Lecture 1, introduction lectur
What is a microbe
Microbe de ned
• A microbe is commonly de ned as a living organism that can be seen by a microscope
(traditional) that range from millimetres in size to 0.2 micrometres. There are several
contradictions to this de nition, including super-sized microbial cells, microbial
communities, and viruses
- A genetic de nition includes single-celled organisms that derived from a single ancestor
Includes prokaryotes (bacteria and archaea), and certain eukaryotes (algae, fungi, and
protozoa)
Key Microbiology Event
Robert Hooke observes the microscopic world (1665
Antonie van Leeuwenhoek observes bacteria with a single lens (1676
Agostino Bassi de Lodi noted cases of microbes associated with pathology (1835
Ignaz Semmelweis observes chlorine reduces pathogens on doctors’ hands (1847
Florence Nightingale shows statistical correlation of sanitation and mortality (1855
Louis Pasteur notes that microbes did not appear spontaneously, and can produce lactic
acid or alcohol (1864, 1857
Ernst Haeckel de nes microbes in a different class than plants and animals (1866
John Tyndall observes that bacterial spores survive boiling, but are killed by cyclic boiling
and cooling (1881
Alexander Flemming discovers penicillin ( rst antibiotic) is made by fungus (1929
William Costerton describe bio lms as the major form of existence of microbes (1978
First sequenced genome
Haemophilus in uenza
Robert Koch’s postulates
Link between infection and diseas
1. The microbe is found in all cases of the disease but is absent from the healthy
individual
2. The microbe is isolated from the diseased host and grown in pure culture
3. When the microbe is introduced into a healthy, susceptible host, the host shows the
same disease
4. The same strain of microbe is obtained from the newly diseased host. When cultured, it
shows the same characteristics as before
Louis Pasteur and Immunizatio
Louis Pasteur is more famous for his work on Immunizations and the smallpox virus.
Given the situation with COVID, and vaccinations, the usefulness of vaccines against
viruses are highly relevant (despite not being microbes).
- Most vaccines inject a damaged or dead (inactivated) virus into the host, so that the
immune system can attack the weakened virus and create antibodies.
- A recent development of mRNA vaccines for COVID skip the recognition phase and help
the host produce the protective proteins
Vaccines vs. Antiseptics/antibiotic
• Vaccines work against viruses, in that they utilize the virus infection mechanism to
produce the antibodies against them. –> ineffective against live bacteri
• Antiseptics (used to clean surfaces) come in two forms: physical and chemica
- Physical antiseptics usually include heat (burner ame, autoclave
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, - Chemical antiseptics are molecules kill not only bacteria, but also the host if ingested
• Antibiotics (usually formed by living organisms) are chemicals that would kill the
microbes but leave the host unharmed. Due to host variability, this has been adapted for
killing > 99.9% of microbes. If this percentage is less than 99.9%, it is known as
antimicrobials (instead of antibiotics)
Support Ecosystem
• Aerobic environments are abundant with oxygen
• Microaerophilic environments have reduced oxygen levels and may led to multiple forms
of metabolism
- Capnophilic (CO2 loving) environments are a form of microaerophilic environments.
