B 4509-Microbiology

Lecture 1: Introduction to Microbiology

Dr Liteboho D. Maduna

Department of Biology
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What is Microbiology?

• Microbiology: The study of living things too small to be seen

without magnification
• some < 1mm, some macroscopic
• Microorganisms or microbes -microscopic organisms
• Commonly called “germs, bugs, viruses, agents…” but not all terms
are accurate.
• These organisms are relatively simple in their construction and lack
highly differentiated cells and distinct tissues
• Not all cause disease (most of them are benign)
• Many of them are useful or even essential for human life
 Importance of Microorganisms

 Microorganisms are foundation for all life on Earth

 Have existed for ~3.5 billion years
 Plants, animals, modern microorganisms all evolved from ancestral bacteria
 Our life depends on their activities
• Play a major role in recycling essential elements
• Source of nutrients and some carry out photosynthesis
• Benefit society by their production of food, beverages, antibiotics, and
vitamins
• Some cause disease in plants and animals
Members of Microbial World
 Members of the Microbial World

 Enormous numbers
• Bacterial species outnumber mammalian
species by factor of 10,000!
• Present in all environments on Earth
• Considerations of biodiversity typically
overlook enormous contribution of
microbes
• Less than 1% of all microbial species can be
grown and studied in laboratory
Classification of Microorganisms

 Two basic cell structures

• Prokaryotes do not have a membrane-
bound nucleus
• Eukaryotes have a membrane-bound
nucleus and organelles
 All living things can be classified into one of
three groups, or domains
1. Bacteria
2. Archaea
3. Eukarya
 Organisms in each domain share certain
important properties
Classification of Microorganisms
Microbial sizes

 Microorganisms vary in size - 1µm to 200 nm.

 Enormous range
• Largest eukaryotic cells ~a million times larger than smallest
viruses
 Wide variations even within a group
• Bacterium ~600 µm x 80 µm discovered in mid 1990s
• Visible to naked eye
• Bacterium 70 times larger in volume discovered in 1999
• Eukaryotic cell ~1 µm found
• Similar in size to typical bacteria
Microbial sizes

Nucleus

Small Proteins Viruses Mitochondria

molecules
Prion fibril

Atoms Lipids Ribosomes Smallest Most Most eukaryotic cells Adult roundworm
bacteria bacteria
Human height
Electron microscope

Light microscope

Unaided human eye

0.1 nm 1 nm 10 nm 100 nm 1 µm 10 µm 100 µm 1 mm 1 cm 0.1 m 1m 10 m

The basic unit of length is the meter (m), and all These units of measurement correspond to units
other units are fractions of a meter. in an older but still widely used convention.
nanometer (nm) = 10–9 meter = .000000001 meter 1 angstrom (Å) = 10–10 meter
micrometer (µm) = 10–6 meter = .000001 meter 1 micron (µ) = 10–6 meter
millimeter (mm) = 10–3 meter = .001 meter
1 meter = 39.4 inches
Naming Microorganisms: Scientific Names

 Binomial System of Nomenclature: two words

• Genus (capitalized)
• Specific epithet, or species name (not capitalized)
• Genus and species always italicized or underlined
• e.g Escherichia coli
• May be abbreviated (E. coli)
Domain Bacteria

 Bacteria
• Single-celled prokaryotes
• Prokaryote = “prenucleus”
• No membrane-bound nucleus
• No other membrane-bound organelles
• DNA in nucleoid
• Most have specific shapes (rod, spherical, spiral)
• Rigid cell wall contains peptidoglycan (unique to
bacteria)
• Multiply via binary fission
• Many move using flagella
Domain Archaea

 Archaea
• Like Bacteria, Archaea are prokaryotic
• Similar shapes, sizes, and appearances to
Bacteria
• Multiply via binary fission
• May move via flagella
• Rigid cell walls
 However, major differences in chemical composition
• Cell walls lack peptidoglycan
• Ribosomal RNA sequences different
 Many are extremophiles
• High salt concentration, temperature
Domain Eukarya

