Microbiology lecture 1 13-4-2021
Chapter 1:
Microbe – microorganism
• A microbe is commonly defined as a living organism that can be seen by a microscope
(traditional) that range from millimeters in size to 0.2 micrometers.
• There are several contradictions to this definition, including super-sized
microbial cells, microbial communities, and viruses
• A genetic definition includes single-celled organisms that derived from a single
ancestor.
• Includes prokaryotes (bacteria and archaea), and certain eukaryotes (algae,
fungi, and protozoa).
KEY microbiology events
• 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 defines 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 (first antibiotic) is made by fungus (1929)
• William Costerton describe biofilms as the major form of existence of microbes
(1978)
First sequenced genome
bacteria
Robert Koch’s postulates link between infection and disease
• 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
1
, • 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 immunization
• 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 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/antibiotics
• Vaccines work against viruses, in that they utilize the virus infection mechanism to
produce the antibodies against them. – ineffective against live bacteria
• Antiseptics come in two forms: physical and chemical
• Physical antiseptics usually include heat (burner flame, autoclave)
• Chemical antiseptics are molecules that kill not only bacteria, but also the
host if ingested. (f.e. ethanol for cleaning surfaces)
• Antibiotics 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.
Support ecosystems
• 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 biofilm, any or all of these environments can exist
simultaneously.
endosymbiosis & Nitrogen
cycle
five kingdom scheme
2
,Three kingdom scheme (tree of life)
• Eukarya (eukaryotes) – multi-celled organisms
• 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
Proposed by Carl Woese
Chapter 2:
The microbial cell gram positive/ gram negative
Bacterial cell shapes and arrangements
The gram stain
3
, Chapter 3:
The microbial cell
• 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:
• Thick, complex outer envelope (cell wall or membrane, with or without thick
peptidoglycan layer)
• Compact genome
• 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 cell
• Water, 70% by mass
• Proteins, 16% by mass
• RNA, 6% by mass (0.7% mRNA)
• Phospholipids (membrane) 3% by mass
• Lipopolysaccharides (outer membrane) 1% by mass
• DNA, 1% by mass
• In biofilms, the water content of the structure can be closer to 80 – 90% water.
Cell Fractionation
• 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).
Membrane components
• Membrane lipids (phospholipids) form a bilayer that separates water environments
of the internal cell and surrounding exterior environment
• Membrane proteins
• Provide structural support
• Detect environmental signals
• Secrete virulence factors and communication signals
• Function with ion transport and energy storage
• Thick peptidoglycan structure is a target for several antibiotics (against gram positive
bacteria)
Methods of transport across the membrane
• Passive diffusion – small, uncharged molecules
4
Chapter 1:
Microbe – microorganism
• A microbe is commonly defined as a living organism that can be seen by a microscope
(traditional) that range from millimeters in size to 0.2 micrometers.
• There are several contradictions to this definition, including super-sized
microbial cells, microbial communities, and viruses
• A genetic definition includes single-celled organisms that derived from a single
ancestor.
• Includes prokaryotes (bacteria and archaea), and certain eukaryotes (algae,
fungi, and protozoa).
KEY microbiology events
• 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 defines 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 (first antibiotic) is made by fungus (1929)
• William Costerton describe biofilms as the major form of existence of microbes
(1978)
First sequenced genome
bacteria
Robert Koch’s postulates link between infection and disease
• 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
1
, • 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 immunization
• 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 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/antibiotics
• Vaccines work against viruses, in that they utilize the virus infection mechanism to
produce the antibodies against them. – ineffective against live bacteria
• Antiseptics come in two forms: physical and chemical
• Physical antiseptics usually include heat (burner flame, autoclave)
• Chemical antiseptics are molecules that kill not only bacteria, but also the
host if ingested. (f.e. ethanol for cleaning surfaces)
• Antibiotics 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.
Support ecosystems
• 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 biofilm, any or all of these environments can exist
simultaneously.
endosymbiosis & Nitrogen
cycle
five kingdom scheme
2
,Three kingdom scheme (tree of life)
• Eukarya (eukaryotes) – multi-celled organisms
• 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
Proposed by Carl Woese
Chapter 2:
The microbial cell gram positive/ gram negative
Bacterial cell shapes and arrangements
The gram stain
3
, Chapter 3:
The microbial cell
• 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:
• Thick, complex outer envelope (cell wall or membrane, with or without thick
peptidoglycan layer)
• Compact genome
• 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 cell
• Water, 70% by mass
• Proteins, 16% by mass
• RNA, 6% by mass (0.7% mRNA)
• Phospholipids (membrane) 3% by mass
• Lipopolysaccharides (outer membrane) 1% by mass
• DNA, 1% by mass
• In biofilms, the water content of the structure can be closer to 80 – 90% water.
Cell Fractionation
• 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).
Membrane components
• Membrane lipids (phospholipids) form a bilayer that separates water environments
of the internal cell and surrounding exterior environment
• Membrane proteins
• Provide structural support
• Detect environmental signals
• Secrete virulence factors and communication signals
• Function with ion transport and energy storage
• Thick peptidoglycan structure is a target for several antibiotics (against gram positive
bacteria)
Methods of transport across the membrane
• Passive diffusion – small, uncharged molecules
4