• Anaerobic environments are lacking in oxygen
• Strict anaerobic environments are completely void of oxygen (oxygen is lethal)
Within a growing bio lm, any or all of these environments can exist simultaneously
Serial Endosymbiosis Theor
1. A prokaryote ingested some aerobic bacteria. The aerobes were. Protected and
produced energy fo the prokaryote
2. Over a long time, the aerobes become mitochondria, no longer able to live on their
own (animal cell)
3. Some primitive prokaryotes also ingested cyanobacteria, which contain photosynthetic
pigments
4. The cyanobacteria become chloroplasts, no longer able to live other own (plant cell)
Five Kingdom Schem
Three Kingdom Scheme (Tree of Life
• Eukarya (eukaryotes) – multi-celled organism
• Bacteria (common bacteria) – single celled organisms, of which proteobacteria
(mitochondria) and cyanobacteria (chloroplasts) were derived
• Archaea – (rare bacteria) including thermophiles, sulfur oxidizers, that are not
susceptible to antibiotics
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, Bacterial Cell Shapes and Arrangements
The microbial cel
Gram positive and gram negative bacteria. Main difference is layer of Peptidoglycan
layer in gram positive bacteria (also in negative but much thinner). Antibiotics attack the
gram positive bacteria because of the thick Peptidoglycan layer and they will leave gram
negative alone. Therefore, selective targeting can be used. Gram negatives are easier to
kill because of the thin layer, so we don’t need antibiotics for these ones
To grow and multiply, a microbial cell must obtain nutrients faster than its competitors (or
share them for mutual advantage, like symbiotes with plants
Most bacteria share these 3 traits
1. Thick, complex outer envelope (cell wall or membrane, with or without thick
peptidoglycan layer)
2. Compact genome
3. Tightly coordinated functions
In contrast
- Archaea have unique membrane and envelope structures to allow survival in extremes
- Eukaryotic cells have extensive membranous (internal) organelles
Components of an average Bacterial Cel
• Water, 70% by mas
• Proteins, 16% by mas
• RNA, 6% by mass (0.7% mRNA
• Phospholipids (membrane) 3% by mas
• Lipopolysaccharides (outer membrane) 1% by mas
• DNA, 1% by mas
In bio lms, the water content of the structure can be closer to 80 – 90% water
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, Cell Fractionatio
It is possible to separate components of a cell based on their mass
- Ultra-centrifugation techniques (high speed) are used to pellet heavier components,
while leaving the lighter components in suspension
- After removing the heavier pellet, the centrifuge speed is increased and a lighter
component is next pelleted. (repeated for all interesting components
Protein separation in gels (SDS-PAGE) works in a similar manner (diffusion, rather than
centrifugation) (separated by charge)
Membrane component
• Membrane lipids (phospholipids) form a bilayer that separates water environments of the
internal cell and surrounding exterior environmen
• Membrane protein
- Provide structural suppor
- Detect environmental signal
- Secrete virulence factors and communication signal
- Function with ion transport and energy storag
Thick peptidoglycan structure is a target for several antibiotics (against gram positive
bacteria
Methods of Transport Across the Membran
• Passive diffusion –> small, uncharged molecules
• Osmosis –> concentration of water balance (internal and external) known as osmotic
pressure
• Membrane permeant weak acids/bases –> cross in uncharged form
• Transmembrane ion gradients –> require transfer proteins to move across membran
- Passive –> move according to concentration gradien
- Active –> move against concentration gradient and requires energ
DNA Transcription and RNA Translation to Proteins (Antibiotics that attack this proces
- Rifampin blocks RNA polymeras
- Tetracycline binds ribosome 30S and blocks tRN
- Erythromycin binds ribosome 50S and blocks peptide elongatio
Specialized Structures on Bacteri
- Adhesion structures: pili and stalk
- Movement structure: rotary agell
Nutrient Supplies limit Growt
• Bacteria have a simple purpose: survive and growth.
