Taxonomy
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VOCABULARY
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Microorganisms: organisms that are too
small to be seen with the unaided eye.
Germs: a rapidly growing cell.
Normal microbiota: microorganisms that are
normally found on or in the body and do not
cause disease.
Pathogen: a microorganism that causes
disease
VOCABULARY
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Bacteriology: a study of bacteria.
Mycology: a study of fungi.
Parasitology: the study of protozoa, worms
(helminthes), and other parasites
Immunology: a study of immunity.
Virology: the scientific study of viruses.
Aseptic
adjective
a: preventing infection
b: free or freed from pathogenic microorganisms
Things cleaned specifically in a way that prevents infection were first described
as "aseptic" in the late 19th century. The word combines the prefix "a-,"
meaning "not," and "septic," from Greek "sēptikos," meaning "putrifying."
"Aseptic" was preceded by more than a century by "antiseptic" (from "anti-,"
meaning "opposing,").
Appertization
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Term of French origin for the process of
destroying all the micro-organisms of
significance in food, i.e. ‘commercial sterility’;
a few organisms remain alive but quiescent.
Named after Nicholas Appert (1752–1841), a
Paris confectioner who invented the process
of canning; he opened the first vacuumbottling factory in 1804.
Fomite
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A fomite is an inanimate object, such as a
keyboard, that might have microorganisms
on it that can be picked up by someone.
"Fomite" is a Latin word for “tinder”.
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Much like tinder is a catalyst of fire, a fomite can
kindle disease.
BENEFITS OF MICROORGANISMS
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Decompose organic wastes
Are producers in the ecosystem by photosynthesis (algae,
cyanobacteria, etc)
Produce industrial chemicals such as ethanol and acetone
Produce fermented foods such as vinegar, cheese, bread,
beer, wine. Fermentation also produces useful products such
as solvents to dissolve substances. To be “probiotic” means
to add microbes to your diet.
Produce products used in manufacturing (e.g. cellulose) and
treatment of diseases (e.g. E coli can make insulin).
Genetic Engineering (recombinant DNA technology)
WHY STUDY MICROORGANISMS?
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Allows humans to prevent food spoilage
Prevent disease occurrence and
transmission
Understanding of aseptic techniques
Number of Bacteria
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You have more bacterial cells living in and on
your body than you have human cells!
If you judge based on cell count or DNA
diversity your physical being is more bacteria
than human. (If you go based on weight,
human cells still predominate.)
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LINNAEUS
Established the system of
scientific nomenclature:
Genus and species.
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NAMING AND CLASSIFYING
MICROORGANISMS
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The first letter of the genus name is always
capitalized, but never the first letter of the
species name.
The genus may be abbreviated with the first
letter, and the species is written out.
The genus and species of an organism is
always either underlined OR italicized: E. coli
or E. coli are both acceptable.
NAMING AND CLASSIFYING
MICROORGANISMS
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Escherichia coli is the name of a common bacterium
normally found in the large intestine of all humans
and animals. If E. coli gets out of that location and
into the small intestine or elsewhere, it can cause
disease.
Staphylococcus aureus is the name of a common
bacterium that is found on human skin. If S. aureus
gets inside of an open wound, it can cause disease.
HOW NAMES ARE CHOSEN FOR
MICROORGANISMS
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Named by location of organism:
Enterococcus faecalis (located in feces)
Named by the shape of organism: Bacillus
megaterium (large rod shape)
Named by the arrangement of organism:
Staphylococcus aureus (clusters of circles)
CLASSIFICATION OF
MICROORGANISMS
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Taxonomy: the science of the classification
of organisms.
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SUPERKINGDOMS
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PROKARYA: Prokaryotes have no nucleus
EUKARYA: Eukaryotes have a nucleus
KINGDOMS: Monera
MONERA
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BACTERIA
VIRUSES
ARCHAEBACTERIA
Bacteria
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Prokaryotes (no nucleus)
Peptidoglycan cell walls
Reproduce by binary fission
For energy, use organic
chemicals, inorganic
chemicals, or photosynthesis
Normal
microbiota
are nonpathogenic
Figure 1.1a
BACTERIA
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Three main types
– Gram positive
– Gram negative
– Acid fast
Main shapes
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cocci (ball shaped)
vibrio (comma shaped)
bacillus (rod shaped)
spirochetes (spiral shape)
Arrangements of the cocci
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staphylococcus (clusters like grapes)
 Example: Staphylococcus aureus
diplococcus (pairs of two)
tetrads (groups of four)
streptococcus (chains like bead necklace)
 Example: Streptococcus pyogenes
(“strep throat”)
Viruses
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Acellular
Consist of DNA or RNA core
Core is surrounded by a protein
coat
Coat may be enclosed in a lipid
envelope
Viruses are replicated only when
they are in a living host cell
(obligate intracellular parasites)
Figure 1.1e
VIRUSES
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HIV
Common cold virus
Hepatitis A
VIRUSES
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Vaccines can prevent some viral
infections, but antibiotics are
ineffective for treatment after infection.
