Chapter One: The Microbial World and You

Microbes in Our Lives

• What is microbiology?
• Study of microorganisms (also called microbes) and viruses
• What are microorganisms?
• Organisms that are too small to be seen with the unaided eye
• Microbe versus Germ
 Microbes: organism that cannot see with naked eye
 Germ: rapidly growing cell (cancer, hair, skin…); apply for any cell
• Microbes include bacteria, fungi, protozoa, microscopic algae, and viruses

• A few are pathogenic (disease-producing)

• Decompose organic waste
• Generate oxygen by photosynthesis
• Produce chemical products such as ethanol, acetone, and vitamins
• Produce fermented foods such as vinegar, cheese, and bread
• Produce products used in manufacturing (cellulose; blue color of jeans: E. coli bacteria produces indigo from
tryptophan) and disease treatment (insulin)

• Knowledge of microorganisms allows humans to

• Prevent food spoilage
• Prevent disease
• Understand causes and transmission of disease to prevent epidemics
• Led to aseptic techniques to prevent contamination in medicine and in microbiology laboratories

The Microbiome
• An adult human is composed of 30 trillion body cells
• Harbors another 40 trillion bacterial cells
• The microbiome is a group of microbes that live stably on/in the human body
• Help to maintain good health
• Prevent growth of pathogenic microbes
• Help train the immune system to discriminate threats

• Normal microbiota is the collection of acquired microorganisms on or in a healthy human being

• Begin to be acquired as newborns
• May colonize the body indefinitely
• May colonize the body fleetingly (making them transient microbiota)
• Colonization can only occur at body sites that provide nutrients and the right environment for the microbes to
flourish(grow)

Naming and Classifying Microorganisms

• Carolus Linnaeus
• Established the system of scientific nomenclature in 1735
• Means of communicating to others about specific organisms.
• Binomial system
• Each organism has two names: the genus and specific epithet
• Are italicized or underlined
• Genus (genera): The first name, which is always capitalized
• Species name (specific epithet): The second name is not capitalized.
• Are “Latinized” and used worldwide
• May be descriptive or honor a scientist
Scientific Names
• Staphylococcus aureus
• Describes the clustered (staphylo-) spherical (coccus) cells
• Describes the gold-colored (aureus) colonies
• Escherichia coli
• Honors the discoverer, Theodor Escherich
• Describes the bacterium’s habitat–the large intestine, or colon.

• After the first use, scientific names may be abbreviated with the first letter of the genus and the specific epithet:
• Escherichia coli and Staphylococcus aureus are found in the human body
• E. coli is found in the large intestine, and S. aureus is on skin

Prokaryotes:
• Bacteria (1st domain)
• Archaea (2nd domain)
Eukaryotes: (3rd domain)
• Fungi
• Protozoa
• Algae
• Multicellular Animal Parasites
Bacteria
Prokaryotes: “Prenucleus”
(before nucleus)
No membrane bound
nucleus
Unicellular (1 cell)
Different shapes (bacillus)
Peptidoglycan cell walls
Divide via binary fission (2
steps)
Some bacteria have flagella
for “swimming”
Derive nutrition from organic
chemicals or inorganic
chemicals or photosynthesis
Virus: is not in these 3 domains
Types of Microorganism
Archaea Viruses
Prokaryotes Neither prokaryotes or eukaryotes
No membrane bound nucleus -Consist of DNA or RNA core
-Core is surrounded by a protein
coat
+Coat may be enclosed in a lipid
envelope
Unicellular (1 cell) Acellular (no cell)
Lack peptidoglycan cell walls May lack cell wall
entirely
Divide via binary fission (2 steps) -Are replicated only when they are in
a living host cell
+Obligate intracellular parasites
+Inert outside living hosts
Often live in extreme environments:
-Methanogens (high methane)
-Extreme halophiles: high salt
-Extreme thermophiles: high temp
Generally not known to cause disease in humans
(cuz human can’t live in these environment)