- In the absence of nutrients, bacteria go into “survival” mode
- In the abundance of nutrients, bacteria go into a “replication” mode
- Heterotrophy uses nutrients to produce CO
- Autotrophy uses CO2 to produce nutrient
Life Cycle of Bacteria Cultur
- Lag phase: small number of bacteria may be replicating, but mostly stays the sam
- Log phase (exponential phase): lots of bacteria are doubling/replicatin
- Stationary phase: More bacteria use the nutrients, so replicating stops
- Death phase: Not enough nutrients to overcome the toxins so bacteria die
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What is a microbe
Microbe de ned
• A microbe is commonly de ned as a living organism that can be seen by a microscope
(traditional) that range from millimetres in size to 0.2 micrometres. There are several
contradictions to this de nition, including super-sized microbial cells, microbial
communities, and viruses
- A genetic de nition includes single-celled organisms that derived from a single ancestor
Includes prokaryotes (bacteria and archaea), and certain eukaryotes (algae, fungi, and
protozoa)
Key Microbiology Event
Robert Hooke observes the microscopic world (1665
Antonie van Leeuwenhoek observes bacteria with a single lens (1676
Agostino Bassi de Lodi noted cases of microbes associated with pathology (1835
Ignaz Semmelweis observes chlorine reduces pathogens on doctors’ hands (1847
Florence Nightingale shows statistical correlation of sanitation and mortality (1855
Louis Pasteur notes that microbes did not appear spontaneously, and can produce lactic
acid or alcohol (1864, 1857
Ernst Haeckel de nes microbes in a different class than plants and animals (1866
John Tyndall observes that bacterial spores survive boiling, but are killed by cyclic boiling
and cooling (1881
Alexander Flemming discovers penicillin ( rst antibiotic) is made by fungus (1929
William Costerton describe bio lms as the major form of existence of microbes (1978
First sequenced genome
Haemophilus in uenza
Robert Koch’s postulates
Link between infection and diseas
1. The microbe is found in all cases of the disease but is absent from the healthy
individual
2. The microbe is isolated from the diseased host and grown in pure culture
3. When the microbe is introduced into a healthy, susceptible host, the host shows the
same disease
4. The same strain of microbe is obtained from the newly diseased host. When cultured, it
shows the same characteristics as before
Louis Pasteur and Immunizatio
Louis Pasteur is more famous for his work on Immunizations and the smallpox virus.
Given the situation with COVID, and vaccinations, the usefulness of vaccines against
viruses are highly relevant (despite not being microbes).
- Most vaccines inject a damaged or dead (inactivated) virus into the host, so that the
immune system can attack the weakened virus and create antibodies.
- A recent development of mRNA vaccines for COVID skip the recognition phase and help
the host produce the protective proteins
Vaccines vs. Antiseptics/antibiotic
• Vaccines work against viruses, in that they utilize the virus infection mechanism to
produce the antibodies against them. –> ineffective against live bacteri
• Antiseptics (used to clean surfaces) come in two forms: physical and chemica
- Physical antiseptics usually include heat (burner ame, autoclave
1
.
fi fi.
fl )
?
fi e
s
fi .
fi)
n
e
fi s
e
.
.
fi fl )
)
a
)
.
l
)
)
)
)
.
, - Chemical antiseptics are molecules kill not only bacteria, but also the host if ingested
• Antibiotics (usually formed by living organisms) are chemicals that would kill the
microbes but leave the host unharmed. Due to host variability, this has been adapted for
killing > 99.9% of microbes. If this percentage is less than 99.9%, it is known as
antimicrobials (instead of antibiotics)
Support Ecosystem
• Aerobic environments are abundant with oxygen
• Microaerophilic environments have reduced oxygen levels and may led to multiple forms
of metabolism
- Capnophilic (CO2 loving) environments are a form of microaerophilic environments.
• Anaerobic environments are lacking in oxygen
• Strict anaerobic environments are completely void of oxygen (oxygen is lethal)
Within a growing bio lm, any or all of these environments can exist simultaneously
Serial Endosymbiosis Theor
1. A prokaryote ingested some aerobic bacteria. The aerobes were. Protected and
produced energy fo the prokaryote
2. Over a long time, the aerobes become mitochondria, no longer able to live on their
own (animal cell)
3. Some primitive prokaryotes also ingested cyanobacteria, which contain photosynthetic
pigments
4. The cyanobacteria become chloroplasts, no longer able to live other own (plant cell)
Five Kingdom Schem
Three Kingdom Scheme (Tree of Life
• Eukarya (eukaryotes) – multi-celled organism
• Bacteria (common bacteria) – single celled organisms, of which proteobacteria
(mitochondria) and cyanobacteria (chloroplasts) were derived
• Archaea – (rare bacteria) including thermophiles, sulfur oxidizers, that are not
susceptible to antibiotics
2
.