 Eukarya
• Eukaryotes = “true nucleus”
• Membrane-bound nucleus and other
organelles
• More complex than prokaryotes
• Microbial members include fungi,
algae, protozoa
• Algae and protozoa also termed
protists
• Some multicellular parasites
including helminths (roundworms,
tapeworms) considered as well
Domain Eukarya

 Fungi
• Diverse group
• Single-celled (e.g., yeasts) or multicellular (e.g., molds,
mushrooms)
• Energy from degradation of organic materials
• Primarily live on land
.
Domain Eukarya

 Algae
• Diverse group
• Single-celled or multicellular
• Photosynthetic
• Contain chloroplasts with
chlorophyll or other pigments
• Primarily live in water
• Rigid cell walls
• Many have flagella
• Cell walls, flagella distinct
from those of prokaryotes
Domain Eukarya

 Protozoa
• Diverse group
• Single-celled
• Complex, larger than prokaryotes
• Most ingest organic compounds
• No rigid cell wall
• Most motile
Domain Eukarya

 Parasitic helminths are worms that

live at the expense of a host

 Adult stage can usually be seen

without magnification

 Eggs and larvae are microscopic

 Helminths include roundworms,

tapeworms, and flukes
Acellular Infectious Agents

 Viruses, viroids, prions

 Acellular infectious
agents
 Not alive
 Not microorganisms, so
general term microbe
often used to include
them
Acellular Infectious Agents

 Viruses
• Nucleic acid packaged in protein coat
• Variety of shapes
• Infect living cells, termed hosts
• Multiply using host machinery,
nutrients
• Inactive outside of hosts: obligate
intracellular parasites
• All forms of life can be infected by
different types
Acellular Infectious Agents

 Viroids
• Simpler than viruses
• Require host cell for replication
• Consist of single short piece of RNA PSTV

• No protective protein coat

• Cause plant diseases
• Cause brain diseases in mammals
 The RNA molecule contains no protein-encoding
genes, and the viroid is therefore totally T7 DNA

dependent on host functions for its replication!

 Human pathogen: Hepatitis D pathogen PSTV

1 um
Acellular Infectious Agents
 Prions
• Infectious proteins: misfolded versions of normal cellular proteins
found in brain
• Misfolded version forces normal version to misfold
• Abnormal proteins bind to form fibrils
• Cells unable to function
• Prions propagate by converting normal proteins into the prion
version
• Transmissible and create spongiform pathological changes in the
brain resulting in encephalopathy (i.e. causing brain damage)
• Cause several neurodegenerative
diseases in humans, animals
• Resistant to standard sterilization
procedures
Every Rule Has an Exception

 Extremes of size
• Enormous prokaryote; tiny eukaryote
• Smallest prokaryote ~400 nm, contains ~1/10th as much DNA as
E. coli
 Internal structures
• Prokaryotic Planctomyces have membrane surrounding nucleoid; carry out endocytosis
Copyright © 2016 McGraw-Hill Education. Permission required for reproduction or display.
Copyright © 2016 McGraw-Hill Education. Permission required for reproduction or display.
Copyright © 2016 McGraw-Hill Education. Permission required for reproduction or display.

Epulopiscium
(prokaryote)

Paramecium
(eukaryote)

1 µm
0.2 mm Courtesy of Reinhard Rachel and Harald Huber, University of Regensburg,
Courtesy of Dr. Heide N. Schulz/Max Planck Institute for Marine Microbiology Germany

Courtesy of Esther R. Angert

0.1mm
The Historical Foundations of Microbiology

 Science of Microbiology born in 1674

 Key to the study of microorganisms was the development of the
microscope
 Tools to study microorganisms: microscopes, culture techniques,
molecular genetics, genomics
 Earliest record of microbes was from the work of Robert Hooke in
the 1660s
 The most detailed observations of microbes was possible only after
Antonie van Leeuwenhoek created the single-lens microscope,
further perfected by Ernst Abbé abd Carl Zeiss (~late 19th century)
 Leeuwenhoek is known as the father of bacteriology & protozoology
The Historical Foundations of Microbiology

