Microbiology: study of microbes
Microbes: too small to see clearly be unaided eye
Pathogens: cause infectious disease
Children = most vulnerable as have less developed immune system, LMIC
Bacteria in Food:
+ Cycle carbon + phosphate + Food requires microbial activity
- Food borne disease + Food spoilage
3 Domains:
1. Bacteria:
• Disease causing prokaryotes
• First life forms on earth
• Size depends on nutrient availability
2. Archaea:
• Different molecular organisation to bacteria
• No peptidoglycan in cell wall
• Largely proteinaceous coat
• Ether linked lipids built from peptide chains
• Anaerobes + some obligate anaerobes
• Produce methane
3. Eukaryota:
All organisms except bacteria + blue-green fungi
Cellular properties: compartmentalisation, metabolism, evolution
Some cells: motility, differentiation, communication
Microbial cell sizes:
Viruses 0.01-0.2um
Bacteria 0.2-5um
Yeast 5 – 10um
Eukaryotes 5-100um
Algae 10-100um
Protists 50-1000um
Smaller cells = faster rate of nutrient exchange = faster growth = faster mutation rate = greater
evolutionary possibilities
Bacterial Cell Membrane:
• Positive inside cell
➔ Protein anchor
➔ Prevents bursting
➔ Respiration + photosynthesis
Bacterial Cell Wall:
• Coccus, rod, spirillum, librio, spirochete, filamentous, stalk, hypha
• Diplococci/streptococci
➔ Prevents osmotic lysis
1. Gram +ve: thick peptidoglycan, lipoteichoic + teichoic acid, wall associated proteins
Retains dye -> purple
2. Gram -ve: thin peptidoglycan, outer membrane = lipids, proteins, lipopolysaccharides
, Dye washed out -> pink
3. Mycobacterial: thin peptidoglycan, mycolic acid
4. Archaeal: pseudopeptidoglycan, S-layer = proteins + glycoproteins
Gram staining: crystal violet stain -> add iodine -> wash with ethanol -> counter stain with
safranin
Peptidoglycan structure: GM polymer linked via peptide bridges
G (N-Acetylglucosamine) + M (N-Acetylmuramic acid
G + M are alternating
Lysozymes -> break peptide bond -> cell wall loses structure -> kills bacteria
Capsule: made of polysaccharides
➔ Increases size -> protect from phagocytisus
➔ Protects from desiccation
➔ Surface attachment
Fimbriae: short, thin, hair-like appendages
➔ Recognition + surface attachment
Flagella: made of flagellin protein
1. Monotrichous: 1 polar flagellum
2. Amphitrichous: 1 flagellum at each pole
3. Lophotrichous: cluster of flagellum at 1 or both poles
4. Peritrichous: flagella spread out over entire cell surface
Pili: long, thick + less numerous hair-like appendages made of pili protein
➔ Surface attachment
➔ Sex pili: pass genetic material
Bacterial Cytoplasm: gelatinous material = ribosomes, nucleoid, cellular inclusions, macromolecules,
organic molecules, inorganic ions
Nucleoid: irregularly shaped region containing genophore
Plasmid: small circles of DNA + replicate independently of nucleoid
➔ Transfer DNA between species
Cellular inclusions: granules of organic + inorganic material reserved for the future e.g. glycogen,
sulphur + polyphosphate granules
Magnetosomes: store Fe in magnetite form in some pecialist bacteria
➔ Orients cells in magnetic fields
Gas Vesicles: arranged in bundles -> buoyancy e.g. cyanobacteria
Endospores: produced by some gram-ve bacteria -> survival mechanism
Cell differentiates -> spores -> chromosome + other survival apparatus migrates into spore ->
spore attaches to surface + waits for adverse conditions to end
+ Survive long time
+ Stores sulphur
+ Resistance to drying, radiation + chemicals
+ Specialised proteins protect DNA
+ Contain calcium carbonate CaCO3 -> binds to H2O molecules -> dehydrates endospore ->
stabilises DNA
Prokaryote Eukaryote
Cell size < 5um >5um
Number of chromosomes 1-2 >1
, Cell wall Thin + peptidoglycan Thick (plant cells) or absent
Ribosomes in cytoplasm 70S 80S
Ribosomes within organelles No 70S
Cilia No Yes
Flagella Helical arrangement 9:2 Fibril arrangement
Cell division Binary Fission Mitosis
Nutrients: provide all elements involved in cell membrane synthesis
Macroelements: required in large amounts in all cells
C, O, H, N, P -> amino acids, DNA, carbohydrates
S (cysteine, methionine), K (enzyme activity), Ca (cell wall stability), Mg (ribosomes, membrane), Fe
(ET proteins)
Microelements: required in small amounts by some organisms e.g. Cu, Zn, Ni
Bacterial Sampling:
Culture media: nutrient solutions containing all elements required for growth
