Introduction to Microbiology

TERMINOLGY
1. Microbiology
2. Spontaneous generation
3. biogenesis
4. fermentation
5. bioremediation
6. bioaugmentation
7. pasteurization
8. Biotechnology
9. vaccination
10. bacteriology
11. genomics
12. Immunology
 Terminology cont.
13.Chemotherapy
14.Virology
15.Microbial genetics
16.Mycology
17.Aseptic techniques
18.Germ theory of disease
19.Molecular biology
20.Recombinant DNA Techniques
 Definition of Microbiology
• Microbiology is the study of
microorganisms which must be viewed
with the aid of a microscope or electron
microscope. It includes microorganisms
such as bacteria, viruses, viroids, yeast,
molds, protozoans, algae, fungi and other
very small organisms.
  Microbiology is the Science that studies
What is Microbiology? Microorganisms.
 Microorganisms, roughly, are those living things
that are too small to be seen with the naked eye.
 Microorganisms cannot be distinguished
Phylogenetically from “Macroorganisms”
 For example, many fungi are microorganisms, as
well as all bacteria, all viruses, and most protists.
 Microbiology is more a collection of techniques:
• Aseptic technique
• Pure culture technique
• Microscopic observation of whole organisms
 A microbiologist usually first isolates a specific
microorganism from a population and then
cultures it.
Scale of Microbes
 History of Microbiology
• 1665 Robert Hooke-1st to develop cell.
• 1838-1839- Theodor Schawnn and Matthias -development of cell
theory
• 1673 Anton Van Leeuwenhoek- 1st to view microorganism ie.
Bacteria and protozoa
• Spontaneous Generation: life arise from non living matter
• 1668 Francisco Redi- oppose theory of spontaneous generation.
 Spontaneous Generation
Many believed spontaneous generation:
life can arise from non-living matter
Snakes from horse hairs in stagnant water
Mice from grain and cheese wrapped in a sweater
Maggots from rotting meat
Fleas from hair
Flies from fresh and rotting fruit
Mosquitoes from stagnant pondwater
Locusts from green leaves
Raccoons from hollow tree trunks
Termites are generated from rotting wood
- 1745 John Needham-claimed that microbes developed
spontaneously from fluids.
• 1765 Lazzaro Spallanzani- showed that when the nutrient fluid
were boiled their was no microbial growth
• Anthon Lavoisier- showed the importance of oxygen to life.
• Biogenesis- the theory that living things arise only from pre-
existing cells.
• 1858-Rudolf Virchow- living things can only arise from preexisting
cells
• 1861- Louis Pasteur- demonstrated that microorganisms are
present in the air and can contaminate sterile solutions, but air itself
cannot create microbes. He also demonstrated that microbial life
could be destroyed by heat and that methods can be devised to
block access of airborne microorganism to nutrient environments.
• Golden Age of microbiology (1857-1914)
• Microbiology became a science
• Major discoveries: fermentation, pasteurization, germ theory of
disease, vaccination
• Fermentation and Pasteurization
• Pasteur discovered the use of yeast in fermentation and the
action of bacteria in food spoilage and souring forming vinegar-
acetic acid. He discovered the process of pasteurization
(process of mild heating to kill particular spoilage microorganism
or pathogens)
• The germ theory of Disease-the principle that microorganisms
may cause disease
• 1860’s Joseph Lister-applied the germ theory to medical
procedures. Lister was the 1st to use disinfectants to treat
surgical wounds preventing infections caused by
microorganism.
• 1876 Robert Koch- was the 1st to prove that bacteria actually
cause disease. He discovered rod shaped bacteria called Bacillus
anthracis in the blood of cattle that died from anthrax.
• 1798- Edward Jenner- discovered vaccine against small pox.
• 1880-Pasteur discovered that a virulent bacteria could be used as a
vaccine for the fowl cholera. Modern vaccine are prepared from
virulent microorganism or killed pathogens, from isolated
components of pathogens or by recombinant DNA techniques.
• The birth of chemotherapy
• Chemotherapy refers to the chemical treatment of non
infectious disease such as cancer using chemical substances
• 1910-Paul Ehrlich- 1st to use chemotherapy – introduced an
arsenic containing chemical called salvarsan to treat syphilis
• 1928 Alexander Fleming- observed that the Penicillin fungus
inhibited the growth of bacteria culture.
 Modern Microbiology
• Bacteriology- the study of bacteria
• Mycology-the study of fungi, includes medicinal, agricultural and
ecological branches.

