Chapter 1: The Microbial
World and You
Microbiology:
The study of microorganisms.
Microorganisms: Small living organisms that
generally can not be seen with the naked eye.
Include:
Bacteria
Fungi (yeasts and molds)
Protozoa
Algae
Multicellular parasites
Also include nonliving infectious agents:
Viruses
 Prions
Microbes are Essential for Life on
Earth: Have many important and beneficial
biological functions:
 Photosynthesis: Algae and some bacteria
capture energy from sunlight and convert it to
food, forming the basis of the food chain.
 Decomposers: Many microbes break down
dead and decaying matter and recycle nutrients
that can be used by other organisms.
 Nitrogen Fixation: Some bacteria can take
nitrogen from air and incorporate it into soil.
Important and beneficial biological
functions of Microbes:
 Digestion: Animals have microorganisms in
their digestive tract, that are essential for
digestion and vitamin synthesis.
 Cellulose digestion by ruminants (cows, rabbits,
etc.)
 Vitamin K and B synthesis in humans.
 Medicine: Many antibiotics and other drugs
are naturally synthesized by microbes.
 Penicillin is made by a mold.
Important and beneficial biological
functions of Microbes:
 Food Industry: Many important foods and
beverages are made with microbes:
 Alcoholic beverages (Wine, beer, rum, whiskey)
 Bread
 Vinegar
 Soy sauce
 Cheese
 Pickles, olives, sauerkraut
 Yogurt
 Buttermilk
 Sour cream
 Coffee
 Chocolate
 Hams, sausages
Important and beneficial biological
functions of Microbes:
 Genetic Engineering: Recent advances in
gene splicing allow us to design recombinant
microbes that produce important products:
 Human growth hormone (Dwarfism)
 Insulin (Diabetes)
 Blood clotting factor (Hemophilia)
 Recombinant vaccines
Hepatitis A and B vaccines
 Human hemoglobin (Emergency blood substitute)
 Taxol (Breast and ovarian cancer)
 Erythropoietin (Anemia)
 Monoclonal antibodies (Disease diagnosis and
prevention).
Important and beneficial biological
functions of Microbes:
 Medical Research: Microbes are well suited
for biological and medical research for several
reasons:
 Relatively simple and small structures, easy to study.
 Genetic material is easily manipulated.
 Can grow a large number of cells very quickly and
at low cost.
Short generation times make them very useful to
study genetic changes.
Microbes and Disease: Most microbes are
either beneficial or harmless to humans.
 Less than 1% of microbes cause disease.
 In 1962, the surgeon general of the United
States stated: “The war against infectious
diseases has been won”.
Today it is clear that this was overly optimistic:
 Emerging diseases: New diseases like AIDS,
hantavirus, Ebola fever, Lyme disease, Hepatitis C,
and others that did not exist a few years ago.
 Antibiotic and Drug Resistance: Many old
diseases are becoming resistant to traditional
therapies: Tuberculosis, gonorrhea, malaria, etc.
 Today infectious diseases cause 50% of the
52 million worldwide deaths per year.
Infectious Diseases Causing Most
Deaths Worldwide in 1998
Disease
Cause
Deaths/year
Acute Respiratory*Bacterial or viral 4,400,000
Diarrheal diseases Bacterial or viral 3,200,000
TuberculosisBacterial
3,100,000
Malaria
Protozoan
3,100,000
Hepatitis B
Viral
2,000,000
Measles
Viral
1,500,000
AIDS
Viral
1,000,000
Neonatal Tetanus Bacterial
600,000
*: Pneumonia, bronchitis, influenza, etc.
Neonatal tetanus kills over 600,000 infants every year.
Source: Tropical Medicine and Parasitology, 1997.
Microbes and Disease in Human
History
 Bubonic Plague (Black death): Several
devastating epidemics throughout history.
• High mortality: Up to 80% of those infected die.
• 1347-1351: Over 75 million died in Europe,
Asia, and Africa.
• Over 25% of population of Europe died.
• Cause was unknown for over 500 years, leading
to superstition, persecution, and hysteria.
• Bacterial disease transmitted by rat fleas.
• Rare today but still occurs:
• 10-15 cases/year in U.S.