 Antony van Leeuwenhoek (1632–1723)

• Fabric merchant
• Made simple magnifying glass
• Studied lake water
• Observed ‘animalcules’!
 Robert Hooke
• Also credited with discovery
• Described ‘microscopical
mushroom’ (common bread
mold) in 1665
The Theory Spontaneous Generation

 Early scientists tended to explain natural phenomena by a mixture of

belief, superstition, and argument
 Spontaneous Generation
• “Life arises spontaneously from non-living material”
• This notion had been posited by Aristotle (382-322 B.C.) and other
Greek philosophers to explain decay and appearance of animals
such as flies and frogs
• Aristotle proposed that life arose from nonliving material if the
material contained pneuma (“vital heat”).
• As evidence, he noted several instances of the appearance of animals
from environments previously devoid of such animals, such as the
seemingly sudden appearance of fish in a new puddle of water
The Theory Spontaneous Generation

 Spontaneous Generation
• Concept had supporters and detractors
• Detractors included
A. Francesco Redi
B. Louis Pasteur
C. John Tyndall
• Each contributed to disproving the idea
The Dispute Over Spontaneous Generation
 Italian biologist Francesco Redi (1626-1697)
• discredited spontaneous generation
 Demonstrated worms on rotting meat came from
eggs of flies landing on meat (1668)
• Placed meat in two jars
• Covered one jar with gauze
• Gauze prevented flies from depositing eggs
• No eggs  no worms
 However, Leeuwenhoek’s communications on
microorganisms renewed the controversy.

• Took another 200 years to convincingly disprove spontaneous generation of

microorganisms
• One reason: conflicting results between laboratories
But Could Spontaneous Generation Be True for Microorganisms?

 Some scientists proposed that microbes arose by spontaneous

generation but larger organisms did not.
 They pointed out that boiled extracts of hay or meat gave rise to
microorganisms after sitting for a while.
 John Needham (1713-1781)
• suggested that the organic matter in these extracts contained a
“vital force” that could confer the properties of life on nonliving
matter
• His experiment:
• mutton broth in flasks boiled sealed
• results: broth became cloudy and contained microorganisms
The Dispute Over Spontaneous Generation

 Lazzaro Spallanzani (1729-1799)

• Father Spallanzani contradicted Needham’s results
• Experiment: sealed glass flasks that contained water and seeds and then
placed the flasks in boiling water for about 45 minutes.
• broth in flasks sealed boiled
• results: no growth of microorganisms
• He proposed that air carried germs to the culture medium but also
commented that external air might be required for growth of animals
already in the medium.
• The supporters of spontaneous generation responded that heating the air
in sealed flasks destroyed its ability to support life, and therefore did not
discredit the theory of spontaneous generation.
The Dispute Over Spontaneous Generation

 French chemist Louis Pasteur tried to settle the matter of

spontaneous generation
 Considered “father of modern microbiology”
 Demonstrated air is filled with microorganisms
 If a piece of the cotton was placed in sterile medium after air had
been filtered through it, microbial growth occurred
 Filtered air through cotton plug
• Observed trapped microorganisms
• Many looked identical to those found in broths
Louis Pasteur

 Developed swan-necked flask

• Boiled infusions remained sterile despite opening to air
• Ended arguments that unheated air or broths contained “vital force”
necessary for spontaneous generation
 Biogenesis describes the production of living things from other living
things Air escapes from Microorganisms from
open end of flask. air settle in bend.