• Parasitology- the study of protozoa and parasitic worms

• Genomics-the study of an organism’s genes. This have allowed

scientist to classify bacteria and fungi according to their genetic
relationships with other bacteria, fungi and protozoa
• Immunology- the study of immunity
• Virology-the study of virus. In 1892 Dmitri Iwanowski reported that
the organism that causes mosaic disease of tobacco was so small
that it passed through it filters fine enough to stop all know bacteria.
Wendett Stanley was the 1st to characterize a virus.
• Recombinant DNA technology/ genetic engineering- the
manufacturing and manipulation of genetic material in vitro.
• Paul Berg- showed that fragments of human or animal
DNA(genes) that code for important proteins can be
attached to bacteria DNA. When injected in bacteria it
can make large amounts of the desired proteins.
• 1941- George Beadle and Edward Tatum-
demonstrated the relationship between genes and
enzymes.
• 1944- Qswald Avery, Colin MacLeod and Maclyn Mc
Carty –established DNA as the genetic material
• 1953- James Watson and Francis Crick-proposed a
model for the structure and replication of DNA
• 1961- Francois Jacob and Jacques Monod –
discovered messenger RNA, a chemical involved in
protein synthesis and later made the 1st major discoveries
about the regulation of gene functions in bacteria.
 What is the importance of studying
microbiology?
Biomedical research
• Human insulin production : recombinant DNA
techniques have resulted in insertion of the gene
for insulin production into bacterium. The
bacterium can produce human insulin
inexpensively.
• Vaccine production- microorganism can be used
as vaccines. Some microbes can be genetically
engineered to produce compounds of vaccines.
• See pg 529 table 18.1
Environmental application
• - microorganisms forms the basis of food chains

• - nitrogen cycle: helps break down waste in the soil and incorporate
nitrogen gas from the air in organic compounds.
• - Recycling of vital elements eg. N, S

• - bacteria decompose material and release carbon dioxide into the

atmosphere for use by plants.

• - important in sewage treatment: organic material in sewage is

decomposed by bacteria into carbon dioxide, nitrates, phosphates,
sulphates and other organic compounds in a waste water treatment plant.

• - they are important in BIOREMEDIATION

• - Biological Control of pest

 human body function: use in digestion and in the synthesis of vitamins
such as B and K

Helps us to understand and treat diseases ie. Cholera, sars, aids, STI

Industry –
• Use in food industry for the production of vinegar, alcoholic beverages,
soy sauce, cheese, yogurt, bread Eg (yeast: Saccharomyces
cerevisae) use for fermentation, Lactobacillus - dairy production
• Use in genetic engineering: microbes are manipulated to produce
substances that helps them to synthesize substances such as
cellulose, digestive aids, and important therapeutic substances such as
insulin.
• Food pathogens- are responsible for millions of cases of infectious
gastrointestinal each year, costing billions of dollars in medical care
and lost productivity.
 Microbes at Work
1. Agriculture - used to control crop insects.

2. Bioremediation - a field of environmental biotechnology

where bacteria are used to clean up toxic wastes. Ex. Oil spills.

3. Pharmacology - developing anti-microbics (antibiotics and

other chemotherapeutic substances) to destroy pathogens.

4. Vaccines - developing weakened strains of pathogenic

bacteria or viruses in order to protect (immunize) against
infection.
5. Forensics - analyzing DNA left as evidence in criminal
investigations (PCR test).

6. Genetic engineering - transfer of genes (DNA) from one

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organism to another
 Examples of food pathogens
1. Mycotoxins- Molds produce mycotoxins, which are secondary metabolites that
can cause acute or chronic diseases in humans when ingested from
contaminated foods. Potential diseases include cancers and tumors in different
organs .

2. Vibrio species are prevalent in estuarine and marine environments, and seven
species can cause foodborne infections associated with seafood. Ie Vibrio
cholerae

3. Staphylococcus aureus is a common cause of bacterial foodborne disease

worldwide. Symptoms include vomiting and diarrhea that occur shortly after
ingestion of S. aureus toxin-contaminated food. The symptoms arise from
ingestion of preformed enterotoxin, which accounts for the short incubation time.
Staphylococcal enterotoxins are superantigens and, as such, have adverse
effects on the immune system.

4. Salmonella- acquired by animal to human transmission though consumption of

undercooked food products derived from livestock or domestic fowl.
 Microbes & Disease
Microbes both cause and prevent diseases
Microbes produce antibiotics used to treat diseases
The single most important achievement of modern medicine is the ability to treat
or prevent microbial disease
Most of this course will consider the physiology of microbes and their role in
disease
The Germ Theory of Disease = Microbes cause disease!
(yes, it wasn’t so long ago that humans didn’t know this)
 Pathogens and Diseases
Bacillus anthracis Anthrax

Brodetella pertusis Whooping cough (pertusis)

Chlamydia trachomatis Trachomas (blindness), etc.