• Last epidemic occurred in India in 1994.
Left: Swollen lymph nodes in bubonic plague infection.
Right: Infected flea bite with eschar and carbuncle.
Source: Tropical Medicine and Parasitology, 1997.
Worldwide Distribution of Plague
++: Frequent transmission
+/-: Infrequent transmission.
Source: Tropical Medicine and Parasitology, 1997.
 Smallpox: One of deadliest human
infectious diseases throughout history.
• Caused by smallpox virus.
• First known case in 1175 B.C.: Egyptian
pharaoh Ramses V died from smallpox.
• Several hundred million deaths through history.
• Up to 90% of Native American population was
killed by smallpox and other diseases (measles
and plague) introduced during European
conquests.
• Native population of Central and South America dropped
from 130 million to about 1.6 million over several decades.
• Smallpox was used as a biological weapon by British
colonists in North America.
• 600,000 deaths/year in Europe from 1500-1700.
Smallpox infection in a small child.
Disease was eradicated worldwide by immunization in 1977.
Source: Microbiology Perspectives, 1999.
 Smallpox (Continued)
• 75% of survivors were severely scarred and/or
blinded.
• An effective vaccine was developed in 1870s by
Edward Jenner, using a related virus (cowpox).
• Smallpox was the first and only viral disease to
be completely eradicated (1977).
• Worldwide immunization campaign in 1960s.
• Only infects humans.
Tuberculosis (TB): Caused by a bacterium
that mainly infects lungs but may spread to other
parts of body.
• Leading killer of world’s infectious diseases:
• 3 million die worldwide every year.
• Over 1 million killed in U.S. between 1930-49.
• One out of three people infected worldwide.
• In U.S. 10 million people are presently infected, but only
5% will develop active disease.
• Most healthy individuals can contain infection.
• Treatment: Antibiotics for up to one year.
• After introduction of antibiotics, TB declined from 1950s
to 80s, and then started to increase again.
• Low patient compliance with treatment has caused
antibiotic resistant TB.
• AIDS epidemic has caused an increase in cases.
Tuberculosis is leading killer among infectious diseases
worldwide. Patient with lymph node necrosis.
Photo by Dr. I. Small
 Childbirth Fever: Common nosocomial
(hospital acquired) infection.
• Bacterial infection of the uterus as a result of
childbirth or abortion.
• Transmitted by hands and instruments of
physicians and midwives.
• Extremely common before the 1900s.
• About 1 in 17 women who gave birth would become
infected (fever, chills, delirium, and death).
• Cause was unknown.
• Austrian doctor Semmelweiss showed that washing
hands and instruments with a disinfectant solution
greatly reduced cases.
• Today common in women who have illegal
abortions, especially in third world countries.
 AIDS: Acquired Immune Deficiency
Syndrome.
• First cases reported in 1981 at UCLA.
• Cause: Human Immunodeficiency Virus (HIV)
• Transmitted by sexual contact, blood transfusions,
mother-to-child, and infected needles.
• Destroys an individual’s immune system, making
them susceptible to many infectious diseases and
cancer.
• Number of cases has grown rapidly during the last
two decades. As of 2001:
• Over 900,000 infected individuals in the U.S.
• Over 40 million deaths worldwide.
African AIDS patient with slim disease
Source: Tropical Medicine and Parasitology, 1997
Endemic Kaposi’s Sarcoma, nodular form in an AIDS patient.
Source: AIDS, 1997.
Extensive symmetric tumor lesions of Kaposis’s sarcoma in an
AIDS patient.
Source: AIDS, 1997
Oral candidiasis (yeast infection) in an AIDS patient
Source: Atlas of Clinical Oral Pathology, 1999
History of Microbiology
Early Studies
Before 17th century, study of microbiology was
hampered by the lack of appropriate tools to
observe microbes.
 Robert Hooke: In 1665 built a compound light
microscope and used it to observe thin slices of
cork. Coined the word cell.
 Anton van Leeuwenhoeck: In 1673 was the first
person to observe live microorganisms which he
called “animalcules” (bacteria, protozoa), using
single-lens microscopes that he designed.