Years Hours/days

1 Broth sterilized— 2 Broth allowed 3 Broth stays sterile 4 Flask tilted so that 5 Bacteria multiply
air escapes. to cool slowly— indefinitely. the sterile broth comes in broth.
air enters. in contact with micro-
organisms from air.
Pasteur's test of spontaneous generation.
By sterilizing a food source and keeping it isolated from the outside, Pasteur observed no putrefaction of the food source (top
panel). Upon exposure to the outside environment, Pasteur observed the putrefaction of the food source (bottom panel). This
strongly suggested that the components needed to create life do not spontaneously arise.
Final Blow to Spontaneous Generation
 Louis Pasteur experiment brought into existence the germs theory of
disease (means germs are responsible for the disease not the inert
mater) and ended the spontaneous generation theory
 Some scientists remained skeptical
 Pasteur’s results not fully reproducible
 English physicist John Tyndall finally explained conflicting data
• Proved Pasteur correct
• Sterilizing broths required different times
• Some sterilized in 5 minutes
• Others not despite 5 hours!
• Realized broths made from hay contained heat-resistant microbes
• Labs with contaminations used broths made from hay
Final Blow to Spontaneous Generation

 In same year (1876), German botanist Ferdinand Cohn discovered endospores

• Heat-resistant form of bacteria
 Extreme heat resistance of endospores explains differences between Pasteur’s
results and those of other investigators
• Pasteur used broths made with sugar or yeast extract
• Highlights importance of reproducing all conditions as closely as possible when
conducting research
 These early microbiologists not only disproved spontaneous generation but also
contributed to the rebirth of microbiology.
 They developed liquid media and the methods for sterilizing it so that microbes
could be cultured.
 These techniques were next applied to understanding the role of microorganisms in
disease
The Role of Microorganisms in Disease

 Role of microorganisms in disease was not immediately obvious

 For hundreds of years, infectious diseases believed to be due to
supernatural forces or imbalances of 4 bodily- fluid ‘humors’
• Blood, phlegm, Yellow bile [choler], and black bile [melancholy])
in disease had been widely accepted since the time of the Greek
physician Galen (129–199).
 Support for the idea that microorganisms cause disease—that is, the
germ theory of disease—began to accumulate in the early nineteenth
century from diverse fields

35
Evidence for the Relationship between Microorganisms and
Disease

 Agostini Bassi (1773-1856)

• showed that a disease of silkworms was caused by a
fungus
 M. J. Berkeley (ca. 1845)
• demonstrated that the great Potato Blight of Ireland was
caused by a water mold
 Heinrich de Bary (1853)
• showed that smut and rust fungi caused cereal crop
diseases
 More Evidence…

 Louis Pasteur
• demonstrated microorganisms carried out fermentations, helping French wine
industry
• developed pasteurization to avoid wine spoilage by microbes
• showed that the pébrine disease of silkworms was caused by a protozoan
 Joseph Lister
• provided indirect evidence that microorganisms were the causal agents of
disease
• developed a system of surgery designed to prevent microorganisms from
entering wounds as well as methods for treating instruments and surgical
dressings
• his patients had fewer postoperative infections 37
Final Proof…

• Robert Koch (1843-1910)

– established the relationship
between Bacillus anthracis and
anthrax
– used criteria developed by his
teacher Jacob Henle (1809-1895)
– these criteria now known as Koch’s
postulates
• still used today to establish the
link between a particular
microorganism and a particular
disease

38
Koch’s Experimentation
1. Koch developed a staining technique to
examine human tissue. Mycobacterium
tuberculosis could be identified in
diseased tissue.
2. Koch grew M. tuberculosis in pure
culture on coagulated blood serum.
3. Koch injected cells from the pure culture
of M. tuberculosis into guinea pigs. The
guinea pigs subsequently died of
tuberculosis.
4. Koch isolated M. tuberculosis in pure
culture on coagulated blood serum from
the dead guinea pigs 39
Koch’s Postulates

1. The microorganism must be present in every case of the disease

but absent from healthy organisms.
2. The suspected microorganisms must be isolated and grown in a
pure culture.
3. The same disease must result when the isolated microorganism
is inoculated into a healthy host.
4. The same microorganisms must be isolated again from the
diseased host.

