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MICROBIOLOGY LECTURE
MICROORGANISMS
These are organisms that are too small to be seen with the unaided eye. A layperson calls
them “germs”, which is a word that is derived from “germinate”, and refers to a rapidly
growing cell. Normal microbiota: microorganisms that are normally found on or in the
body and do not cause disease. The proper term for a microorganism that causes disease
is PATHOGEN. The prefix “patho” means “disease”, and “gen” means “generating”.
Types of pathogens include fungi (plant molds and yeasts), protozoa (single celled
animals), viruses (the smallest; they can fit inside the nucleus of a bacteria), helminthes
(worms), and bacteria. Not all microorganisms are pathogens; many are useful in the
environment and to humans.
Bacteriology: a study of bacteria.
Mycology: a study of fungi.
Parasitology: the study of protozoa, parasites, and worms (helminthes).
Immunology: a study of immunity.
Virology: the scientific study of viruses.
BENEFITS OF MICROORGANISMS
1. Decompose organic wastes
2. Are producers in the ecosystem by photosynthesis (algae, cyanobacteria, etc)
3. Produce industrial chemicals such as ethanol and acetone
4. 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.
5. Produce products used in manufacturing (e.g. cellulose) and treatment of diseases
(e.g. E coli can make insulin).
6. Genetic Engineering (recombinant DNA technology)
7. Normal microbiota: normally found on humans, etc, and do not cause disease
except in immunocompromised people (immune system is not strong).
WHY STUDY MICROORGANISMS?
1. Allows humans to prevent food spoilage
2. Prevent disease occurrence and transmission
3. Understanding of aseptic techniques to prevent contamination in medical practice,
surgery, laboratories, patient handling, food and medicine preparation.
a. NOSOCOMIAL DISEASES are those acquired in a hospital.
NAMING AND CLASSIFYING MICROORGANISMS
LINNAEUS (a Swedish Botanist) established the system of scientific nomenclature.
Each organism has two names: GENUS (from the word “genre”, meaning “more than
one”) and an epitaph, also known as the SPECIES (specific name unique to that organism
type).
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.
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
Named by location of organism: Enterococcus faecalis (located in feces)
Named by the shape of organism: Bacillus megaterium (rod shaped and large)
Named by the arrangement of organism: Staphylococcus aureus (clusters of circles)
CLASSIFICATION OF MICROORGANISMS
Taxonomy: the science of the classification of organisms.
SUPERKINGDOMS
1. PROKARYA: Prokaryotes have no nucleus
2. EUKARYA: Eukaryotes have a nucleus
KINGDOMS
1. MONERA
a. BACTERIA
i. Prokaryotes: no nucleus
ii. Peptidoglycan cells walls: a substance that makes them strong
iii. Binary fission: reproduce by splitting in two
iv. Diverse energy requirements: For energy, use organic chemicals
(contains carbon), inorganic chemicals (no carbon), or
photosynthesis (use chlorophyll and sunlight to make food).
v. Normal microbiota are non-pathogenic
vi. Three main types
1. Gram positive
2. Gram negative
3. Acid-fast
vii. Main shapes
1. cocci (ball shaped)
2. vibrio (comma shaped)
3. bacillus (rod shaped)
4. spirochetes (spiral shape)
viii. Arrangements of the cocci
1. staphylococcus (clusters like grapes; example is
Staphylococcus aureus)
2. diplococcus (pairs of two)
3. tetrads (groups of four)
4. streptococcus (chains like a bead necklace; example is
streptococcus pyogenes = “strep throat”)
b. VIRUSES
i. These are the smallest of all microbes; hundreds of viruses can fit
into one bacterium!
ii. They are acellular (no cells)
iii. They consist of a core of a fragment of nucleic acid: either DNA or
RNA (not both). The RNA viruses don’t have stable genes and
they mutate frequently.
iv. The core is surrounded by a protein coat called a capsid, made up
of capsomeres. The capsid may be surrounded by an envelope
made up of lipid.
v. Viruses are only replicated when they are living in a host cell.
vi. They don’t have their own metabolism; they use host cells for metabolism.
vii. They are obligate intracellular (must live inside host cell) parasites (live at
the expense of the host, which it weakens or kills).
viii. Even when you kill a virus, it can leave behind an active particle.
ix. Examples of viral diseases range from the deadly HIV to the
common cold virus. Hepatitis A is a virus that can remain viable
(living) even outside of the host for long periods of time; it spreads
through fecal contamination (food workers who do not wash their
hands after a bowel movement).
x. 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.
c. ARCHAEBACTERIA
i. Prokaryotic
ii. Lack peptidoglycan
iii. Live in extreme environments: deep sea, salt, heat, cold
1. Methanogens: can make methane gas (flatulence!). They can live
in animal bodies (cattle, etc), contributes to global warming.
