise to use of the term flora for microbes.
b. This term has been replaced by microbiota.
c. Microbes normally present in and on the human body are called normal microbiota.
d. Normal Microbiota: Fig. 7.
i. Are normally found on the skin, in the oral-nasal cavities, in the respiratory tract,
digestive tract, and urogenital tract.
ii. Are normally not found in the blood, CSF, muscle, nervous tissue, or bone.
iii. Prevent growth of pathogens by competing with them for resources.
iv. Secrete toxins that inhibit the growth of pathogens (microbial antagonism).
v. Produce nutrients and growth factors such as folic acid and vitamin K that humans
utilize.
vi. Do not normally cause disease.
e. Biofilms.
i. Microbes forming complex layers on surfaces.
f. Resistance is the ability of the body to ward off disease.
i. Resistance factors include skin, stomach acid, immune system.
g. Infectious Diseases.
i. When a pathogen overcomes the host’s resistance, disease results.
1. An infectious disease is a disease caused by a pathogenic microbe.
ii. Emerging Infectious Diseases (EID): New or changing diseases that are increasing or
have the potential to increase in incidence.
iii. Reasons that EID’s exist include microbial adaptation/mutation, global human travel,
humans moving into previously uninhabited locations, and global climate change.
Examples of EID’s include:
1. West Nile encephalitis (West Nile Virus).
a. First diagnosed in the West Nile region of Uganda in 1937.
b. Appeared in New York City in 1999.
2. Bovine Spongiform Encephalopathy (Mad Cow Disease).
a. Caused by a prion.
b. A prion also causes Creutzfeldt-Jakob disease (CJD).
c. Variant CJD (vCJD) in humans is related to cattle fed sheep/cattle offal for
protein that have then entered the human food supply.
3. Escherichia coli O57:H7.
a. Toxin-producing strain of E. coli.
b. First seen in 1982.
c. Leading cause of diarrhea worldwide.
4. Antibiotic resistant bacteria (Staphylococcus, etc.).
5. Invasive group A Streptococcus (Flesh eating bacteria).
a. Rapidly growing bacteria cause extensive tissue damage.
b. Increased incidence since 1995.
6. Ebola hemorrhagic fever (Ebola virus).
a. Causes fever, hemorrhaging, and blood clotting.
b. First identified near Ebola River, Congo.
c. Outbreak every few years.
7. Hantavirus pulmonary syndrome.
a. Fist identified in 1951 in Korea as cause of hemorrhagic fever and named
for Hantaan River.
b. A new disease involving respiratory symptoms was seen in the U.S. in
1995.
i. The U.S. virus, called Hantavirus Sin Nombre virus, probably
came to the U.S. with rats around 1900.
8. Acquired immunodeficiency syndrome (AIDS).
a. Human immunodeficiency virus (HIV).
b. First identified in 1981.
c. Worldwide epidemic infecting 40 million people; 14,000 new infections
everyday.
d. Sexually transmitted disease affecting males and females.
e. In the U.S., HIV/AIDS in people 13-24 years of age: 44% are female and
63% are African American.
9. Anthrax.
a. Bacillus anthracis.
b. In 1877, Koch proved B. anthracis causes anthrax.
c. Veterinarians and agricultural workers are at risk of cutaneous anthrax.
d. In 2001, dissemination of B. anthracis via mail infected 22 people.
10. Salmonella.
a. Outbreaks have recently occurred in cantaloupe, peanut butter, mangoes,
alfalfa sprouts, etc.