40
 41
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 Limitations of Koch’s Postulates
1. Some infectious agents cannot be readily isolated or grown in the
laboratory
• Treponema pallidum (syphillis)
• Mycobacterium leprae (leprosy)
2. Infected individuals do not always have symptoms
• Examples: Polio, Cholera
3. Suitable animal hosts not always available for testing
4. Some pathogens may cause several different diseases (polymicrobial
diseases)
• Streptococcus pyogenes: Scarlet fever, sore throat, skin infections, bone
infections, etc.
• Mycobacterium tuberculosis: Causes disease of lungs, skin, bones, and
internal organs
The Development of Techniques for Studying Microbial Pathogens

• Koch’s work led to discovery or development of:

– agar
– Petri dishes
– nutrient broth and nutrient agar
– methods for isolating microorganisms

43
Other Developments…

 Charles Chamberland (1851-1908)

• developed porcelain bacterial filters used by Ivanoski and Beijerinck to
study tobacco mosaic disease
• determined that extracts from diseased plants had infectious agents
present which were smaller than bacteria and passed through the
filters
• infectious agents were eventually shown to be viruses
 Edward Jenner (ca. 1798)
• used a vaccination procedure to protect individuals from smallpox
 Pasteur and his coworkers
• developed vaccines for chicken cholera, anthrax, and rabies
44
Golden Age of Microbiology

 As spontaneous generation was disproved, Golden Age of

Microbiology was born
 The principle that microorganisms cause diseases is known as
Germ Theory of Disease.
• Most pathogenic bacteria identified (1875–1918)
• Work on viruses began
• Understanding that microscopic agents could cause disease led
to control efforts
• Huge improvements in past century in human health
• Antibiotics to treat infectious diseases
• Vaccines to prevent diseases
Historical Events in Microbiology

 Some major
milestones in
microbiology in
relation to other
historical
events
 The Scientific Method

1. Make an observation
2. Develop a testable explanation called an hypothesis
3. Design experiments to test the hypothesis
4. Do the experiment, collect and analyze data
5. Draw a conclusion
6. Communicate methods, results and conclusions
 A scientific theory is an explanation supported by a large
amount of evidence.
 Microbiology: A Human Perspective

 We could not survive without microorganisms

 Numerous benefits
 Examples include nitrogen fixation, oxygen production,
degradation of materials (e.g., cellulose, also sewage
and wastewater)
 But microorganisms have also killed more people than
have ever been killed in war
 Have even been used as weapons and could be used in
bioterrorism attacks
 Host-Microbe Interactions

 All surfaces of human body populated by microorganisms

 Beneficial microbes
• Termed normal microbiota or normal flora
• Prevent diseases by competing with pathogens
• Development of immune system response
• Aid in digestion
 Pathogens
• Damage body tissues  disease symptoms
 Microorganisms in the Environment

 Recycling of nutrients
 Oxygen production through photosynthesis
 Nitrogen fixation
 Decomposers of material
• Cellulose degraded in the environment and in the
digestive tracts of ruminants
 Applications of Microbiology

 Food production
• Baking bread using yeast
• Egyptian bakers as early as 2100 B.C.
• Fermentation of grains to produce beer
• Egyptian tombs revealed as early as 1500 B.C.
• Fermentation of milk  yogurt, cheeses, buttermilk
 Biodegradation
• Degrade PCBs, DDT, trichloroethylene and others
• Help clean up oil spills
• Bioremediation: using microorganisms to hasten decay of pollutants
Applications of Microbiology

 Bacteria synthesize commercially valuable products

 Examples include:
• Cellulose (stereo headsets)
• Hydroxybutyric acid (manufacture of disposable diapers and
plastics)
• Ethanol (biofuel)
• Hydrogen gas (possible biofuel)
• Oil (possible biofuel)
• Insect toxins (insecticides)
• Antibiotics (treatment of disease)
• Amino acids (dietary supplements)
Applications of Microbiology