Antibiotics work by interfering with cell
wall synthesis or metabolism; since
viruses don’t have these things, they
are not effective.
There are medicines that treat but
don’t cure viruses, such as acyclovir
for Herpes Simplex 1.
ARCHAEBACTERIA
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Prokaryotic
Lack peptidoglycan
Live in extreme
environments
Include:
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Methanogens
Extreme halophiles
Extreme thermophiles
Figure 4.5b
KINGDOMS: Protista
PROTISTA
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ALGAE
PROTOZOA
FUNGI
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Molds (multicellular)
Yeasts (single-celled)
Algae
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Eukaryotes
Cellulose cell walls
Use photosynthesis for
energy
Produce molecular
oxygen and organic
compounds
Figure 1.1d
Protozoa
 Eukaryotes
 Absorb
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or ingest organic
chemicals
 Classified according to their
motility (movement) by
pseudopods (false foot), cilia
(hairs) or flagella (tail).
 Diseases caused by protozoa
include malaria (carried by
mosquitoes) and ameobiasis
(food and water poisoning).
Figure 1.1c
Fungi
FUNGI
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Eukaryotes: have a nucleus in the cell
Cell walls made of chitin or cellulose
Although mushrooms look like plants, they are not
because they do not use photosynthesis for food. Fungi
are not phototrophic.
They are heterotrophic: Use organic chemicals for
energy, not photosynthethesis.
Not as diverse as bacteria
Two types:
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Yeasts: unicellular, no mycelia (root-like structures)
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Saccharomyces (Baker’s and Brewer’s yeast)
Candida albicans (vaginal yeast infections)
Molds and mushrooms: multicellular, consisting of masses
of mycelia which are composed of filaments called hyphae.
Figure 1.1b
KINGDOM: Plantae
PLANTAE (plants)
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Plants are photosynthetic (use sunlight to make
food).
That means they are autotrophs (make their
own food)
They have roots, stems, and leaves (unlike
algae)
They do not cause many microbiological
diseases; not covered in this course.
Kingdom: Animalia
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ANIMALIA (animals): We will just cover
multicellular animal parasites.
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HELMINTHES
– Flat worms
– Tapeworms
NEMATODES
– Roundworms
Multicellular Animal Parasites
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Eukaryote
Multicellular animals
Parasitic flatworms
and tapeworms are
called Helminthes.
Roundworms are
called Nematodes.
Microscopic stages in
life cycles.
Figure 12.28
TAXONOMY
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Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
TAXONOMY
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Dashing
King
Phillip
Came
Over
From
Greece
Singing
Microorganisms:
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Figure 1.1
MICROBES COMPARISON CHART
BACTERIA
Prokaryotic
Peptidoglycan cell walls
Reproduced by binary fission
Uses organic (heterotrophs) and inorganic chemicals (chemoheterotrophs) or
photosynthesis (autotrophs) for energy
Shapes are rod, coccus, spiral
ARCHAEA
Prokaryotic; these are bacteria that:
Lack peptidoglycan
Live in extreme environments
Include methanogens (love methane gas), extreme Halophiles (love salt),
extreme thermophiles (love heat and cold)
FUNGI
Eukaryotes
Cell walls have chitin
Heterotrophs: use only organic chemicals for energy
Molds are multicellular; Yeasts are unicellular
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MICROBES COMPARISON CHART
PROTOZOA
Eukaryotes
Heterotrophs: use only organic chemicals for energyMay be motile via
pseudopods, cilia, or flagella
ALGAE
Eukaryotes
Cell wall contain cellulose
Uses photosynthesis for energy (autotrophs); Produces oxygen and organic
food for other species. They are like plants except they don’t have roots,
stems, leaves and can be unicellular.
VIRUSES
Non-cellular intracellular parasites; lives at the expense of host
Contain either DNA or RNA surrounded by a protein coat
May have an envelope
Smallest of all microbes
Replicates in living host cell
Antibiotics do not work; requires antiviral agents
HELMINTHES
AND
NEMATODES
(parasitic worms)
Eukaryotes
Helminthes: parasitic flat worms and tapeworms
Nematodes: parasitic roundworms
They are endoparasites: animals that live inside other animals through fecal
contamination
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VOCABULARY
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Biotechnology: the industrial application of microorganisms,
cells, or cell components to make a useful product.
Microbial ecology: the study of the relationship between
microorganisms and their environment
Microbial genetics: study of the mechanisms by which
microorganisms inherit traits.