History of Microbiology
Spontaneous Generation vs Biogenesis
 Before 1860s many scientists believed in
Spontaneous generation, i.e.: That living
organisms could arise spontaneously from
nonliving matter:
 Mice come from rags in a basket.
 Maggots come from rotting meat.
 Ants come from honey.
 Microbes come from spoiled broth.
History of Microbiology
Spontaneous Generation vs Biogenesis
 Theory of Biogenesis: Belief that living cells can
only arise from other living cells.
 Francesco Redi: In 1668 proved that maggots do
not arise spontaneously from decaying meat.
 Lazaro Spallanzani: In 1765 found that nutrient
broth that had been heated in a sealed flask would
not become contaminated with microbes.
 Some proponents of spontaneous generation argued that
boiling had destroyed the “life force” of air in flask.
 Others argued that microbes were different from other life
forms.
History of Microbiology
Spontaneous Generation vs Biogenesis
Debate was finally settled by Pasteur.
 Louis Pasteur: In 1861 finally disproved
spontaneous generation when he demonstrated
that microorganisms in the environment were
responsible for microbial growth in nutrient broth.
Designed swan neck flasks that allowed air in, but
trapped microbes in neck.
Developed aseptic technique: Practices that prevent
contamination by unwanted microorganisms.
History of Microbiology
Golden Age: 1857-1914
Rapid advances led to the development of
microbiology as a science.
Pasteur’s Contributions to Microbiology:
 Fermentation: Pasteur found that yeasts were
responsible for converting sugar into alcohol in
the absence of air.
Souring and spoilage were caused by bacterial
contamination of beverages.
History of Microbiology
Golden Age: 1857-1914
Pasteur’s Contributions:
 Pasteurization: Developed a process in which
liquids are heated (at 65oC) to kill most bacteria
responsible for spoilage.
 Disease Causes: Identified three different
microbes that caused silkworm diseases.
 Vaccine: Developed a vaccine for rabies from
dried spinal cords of infected rabbits.
 Directed Pasteur Institute until his death in 1895.
History of Microbiology
Golden Age: 1857-1914
Germ Theory of Disease: Belief that microbes
cause diseases. Before, most people believed
diseases were caused by divine punishment,
poisonous vapors, curses, witchcraft, etc.
 Agostino Bassi (1835): Found that a fungus was
responsible for a silkworm disease.
 Ignaz Semmelweis (1840s): Demonstrated that
childbirth fever was transmitted from one patient
to another, by physicians who didn’t disinfect their
hands. He was ostracized by colleagues.
History of Microbiology
Golden Age: 1857-1914
Germ Theory of Disease:
 Joseph Lister (1860): Used disinfectant to treat
surgical wounds, greatly reducing infection rates.
Considered the father of antiseptic surgery.
 Robert Koch (1876): First person to conclusively
prove that a specific bacterium caused a disease.
Germ Theory: One microbe causes one specific
disease.
 Proved that Bacillus anthracis causes anthrax in cattle.
 Later identified bacterium that causes tuberculosis.
History of Microbiology
Modern Microbiology: After 1914
Chemotherapy: Treatment of a disease by using a
chemical substance. Chemical must be more
poisonous to microbe than host.
 Quinine: First known chemical to treat a disease
(malaria). Used by Spanish conquistadors.
 Synthetic Drugs: Made in the laboratory.
 Antibiotics: Produced naturally by fungi and
bacteria.
History of Microbiology
Modern Microbiology: After 1914
 Paul Ehrlich (1910): Search for “magic bullet”.
Discovered salvarsan, an arsenic derivative, was
effective against syphilis.
 Alexander Fleming (1928): Discovered that
penicillin produced by the mold Penicillium
notatum was able to prevent microbial growth.
Penicillin was not mass produced until the 1940s.
 Rene Dubos (1939): Discovered two antibiotics
(gramidin and tyrocidine) produced by bacterium
(Bacillus brevis).
History of Microbiology
Modern Microbiology: After 1914
Problems with Chemotherapy:
 Toxicity
 Drug resistant microbes
Diversity of Microorganisms
I. Bacteria (Sing. Bacterium)
 Small, single-celled (unicellular) organisms.