Eukaryotes Fungi Protozoa Algae Multicellular Animal

Parasites
Distinct membrane Eukaryotes Eukaryotes Eukaryotes Eukaryotes
bound nucleus -Distinct nucleus -Unicellular -Unicellular -Multicellular animals
Membrane bound Chitin cell walls Cellulose cell walls No cell walls
organelles
Cells are larger Absorb organic Absorb or Use photosynthesis for Not strictly microorganisms
than prokaryotes chemicals for energy ingest organic energy (photosynthetic)
chemicals Produces oxygen and
carbohydrates
Moderate Yeasts are unicellular May be motile Found in freshwater, Parasitic flatworms and
environments via saltwater, and soil round worms are called
pseudopods, helminths.
cilia, or flagella -Some microscopic stages
in life cycles
Molds and mushrooms Free-living or Motility either absent or
are multicellular parasitic reduced
-Molds consist of (derive
masses of mycelia, nutrients from a
which are composed of living host)
filaments called hyphae Some are
photosynthetic
Reproduce sexually or Reproduce Reproduce sexually or Sexual reproduction
asexually sexually or asexually
asexually
Classification of Microorganisms
 • Developed by Carl Woese in 1978
• Three domains based on cellular organization
• Bacteria
• Archaea
• Eukarya
• Protists (Protozoa and Algae)
• Fungi
• Plants and Animals
History of Microbiology
• Ancestors of bacteria were the first life on Earth
• The first microbes were observed in 1673
• In 1665, Robert Hooke reported that living things are composed of little boxes or “cells”.
• Marked the beginning of cell theory
• All living things are composed of cells
• All living things come from preexisting cells
• Life continues because of growth and division of cells
• Cells are the smallest unit of life maintaining properties of life

The First Observations

• 1673-1723, Antoni van Leeuwenhoek described live microorganisms that he observed in teeth scrapings, rain
water, and peppercorn infusions. (create microscope)
• Microscopic organisms – “Animalcules”
• Submitted findings to Royal Society of London
• Raised questions – Where did they originate?

The Debate Over Spontaneous Generation

• The hypothesis that living organisms arise from nonliving matter is called spontaneous generation.
According to spontaneous generation, a “vital force” is necessary for life.
• What was the “vital force”? considering as AIR
• The alternative hypothesis, that the living organisms arise from preexisting cells, is called biogenesis.
(Rudolf Virchow, 1858)

• 1668: Francisco Redi (opponent) filled jars with decaying meat. (2 seal jars: s.t grew, unseal jar: nothing grew)
• From where did the maggots come? THE FLY
• What was the purpose of the sealed jars? Prevent fly to lay eggs directly to the meat
• Spontaneous generation or biogenesis? cuz maggots came from preexisting, which is fly

• 1745: John Needham (pro) put boiled nutrient broth into covered flasks (transfer from 1 flask to another)
• From where did the microbes come? From transferred flask
• Spontaneous generation or biogenesis? cuz microbial grow from preexisting cell in the transferred flask

• 1765: Lazzaro Spallanzani boiled nutrient solutions in flasks. (NOT transfer from 1 flask to another)
• Spallanzani vs. Needham
• Spontaneous generation or biogenesis? no microbial grow cuz not contact with preexisting cells.

The Theory of Biogenesis

• 1861: Louis Pasteur demonstrated that microorganisms are
present in the air.
• Experiments disproving spontaneous generation
• Led to the development of aseptic techniques
Nutrient both placed in flask, heated, not seal  microbial growth
Nutrient both placed in flask, heated, seal  NO microbial
growth
problem is he sealed the flask so air cannot come in
Pasteur also used S-shaped flasks
• Keep microbes out but let air in
• Broth in flasks showed no signs of life
• Neck of flasks traps microbes
• Microorganisms originate in air or fluids, not mystical forces
prove that even air can come in but no sign of microbial grow
disprove the spontaneous generation
The Golden Age of Microbiology
• 1857-1914: Period of rapid development
• Beginning with Pasteur’s work, discoveries included the relationship between microbes and disease, immunity,
and antimicrobial drugs

Fermentation and Pasteurization

• Pasteur showed that microbes are responsible for fermentation.
• Fermentation is the microbial conversion of sugar to alcohol in the absence of air by yeast
• Microbial growth is also responsible for spoilage of food and beverages
• Bacteria that use air to spoil wine by turning it to vinegar (acetic acid)

• Pasteur demonstrated that these spoilage bacteria could be killed by heat that was not hot enough to evaporate
the alcohol in wine. (hot enough to kill bacteria but not the wine)
• Pasteurization is the application of a high heat for a short time to kill harmful bacteria in beverages (milk, juices...)