.
.
s
e
fi .
y
.
.
)
s
.
.
.
.
.
.
.
, Bacterial Cell Shapes and Arrangements
The microbial cel
Gram positive and gram negative bacteria. Main difference is layer of Peptidoglycan
layer in gram positive bacteria (also in negative but much thinner). Antibiotics attack the
gram positive bacteria because of the thick Peptidoglycan layer and they will leave gram
negative alone. Therefore, selective targeting can be used. Gram negatives are easier to
kill because of the thin layer, so we don’t need antibiotics for these ones
To grow and multiply, a microbial cell must obtain nutrients faster than its competitors (or
share them for mutual advantage, like symbiotes with plants
Most bacteria share these 3 traits
1. Thick, complex outer envelope (cell wall or membrane, with or without thick
peptidoglycan layer)
2. Compact genome
3. Tightly coordinated functions
In contrast
- Archaea have unique membrane and envelope structures to allow survival in extremes
- Eukaryotic cells have extensive membranous (internal) organelles
Components of an average Bacterial Cel
• Water, 70% by mas
• Proteins, 16% by mas
• RNA, 6% by mass (0.7% mRNA
• Phospholipids (membrane) 3% by mas
• Lipopolysaccharides (outer membrane) 1% by mas
• DNA, 1% by mas
In bio lms, the water content of the structure can be closer to 80 – 90% water
3
fi :
l
s
.
s
.
s
.
)
:
s
l
s
)
.
.
.
.
, Cell Fractionatio
It is possible to separate components of a cell based on their mass
- Ultra-centrifugation techniques (high speed) are used to pellet heavier components,
while leaving the lighter components in suspension
- After removing the heavier pellet, the centrifuge speed is increased and a lighter
component is next pelleted. (repeated for all interesting components
Protein separation in gels (SDS-PAGE) works in a similar manner (diffusion, rather than
centrifugation) (separated by charge)
Membrane component
• Membrane lipids (phospholipids) form a bilayer that separates water environments of the
internal cell and surrounding exterior environmen
• Membrane protein
- Provide structural suppor
- Detect environmental signal
- Secrete virulence factors and communication signal
- Function with ion transport and energy storag
Thick peptidoglycan structure is a target for several antibiotics (against gram positive
bacteria
Methods of Transport Across the Membran
• Passive diffusion –> small, uncharged molecules
• Osmosis –> concentration of water balance (internal and external) known as osmotic
pressure
• Membrane permeant weak acids/bases –> cross in uncharged form
• Transmembrane ion gradients –> require transfer proteins to move across membran
- Passive –> move according to concentration gradien
- Active –> move against concentration gradient and requires energ
DNA Transcription and RNA Translation to Proteins (Antibiotics that attack this proces
- Rifampin blocks RNA polymeras
- Tetracycline binds ribosome 30S and blocks tRN
- Erythromycin binds ribosome 50S and blocks peptide elongatio
Specialized Structures on Bacteri
- Adhesion structures: pili and stalk
- Movement structure: rotary agell
Nutrient Supplies limit Growt
• Bacteria have a simple purpose: survive and growth.
- In the absence of nutrients, bacteria go into “survival” mode
- In the abundance of nutrients, bacteria go into a “replication” mode
- Heterotrophy uses nutrients to produce CO
- Autotrophy uses CO2 to produce nutrient
Life Cycle of Bacteria Cultur
- Lag phase: small number of bacteria may be replicating, but mostly stays the sam
- Log phase (exponential phase): lots of bacteria are doubling/replicatin
- Stationary phase: More bacteria use the nutrients, so replicating stops
- Death phase: Not enough nutrients to overcome the toxins so bacteria die
4
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