Clostridium botulinum Botulism
Clostridium perfringens Gas gangrene & food poisoning
Clostridium tetani Tetanus
Corynebacterium diphtheriae Diphtheria
Escherichia coli Food Poisoning
Gardinerella vaginalis Vaginitis
Helicobacter pylori Stomach ulcer
Haemophilus influenzae Lung infections
Klebsiella pneumoniae Atypical pneumonia
Legionella spp. Legionnaire’s disease
Listeria monocytogenes Damage to fetus
 Pathogens and Diseases
Leprosy Mycobacterium leprae
Tuberculosis Mycobacterium tuberculosis
Atypical pneumonia Mycoplasma pneumoniae
Gonorrhea Neiseria gonorrhoeae
Meningitis Neiseria meningitidis
Plague (older name) Pasteurella pestis
Wound infection Proteus vulgaris
Opportunist (e.g., burns) Pseudomonas aeruginosa
Typhus Rickettsia prowazekii
Rocky Mountain Spotted Fever Rickettsia rickettsii
Typhoid fever Salmonella typhi
Nosocomial infections Serratia marcescens
Traveler’s diarrhea Shigella dysenteriae
TSS, food poisoning, etc. Staphylococcus aureus
Most-common pneumonia Streptococcus pneumoniae
Syphilis Treponema pallidum
Cholera Vibrio cholerae
Plague (newer name) Yersinia pestis
 BACTERIAL PATHOGENS

Neisseria meningitis Yersinia pestis

B. burgdorferi
Borrellia -> Lyme disease

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 BACTERIAL PATHOGENS

Clostridium botulinum. CDC.

Bacillus anthracis
C. tetani -> tetanus

Corynebacterium diphtheriae
Staphylococcus aureus 25
 BACTERIAL PATHOGENS

Mycoplasma “fungus-form”

-> pneumonia
-> Pneumonia, Blindness The smallest bacteria
- 0.2 micrometers

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 VIRAL PATHOGENS

HIV

Ebola

Smallpox Rabies virus

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 EUKARYOTIC PATHOGENS

Plasmodium vivax Giardia lamblia

-> Malaria –> chronic diarrhea

Trichomonas vaginalis –
vaginosis in females and
urethritis in males.

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Types of Microorganisms
 Bacteria
• a.k.a., eubacteria (“true” bacteria)
• a.k.a., domain Bacteria
 Archaeabacteria
• a.k.a., domain Archaea
 Single-celled members of domain Eukarya.
• Protozoa
• Microscopic Algae
• Microscopic Fungi
 Viruses
Two cell types - The Three Domain System

Prokaryotes

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 Microorganisms
2 groups: (1) prokaryotes
(2) eukaryotes

• The smallest organisms are

the bacteria which are
prokaryotic
• Larger and more complex
organisms include the
eukaryotic fungi, algae and
protozoa
 Microorganisms

1. Viruses - consist solely of nucleic acid and protein and

are not technically viable living organisms
2. Bacteria – single cell micro-organism that can exist
either independent or as a parasite, can cause infection
but important in biochemical transformation,
bioremediation, waste disposal
3. Fungi – kingdom of heterotrophic, single cell,
multinucleated organism including yeast, mold and
mushroom.
4. Algae- affect surface water quality and can also produce
microbial toxins, but their overall impact is not as
significant as bacteria and fungi
5. Protozoan- pathogens that directly affect human health
 Viruses
DEFINITION
- obligate, intracellular parasites, meaning that they require a host
cell for their growth and replication.
Characteristics of Viruses
– Particles contains: (1) inner nucleic genome
• outer protein capsid
• sometimes and additional membrane envelope
– particles may or may not be infectious
– infectious particles are called virons and prions
– cannot grow on non living media
– are not sensitive to antibiotics
– contain either DNA or RNA, not both
– can reproduce themselves from their genome (a single nucleic
acid molecule)
– reproduce inside living host and are parasitic
Typical Viral Structure
Viruses are infectious agents with both living and nonliving
characteristics.

1. Living characteristics of viruses

• a. They reproduce at a fantastic rate, but only in living host cells.
• b. They can mutate.

2. Nonliving characteristics of viruses

• a. They are acellular, that is, they contain no cytoplasm or cellular
organelles.
• b. They carry out no metabolism on their own and must replicate
using the host cell's metabolic machinery. In other words, viruses
don't grow and divide. Instead, new viral components are
synthesized and assembled within the infected host cell.
• c. The vast majority of viruses possess either DNA or RNA but not
both.
 General Characteristics of bacteria
• Bacteria are prokaryotic cells
• They are the largest group of unicellular
organisms
• They consist of cell protoplasm contained within
a retaining structure or envelope.
• Typically a few micrometers in length.
• bacteria have a wide range of shapes, ranging
from spheres to rods and spirals.
• Bacteria are vital in recycling nutrients
• Characterized by rapid growth and cell division
under favorable conditions.
 Structure
• Size: about 0.5 to 1 micrometer in
diameter by 1 to 2 micrometer long.