The Germ Theory of Disease

• 1835: Agostino Bassi showed that a silkworm disease was caused by a fungus
• 1865: Pasteur showed that another silkworm disease was caused by a protozoan
• 1840s: Ignaz Semmelweis advocated hand washing to prevent transmission of puerperal fever from one
obstetrical patient to another
• 1860s: Applying Pasteur’s work showing that microbes are in the air, can spoil food, and cause animal diseases,
Joseph Lister used a chemical antiseptic (phenol) to prevent surgical wound infections
• 1876: Robert Koch discovered that a bacterium causes anthrax and provided the experimental steps, Koch’s
postulates, to demonstrate that a specific microbe causes a specific disease

Vaccination
• 1796: Edward Jenner inoculated a person with cowpox virus, who was then immune to smallpox
• Vaccination is derived from the Latin word vacca, meaning cow
• The protection is called immunity

The Birth of Modern Chemotherapy

• Treatment of disease with chemicals is called chemotherapy
• Chemotherapeutic agents used to treat infectious disease can be synthetic drugs or antibiotics
• Antibiotics are chemicals produced by bacteria and fungi that inhibit or kill other microbes

The First Synthetic Drugs

• Quinine from tree bark was long used to treat malaria
• Paul Ehrlich speculated about a “magic bullet” that could destroy a pathogen without harming the host
• 1910: Ehrlich developed a synthetic arsenic drug, salvarsan, to treat syphilis
• 1930s: Sulfonamides (sulfa drugs) were synthesized

A Fortunate Accident – Antibiotics

• 1928: Alexander Fleming discovered the first antibiotic (by accident)
• Fleming observed that Penicillium fungus made an antibiotic, penicillin, that killed S. aureus
• 1940s: Penicillin was tested clinically, and mass produced

Problems with Antimicrobial Chemicals

• Overuse can lead to resistance
• Some drugs can be toxic to humans; especially antivirals
• Research used to overcome these problems has ushered in a Third Golden Age of Microbiology from the late
1980s to the present

Modern Developments in Microbiology

• Bacteriology is the study of bacteria
• Mycology is the study of fungi
• Parasitology is the study of protozoa and parasitic worms
• Immunology is the study of immunity.
• Vaccines and interferons are used to prevent and cure viral diseases.
• A major advance in immunology occurred in 1933 when Rebecca Lancefield classified streptococci based on
their cell wall components

Virology
 • Virology is the study of viruses
• Dmitri Iwanowski in 1892 and Wendell Stanley in 1935 discovered the cause of mosaic disease of tobacco to
be a virus
• Electron microscopes have made it possible to study the structure of viruses in detail

Molecular Genetics
• Microbial genetics: the study of how microbes inherit traits
• Molecular biology: the study of how DNA directs protein synthesis
• Genomics: the study of an organism’s genes; has provided new tools for classifying microorganisms
• Recombinant DNA: DNA made from two different sources.
 In the 1960s, Paul Berg inserted animal DNA into bacterial DNA, and the bacteria produced an animal protein

First Nobel Prizes for Microbiology Research, in Physiology or Medicine

1901 von Bering Diphtheria antitoxin
1902 Ross Malaria transmission
1905 Koch TB bacterium
1908 Metchnikoff Phagocytes
1945 Fleming, Chain, Florey Penicillin
1952 Waksman Streptomycin
1969 Delbrück, Hershey, Luria Viral replication
1997 Prusiner Prions
2005 Marshall & Warren H. pylori & ulcers
2008 zur Hausen HPV & cancer
2008 Barré-Sinoussi & Montagnier HIV