 Biotechnology
• Use of microbiological and biochemical techniques to
solve practical problems
 Genetic engineering
• Introduction of genes into another organism
• Disease-resistant plants
• Production of medications (e.g., insulin for diabetes)
Microorganisms as Model Organisms

 Wonderful model organisms

• Metabolism, genetics same as higher life-forms
• All cells composed of same elements
• Synthesize structures in similar ways
• Replicate DNA
• Degrade foods via metabolic pathways
• “What is true of elephants is also true of bacteria, and
bacteria are much easier to study” (Nobel Prize–
winning microbiologist Dr. Jacques Monod)
Medical Microbiology

 Most microorganisms are not harmful

 Some are pathogens
• Cause disease
• Influenza in 1918–1919 killed more Americans than died in WWI,
WWII, Korean, Vietnam, and Iraq wars combined

• Modern sanitation, vaccination,

and effective antimicrobial
treatments have reduced
incidences of the worst diseases
Past Triumphs

 Viral disease smallpox once a leading killer

• ~10 million deaths over 4,000 years
• Devastating on unexposed populations (e.g., Aztecs in New
World)
• Worldwide eradication attempts eliminated disease
• No reported cases since 1977
 Plague another major killer in history
• ~1/3 of population of Europe (or ~25 million individuals) died
between 1346–1350
• Today, fewer than 100 die worldwide
• Control of rodent population harboring bacterium
• Antibiotics available
Present and Future Challenges

 Despite impressive progress, much work remains

• Especially true for viral diseases and diseases associated
with poverty
• Respiratory infections, diarrheal diseases cause most
illness and deaths in world today
 In United States, ~750 million infections
• ~200,000 deaths
• Cost in tens of billions of dollars
 Present and Future Challenges

 Emerging diseases continue to arise

2019
SARS-COV-2 (COVID-
19)-China
Present and Future Challenges
 Emerging diseases
• Most newly recognized
• Multiple examples
• Monkey Pox
• Severe acute respiratory syndrome (SARS-COV-2)
• Swine flu
• Multidrug-resistant tuberculosis
• Lyme disease
• Hepatitis C
• Acquired immunodeficiency syndrome (AIDS)
• Hemolytic uremic syndrome (E coli O157:H7)
• Hantavirus pulmonary syndrome
• Mad cow disease
• West Nile encephalitis
• Ebola virus
Present and Future Challenges

 Emerging diseases
• Changing lifestyles increase opportunities to spread
• Closer contact with animals (e.g., hantavirus)
• Evolution of infectious agents previously unable to infect humans
(e.g., HIV/AIDS, SARS, Ebola virus)
 Re-emerging diseases
• Vaccination can become victim of own success
• Lack of firsthand knowledge of dangers of diseases can lead people
to fear vaccines more than the diseases
• Diseases such as measles, mumps, whooping cough nearly
eradicated from U.S. but could re-emerge with declining
vaccination rates
 Present and Future Challenges

 Emerging diseases
• Pathogens can become resistant to antimicrobial medications (e.g.,
tuberculosis, malaria)
• Increased travel and immigration
• Many diseases eliminated from developed countries still exist in
many parts of world (e.g., malaria, cholera, plague, yellow fever)
• Changes in population
• Weakened immune systems (e.g., elderly, HIV/AIDS)
• Chronic diseases may be caused by bacteria
• E.g., peptic ulcers caused by Helicobacter pylori
• Possibly indigestion, Crohn’s disease, others
Second Golden Age of Microbiology

 Less than 1% of prokaryotes ever studied

 Most do not grow in lab
 New sequencing approaches revealing enormous
biodiversity of microbial world
• E.g., 1,800 new bacterial species found in Sargasso
Sea
 Major challenges remain
 Exploring microbial world should answer many
fundamental biological questions
-END-