• cells do not usually exist in isolation,

they form colonies.

• Bacterial colonies that can be seen

consist of million of cells

• The overall form of the bacterial cell

is that of a complex envelope that
encloses cell protoplasm.

• Cell appendages from the envelope

protrude into the environment
surrounding the cell.( flagella,
fimbriae and pili)
 Bacterial Form
• Most bacterial
species are either
• Spherical- cocci –
shape like a sphere
• rod-shaped- bacilli –
shape like a cylinder
- have multiple
appendages or
flagella that aid in
locomotion.
• spiral-shaped- spirilla
• pleomorphic-
bacteria without a well
defined shape.
 ARCHAEA
• Prokaryotic
• No peptidoglycan
• 3 groups (1) methanogens- produce
methane as a waste in respiration
• (2) halophiles- live in extreme salt
environment
• (3) thermophiles- live in hot sulphurous
water, hot springs
• Don’t cause disease in humans.
 Fungi
What is a fungi?

• Fungi were once classified as plants, due to the

fact that they are decomposers, pathogens and
plant benefactors.

• Like plants they were believed to be

monophyletic but derived from a algal ancestor
that had lost its ability to photosynthesize.
 Mode of Nutrition
Absorption: The transport of food from their substrate into their cell walls.

3 modes of nutrition: saprophytic, parasitic, symbiotic

(i) Saprophytic Fungi

- feed on the dead remains of plants or animals, or on the waste materials
(such as dung) of other living things. These fungi help to get rid of
organic waste.

(ii) parasitic fungi

- feed on other organisms while they are still alive causing serious
damage to trees and other plants. Eg athelete’s foot , ringworm, dry rot
fungi

(iii) Symbiotic Fungi

- mycorrhiza.

- Lichen
Prostist
 Protozoan Characteristics
• Protozoa are microorganisms classified
as unicellular eukaryotes.

Characteristics:
• Protozoa usually range from 2–50 μm, but
can grow up to 1 mm
• easily seen under a microscope.
• Free living, parasitic
Protozoans
– Mastigophora- protozoa having one or more
flagella.

– Sarcodina- are amoebas, move by

pseudopodia with help of Cytoplasmic streaming

– Ciliophora includes protozoa that move by

means of cilia.

– Apicomplexa -Members form spores at one

stage in their life cycle. For this reason, the group
is also known as Sporozoa.
 Binomial Nomenclature
Examples: Escherichia coli, E. coli, Escherichia spp., and “the genus Escherichia”

The genus name (Escherichia) is always capitalized

The species name (coli) is never capitalized

The species name is never used without the genus name (e.g., coli standing alone,
by itself, is a mistake!)

The genus name may be used without the species name (e.g., Escherichia may
stand alone, though when doing so it no longer actually describes a species)

When both genus and species names are present, the genus name always comes
first (e.g., Escherichia coli, not coli Escherichia)
 Binomial Nomenclature
Both the genus and species names are always italicized (or underlined)—always
underline if writing binomials by hand

The first time a binomial is used in a work, it must be spelled out in its entirety (e.g.,
E. coli standing alone in a manuscript is not acceptable unless you have already
written Escherichia coli in the manuscript)

The next time a biniomial is used it may be abbreviated (e.g., E. for Escherichia)
though this is done typically only when used in combination with the species name
(e.g., E. coli)

The species name is never abbreviated

 Binomial Nomenclature
It is a good idea to abbreviate unambiguously if there is any potential for confusion
(e.g., Enterococcus vs. Escherichia)

These rules are to be followed when employing binomial nomenclature even in your
speech. It is proper to refer to Escherichia coli as E. coli or even as Escherichia, but
it is not proper to call it coli or E.C.!

When in doubt, write the whole thing out (and underline)!

 Gene Therapy
• - is an outcome of recombinant DNA
techniques.
• It involves inserting a missing gene or
replacing a defective one in human cells.
HOW DOES IT WORK?
- The technique uses a harmless virus to
carry the missing or new gene into certain
host cells, where the gene is picked up and
inserted into the appropriate chromosomes.
Uses of Gene therapy:
1.Treat patients with adenosine deaminase
deficiency (ADA) and Severe combined
immunodefficency disease(SCID)
Potential: in the future it may be used to treat
genetic disease such as hemophilia, diabetes,
sickle cell anaemia
2. agriculture: genetically altered strains of
bacteria have been developed to protect fruit
against frost damage, and bacteria are being
modified to control insects that damage crops.
- Bacteria have also been used to improve
the appearance, flavor and shelf life of
fruits and vegetables.
Potential:
Potential agricultural uses includes drought
resistance, resistance to insects and
microbial disease and increase
temperature tolerance in crops.