 Procaryotes: “Before nucleus”.
Lack the following structures:
Nuclear membrane around DNA
Membrane bound organelles
Mitochondria
Chloroplasts
Golgi apparatus
Endoplasmic reticulum
Lysosomes
Kingdom Prokaryotae: Bacteria lack
nucleus and membrane bound organelles
Diversity of Microorganisms
I. Bacteria (Sing. Bacterium)
 Include two groups:
Eubacteria: Peptidoglycan cell walls.
Archaebacteria: Lack peptidoglycan cell walls.
 Shapes: Several forms:
Bacilli: Rod like. (Sing. Bacillus)
Cocci: Spherical. (Sing. Coccus)
Spiral: Corkscrew or curved
Square
Star shaped
Diversity of Microorganisms
I. Bacteria (Sing. Bacterium)
 Divide by binary fission (not mitosis).
 Source of nutrients varies:
Heterotrophs: Consume organic chemicals.
Autotrophs: Make their own food. Include
photosynthetic bacteria.
 Motility: Many can “swim” by using moving
appendages:
Cilia: Small hair like structures
Flagella: Large whip like structures.
 Distinguish between motility and Brownian
motion.
Diversity of Microorganisms
II. Fungi (Sing. Fungus)
 Eucaryotes: “True nucleus”
DNA is surrounded by nuclear membrane.
Cells have membrane bound organelles:
Mitochondria, endoplasmic reticulum, etc.
Cells are larger than those of procaryotes.
 May be unicellular or multicellular:
Unicellular: Yeasts
Multicellular: Molds, mushrooms
 Do not carry out photosynthesis.
 Must absorb organic nutrients from their
environment.
Diversity of Microorganisms
II. Fungi (Sing. Fungus)
 Source of nutrients varies:
Saprotrophs: Decomposers that feed on dead and
decaying matter. Most fungi are decomposers.
Parasites: Obtain nourishment by parasitizing live
animals and plants.
 Cell wall made of chitin.
 May reproduce sexually or asexually.
Diversity of Microorganisms
III. Protozoa (Sing. Protozoan)
 Eucaryotes: “True nucleus”
DNA is surrounded by nuclear membrane.
Cells have membrane bound organelles and are larger
than those of procaryotes.
 Unicellular
 Kingdom Protista
 Sexual or asexual reproduction
 Classified based on locomotion:
Pseudopods: “False feet”. Cytoplasmic extensions.
Example: Amoeba
Protozoa Belong to Kingdom Protista:
Eucaryotic Unicellular or Simple
Multicellular Organisms
Diversity of Microorganisms
III. Protozoa (Sing. Protozoan)
 Classified based on locomotion:
Flagella: Long whip like appendages.
Example: Trichomonas vaginalis, causes trichominiasis, a
sexually transmitted disease.
Cilia: Small hair like appendages
Nonmotile: Do not move in their mature forms.
Example: Plasmodium spp., causative agent of malaria.
Diversity of Microorganisms
IV. Algae (Sing. Alga)
 Eucaryotes: “True nucleus”
 Photosynthetic: Important part of food chain
because produce oxygen and carbohydrates used
by animals.
 Unicellular or multicellular
 Kingdom Protista
 Sexual or asexual reproduction
 Cell walls composed of cellulose
 Found in aquatic environments (oceans, lakes,
rivers), soil, and in association with plants.
Diversity of Microorganisms
V. Viruses
 Acellular infectious agents, not considered
living because they lack cells.
 Obligate intracellular parasites: Viruses can
only reproduce by using the cellular machinery of
other organisms.
 Simple structure:
Protein coat (capsid) with either DNA or RNA, but not
both.
May also have a lipid envelope.
Comparison of Cells and Viruses
Diversity of Microorganisms
VI. Multicellular Animal Parasites
 Eucaryotes: “True nucleus”
 Multicellular animals, usually are visible to the
naked eye.
 Microscopic during some stages of life cycle.
 Spend part or all of their lives inside an animal
host.
 Helminths include:
Flatworms (Platyhelminths): E.g. Tapeworm
Roundworms (Nematodes): E.g. Ascaris, pinworm.