2. Extreme Halophiles: like excess salt
3. Extreme thermophiles: like extreme temperatures (hot and cold)
2. PROTISTA(Protists)
a. ALGAE
i. These are the producers of the ecosystem because they use
photosynthesis to make food; other organisms eat them and get their food
that way. They are at the bottom of the food chain.
ii. Eukaryotes
iii. Produce oxygen that is needed for all other life forms on earth. Without
algae there would not be enough oxygen on earth.
iv. Don’t cause many diseases
b. PROTOZOA
i. Eukaryotes
ii. Larger than bacteria; many bacteria can fit into a protozoa.
iii. Absorb or ingest organic chemicals
iv. Classified according to their motility (movement): by pseudopods (false
foot), cilia (hairs) or flagella (tail).
v. Diseases caused by protozoa include malaria (carried by mosquitoes) and
ameobiasis (food and water poisoning).
3. FUNGI
a. Eukaryotes: have a nucleus in the cell
b. Larger than protozoa.
c. Chitin cell walls or cellulose
d. Although mushrooms look like plants, they are not because they do not
use photosynthesis for food. Fungi are not phototrophic.
e. They are heterotrophic: Use organic chemicals for energy, not
photosynthethesis.
f. Not as diverse as bacteria
g. Two types:
i. Yeasts: unicellular, no mycelia
1. Saccharomyces (Baker’s and Brewer’s yeast)
2. Candida albicans (vaginal yeast infections)
ii. Molds and mushrooms: multicellular, consisting of masses of
mycelia which are composed of filaments called hyphae.
4. PLANTAE (plants)
a. Plants are photosynthetic (use sunlight to make food).
b. That means they are autotrophs (make their own food)
c. They have roots, stems, and leaves (unlike algae)
d. They do not cause many microbiological diseases; not covered in this course.
5. ANIMALIA (animals): We will just cover multicellular animal parasites.
a. Eukaryotes
b. Multicellular animals
c. Endoparasites (animals that live inside other animals through fecal
contamination.
d. Life cycles are seen in stages; they are microscopic.
i. HELMINTHES
1. Flat worms
2. Tapeworms
ii. NEMATODES
1. Roundworms
Taxonomical classification becomes more specific until the organism is uniquely
identified:
Kingdom
Phylum
Class
Order
Family
Genus
Species
Dashing
King
Phillip
Came
Over
From
Greece
Singing
MICROBES COMPARISON CHART
Prokaryotic
Peptidoglycan cell walls
Reproduced by binary fission
Uses organic and inorganic chemicals or photosynthesis for energy
Shapes are rod, coccus, spiral
Prokaryotic
ARCHAEA
Lack peptidoglycan
Live in extreme environments
Include methanogens, extreme Halophiles (love salt), extreme
thermophiles (love heat and cold)
Eukaryotes
FUNGI
Cell walls have chitin
Heterotrophes: use only organic chemicals for energy
Molds and mushrooms are multicellular; consist of masses of mycelia,
which are composed of filaments hyphae.
Yeasts are unicellular
Eukaryotes
PROTOZOA
Absorb or ingests organic compounds
May be motile via pseudopods, cilia, or flagella
Eukaryotes
ALGAE
Cell wall contain cellulose
Uses photosynthesis for energy
Produces oxygen and organic food for other species
Non-cellular intracellular parasites; lives at the expense of host
VIRUSES
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 Eukaryotes
Helminthes: parasitic flat worms and tapeworms
AND
NEMATODES Nematodes: parasitic roundworms
Endoparasites: animals that live inside other animals through fecal
contamination
Microscopic stages of life cycle
Parasite is in the bite of mosquito or bug; spreads infection in body
BACTERIA
MICROBES AND HUMAN WELFARE:
The good things microbes do for us
VOCABULARY
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; originated from Beijerinck and Windogradskyi.