Microbial physiology: the study of the metabolism of
microbes.
Molecular biology: the science of dealing with DNA and
protein synthesis of living organisms.
• Genomics: the study of an organisms genes; used to
classify a microorganisms.
• Bio remediation: bacteria degrade organic matter in
sewage. Bacteria also degrade or detoxify pollutants
such as oil and mercury.
• Genetic engineering: a new technique for
biotechnology. Bacteria and fungi can produce a variety
of proteins including vaccines and enzymes.
• Probiotic: adding microbes to food to cause a benefit.
• Nosocomial diseases: acquired in hospitals; an
infection that develops during the course of a hospital
stay and was not present at the time the patient was
admitted.
• Neonate: newborn
• Immunocompromised: vulnerable to disease caused by
normal microbiota.
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MICROBES AND HUMAN WELFARE
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ECOLOGY
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Bacteria recycle carbon, nutients, sulfates,
and phosphates that can be used by plants
and animals.
BIOREMEDIATION
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This is any process that uses
microorganisms to return the environment
altered by contaminants to its original
condition.
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Used to clean up oil spills.
Used to clean up industrial toxic wastes.
Bioremediation
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Bacteria degrade
organic matter in
sewage.
Bacteria degrade or
detoxify pollutants
such as oil and
mercury
Oil Spills
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INSECTICIDES
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Bacteria can be used in
the place of pesticides.
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Environmentally friendly
Little or no effect on
humans, wildlife,
pollinators and most
other beneficial insects.
PHARMACOLOGY
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Production of pure
chemicals for use as
pharmaceuticals.
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Insulin
Growth factors
Antibodies
FOOD
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Lactobacillus: fermented
foods
Cheese
Pickles
Soy sauce
Sauerkraut
Vinegar
Wine
Yogart
FOOD
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Probiotics: Live
microorganisms which when
administered in adequate
amounts confer a health
benefit on the host. These
are bacteria added to milk,
yogurt, and other foods.
Lactic acid bacteria (LAB)
are the most common
microbes used.
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provides the characteristic
sour taste of fermented
dairy foods
acts as a preservative, by
lowering the pH and
creating fewer opportunities
for spoilage organisms to
grow.
BIOTECHNOLOGY
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The manipulation of
biological organisms to
make products that
benefit human beings.
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Food production
Waste disposal
Mining
Medicine
BIOTECHNOLOGY:
Genetic Engineering
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Restriction enzymes cut the
DNA strands of any
organism at precise points.
This is how the sequence of
a person’s DNA can be
determined.
A specific gene can be
removed from one
bacterium and inserted it
into another using
restriction enzymes.
BIOTECHNOLOGY:
Recombinant DNA Technology
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Transgenic bacteria (bacteria to which a
gene from a different species has been
transferred)
Example: A human gene which codes for a
hormone is transferred to Escherichia coli
bacteria.
Escherichia coli produces this human
hormone along with their own normal
chemical compounds.
RECOMBINANT DNA TECHNOLOGY
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Recombinant DNA is a form of artificial DNA which is
engineered through the combination or insertion of
one or more DNA strands, thereby combining DNA
sequences which would not normally occur together.
It is produced through the addition of DNA into an
existing organism’s genes to alter traits for a specific
purpose, such as immunity.
Bacteria can also be used to produce large
quantities of human insulin.
NORMAL MICROBIOTA
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There are approximately 10 times as many bacterial
cells as human cells in the human body.
Three pounds of E. coli live in our intestines, helping
to digest food that we cannot digest.
These microbes produce folic acid, biotin, and
vitamin K, substances we need to survive but cannot
make ourselves.
Useful microbes compete for nutrients in our body,
keeping out harmful bacteria.
WHY WE HAVE MICROBIAL DISEASES
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Mutation leads to evolution of bacteria
Antibiotic use causes resistance and
evolution of bacteria
Travel exposes us to microbes we are not
used to
Deforestation (removal of trees, especially in
the tropics, Africa, Central America) destroys
the ecosystem and disturbs natural balance
of microbes
Lab Soil Project
This Thursday, bring a soil sample to lab.
 Don’t use really fertile soil…dry is better, but not in an area where no
plants are growing. It is best to get soil close to roots of nearby plants,
and dig down about 2 inches first.
 Fill a 15 ml test tube all the way up with soil.
 Record the place of collection, temperature, and any of the below data
you can collect
LOCATION
 Location
 Latitude
 Longitude
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Lab Soil Project
Date and Time Collected *
 Date
 Time
 Sample Site Descriptors *
SOIL SAMPLE
 Air Temperature (°C)
 Humidity (%)
 Depth (In.)
 Type of Soil
 Soil Temperature (°C)
 pH of Soil
 Water Content (%)
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