Microbes and Human Welfare

Recycling Vital Elements

• Microbial ecology is the study of the relationship between microorganisms and their environment
• Bacteria convert carbon, oxygen, nitrogen, sulfur, and phosphorus into forms used by plants and animals.
Sewage Treatment: Using Microbes to Recycle Water
• Sewage is 99.9% water, with a few hundredths of 1% suspended solids
• Treatment of sewage removes undesirable components so water can be released or reused
• Large solids are removed physically
• Microbes are used to convert left over liquid and organic materials into by-products such as CO2

Bioremediation
Using Microbes to Clean Up Pollutants
• Bacteria degrade organic matter in sewage
• Bacteria degrade or detoxify pollutants such as oil and mercury

Biological Insecticides
Insect Pest Control by Microorganisms
• Microbes that are pathogenic to insects are alternatives to chemical pesticides
• Prevent insect damage to agricultural crops and disease transmission
• Bacillus thuringiensis infections are fatal in many insects but harmless to animals and plants
• The bacteria produce protein crystals toxic to insects
• The toxin gene has been inserted into some plants to confer insect resistance

Biotechnology
• Biotechnology is the use of microbes for practical applications, such as producing foods and chemicals
• Recombinant DNA technology enables bacteria and fungi to produce a variety of proteins, vaccines, and
enzymes
• Missing or defective genes in human cells can be replaced in gene therapy
• Inserting genes for useful enzymes inside bacterial DNA (Ex. E. coli)
• Efficient and fast production of enzyme by bacteria
• Ex. Insulin (hormones control sugar level)
• Genetically modified bacteria are used to protect crops from insects and from freezing

Microbes and Human Disease

Normal Microbiota
• Microbes normally present in and on the human body are called normal microbiota
• Normal microbiota prevents growth of pathogens
• Normal microbiota produces growth factors such as vitamins B and K
• Resistance is the ability of the body to ward off disease
• Resistance factors include skin, stomach acid, and antimicrobial chemicals

Biofilms
• Microbes attach to solid surfaces and grow into masses
• They will grow on rocks, pipes, teeth, and medical implants
• Biofilms can cause infections and are often resistant to antibiotics

Emerging Infectious Diseases

• When a pathogen overcomes the host’s resistance, disease results
• Emerging infectious diseases (EIDs): new diseases and diseases increasing in incidence

• Zika virus disease

• Virus discovered in 1947 in Uganda
• Human epidemics in Micronesia 2007, then in French Polynesia and Brazil in 2013–2015
• Spread by bite of an infected Aedes mosquito; also transmitted by sexual contact
• Infection during pregnancy can result in severe birth defects

• So, what do you know about swine flu?

• Influenza A virus (H1N1)
• First detected in the United States in 2009
• Declared a pandemic, or worldwide large-scale outbreak, by WHO in 2009
• Spread person-to-person
• Mimics seasonal flu

• Avian influenza A (H5N1)

• Primarily in waterfowl and poultry
• Sustained human-to-human transmission has not yet occurred

• Methicillin-resistant Staphylococcus aureus (MRSA)

 1950s: Penicillin resistance developed
 1980s: Methicillin resistance
 1990s: MRSA resistance to vancomycin reported
 VISA: Vancomycin-intermediate-resistant S. aureus
 VRSA: Vancomycin-resistant S. aureus

• Ebola hemorrhagic fever (EHF)

• Ebola virus
• Causes fever, hemorrhaging, and blood clotting
• Transmitted via contact with infected blood or body fluids
• First identified near Ebola River, Congo
• 2014 outbreak in Guinea, hundreds killed
• Over 28,000 infected over 2 years, with 1/3 of those infected dead

• Cryptosporidiosis
 Cryptosporidium protozoa
 First reported in 1976
 Causes 30% of diarrheal illness in developing countries
 In the United States, transmitted via water

• Acquired immunodeficiency syndrome (AIDS)

• Caused by human immunodeficiency virus (HIV)
• First identified in 1981
• Sexually transmitted infection affecting males and females
• Worldwide epidemic infecting 35 million people; 6000 new infections every day
• HIV/AIDS in the United States: 26% are female, and 49% are African American