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 your diet.
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.
CONCEPTS
ECOLOGY
Bacteria recycle carbon, nutientss, sulfates, and phosphates that can be used by plants and
animals.
BIOREMEDIATION
This is any process that uses microorganisms to return the environment altered by
contaminants to its original condition. The ability of bacteria to degrade a variety of
organic compounds is remarkable and has been used in waste processing and
bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often
used to clean up oil spills. Fertilizer was added to some of the beaches in Prince William
Sound in an attempt to promote the growth of these naturally occurring bacteria after the
infamous 1989 Exxon Valdez oil spill. These efforts were effective on beaches that were
not too thickly covered in oil. Bacteria are also used for the bioremediation of industrial
toxic wastes.
INSECTICIDES
Bacteria can also be used in the place of pesticides in the biological pest control. This
commonly involves Bacillus thuringiensis (also called BT), a Gram-positive, soil
dwelling bacterium. Subspecies of this bacteria are used as insecticides under trade
names such as Dipel and Thuricide. Because of their specificity, these pesticides are
regarded as environmentally friendly, with little or no effect on humans, wildlife,
pollinators and most other beneficial insects.
PHARMACOLOGY
In the chemical industry, bacteria are most important in the production of pure chemicals
for use as pharmaceuticals. Understanding of bacterial metabolism and genetics allows
the use of biotechnology to bioengineer bacteria for the production of therapeutic
proteins, such as insulin, growth factors, or antibodies.
FOOD
Bacteria, often Lactobacillus in combination with yeasts and molds, have been used for
thousands of years in the preparation of fermented foods such as cheese, pickles, soy
sauce, sauerkraut, vinegar, wine and yoghurt. Probiotics: adding bacteria to our diet that
are found in milk, yogart, etc. Probiotics are dietary supplements containing potentially
beneficial bacteria or yeast, with lactic acid bacteria (LAB) as the most common
microbes used. LAB have been used in the food industry for many years, because they
are able to convert sugars (including lactose) and other carbohydrates into lactic acid.
This not only provides the characteristic sour taste of fermented dairy foods such as
yogurt, but acts as a preservative, by lowering the pH and creating fewer opportunities for
spoilage organisms to grow. Probiotic bacterial cultures are intended to assist the body's
naturally occurring gut flora to reestablish themselves. They are sometimes
recommended by doctors, and, more frequently, by nutritionists, after a course of
antibiotics, or as part of the treatment for gut related candidiasis. Claims are made that
probiotics strengthen the immune system.
BIOTECHNOLOGY
Biotechnology is the manipulation of biological organisms to make products that benefit
human beings. Biotechnology contributes to such diverse areas as food production, waste
disposal, mining, and medicine. Restriction enzymes in bacteria cut the DNA strands of
any organism at precise points. A specific gene can be removed from one bacterium and
inserted it into another using restriction enzymes. This event is called genetic
engineering. A human gene which codes for a hormone has been transferred to
Escherichia coli bacteria. Although the transgenic bacteria (bacteria to which a gene
from a different species has been transferred) could not use the human hormone, they
produced it along with their own normal chemical compounds. This type of
biotechnology is called recombinant DNA technology.
RECOMBINANT DNA TECHNOLOGY
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. In terms of genetic modification,
recombinant DNA is produced through the addition of relevant DNA into an existing
organismal genome, such as the plasmid of bacteria, to code for or alter different traits for
a specific purpose, such as immunity. Small circles of DNA exist in bacteria, known as
plasmids. These are modified to include the piece of human DNA containing instructions
for making proinsulin. Proinsulin is the precursor for insulin. The bacteria then multiply
and produce large quantities of human proinsulin for humans to use.
NORMAL MICROBIOTA
There are approximately 10 times as many bacterial cells as human cells in the human
body, with large numbers of bacteria on the skin and in the digestive tract. The vast
majority of these bacteria are harmless or beneficial and serve in useful ways.
Three pounds of E. coli live in our intestines, helping to digest food that we cannot
digest.
Other 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
1. Mutation leads to evolution of bacteria
2. Antibiotic use causes resistance and evolution of bacteria
3. Travel exposes us to microbes we are not used to
4. Deforestation (removal of trees, especially in the tropics, Africa, Central
America) destroys the ecosystem and disturbs natural balance of microbes