Chemically defined media: exact chemical composition known
Complex media: digests of complex material – exact chemical composition not known
Batch culture: grown in closed system
Bacterial growth: increase in cell numbers by binary fission
Streaking: produces isolated colonies of bacteria on agar plate
➔ Purification + allows biochemical tests + obtain appropriate colony numbers
Sterilise inoculating loop -> scrape some bacteria off colony -> spread it over agar plate = parallel
lines -> sterilise loop + repeat -> areas of high to low bacterial concentrations
Bacterial Growth:
Binary fission: DNA replication -< cell elongation -> septum formation -> cell separation
Generation time = doubling time
Ideal conditions = constant doubling time = exponential growth
Growth Curve: lag phase -> Log phase -> Stationary phase -> Death phase
VBNC = viable but not culturable -> still cause disease + have low metabolic activity due to stress
Direct microscopic count: uses species microscope counting slide -> count live + dead
1. Total count: stains all bacteria using non-specific dye
2. Viable count: counts active bacteria using fluorescent dye
3. Culturable count: counts cells that form colonies on solid media/ increase turbidity in liquid
media
Culturable count < viable count < direct count
Turbidity: cells scatter light passing through suspension
Antibiotics:
1. Bacteriostatic: stops growth
2. Bactericidal: kills bacteria -> cells still present
3. Bacteriolytic: bursts cells -> releases contents
Nutrient Types:
1. Heterotrophs: organic molecules from other organisms
2. Autotrophs: CO2 carbon source
3. Phototrophs: light -> ATP
4. Chemoorganotrophs: oxidises organic compounds -> ATP
, 5. Chemolithotrophs: oxidises inorganic compounds -> ATP
Oxygen:
1. Obligate aerobes: need O2
2. Obligate anaerobes: O2 = toxic
3. Facultative anaerobes: prefer O2 but don’t need it
4. Aerotolerant anaerobes: O2 has no effect
5. Microaerophilic: need O2 at low concentrations
Temperature:
1. Psychrophiles: 0-20
2. Mesophiles: 20-40
3. Thermophiles: 45-80
4. Hyperthermophiles: >80
pH: acidophiles, neutral zone, alkaliphiles
Osmolarity: solute concentration
1. Mild 1-6%
2. Moderate 7-15%
3. Extreme 15-30% = Halophiles (salt)
Bacterial Disease:
Pathogenicity; ability to cause disease
Virulence: degree of pathogenicity = invasiveness + toxicity = adhesins, invasins, toxins
Infection: bacteria persist in host
Disease: overt damage to host
Primary pathogens: cause disease in absence of immune defects
Opportunistic pathogen: only causes disease when host defences are impaired e.g. Clostridium
difficile (colon infection)
Kochs Postulates:
1. Microorganisms isolated from diseased animal
2. Grown in pure culture
3. Identified under microscope
4. Injected into healthy lab animal
5. Disease reproduces
6. Microorganisms isolated + grown in culture
7. Microorganism identified
Infection Cycle: reservoir -> host -> adherence -> colonisation -> tissue invasion -> tissue damage ->
reservoir/host
1. Reservoir: Pathogens must have 1+ reservoirs
2. Transmission:
a. Direct host-to-host transmission; aerosols, touching kissing
b. Indirect host-to-host transmission: vector borne (living) or vehicle (non-living)
transmission
3. Adherence: stick quickly to host cell surfaces
Streptococci -> adhere to teeth surfaces
Staphylococci -> adhere to shunts + plastic catheters
Non-specific forces -> bacterial adhesins + host receptors acts as anchor -> bacterial aggregation
produces biofilm -> biofilm disperses -> seed new infection sites
Microbes: too small to see clearly be unaided eye
Pathogens: cause infectious disease
Children = most vulnerable as have less developed immune system, LMIC
Bacteria in Food:
+ Cycle carbon + phosphate + Food requires microbial activity
- Food borne disease + Food spoilage
3 Domains:
1. Bacteria:
• Disease causing prokaryotes
• First life forms on earth
• Size depends on nutrient availability
2. Archaea:
• Different molecular organisation to bacteria
• No peptidoglycan in cell wall
• Largely proteinaceous coat
• Ether linked lipids built from peptide chains
• Anaerobes + some obligate anaerobes
• Produce methane
3. Eukaryota:
All organisms except bacteria + blue-green fungi
Cellular properties: compartmentalisation, metabolism, evolution
Some cells: motility, differentiation, communication
Microbial cell sizes:
Viruses 0.01-0.2um
Bacteria 0.2-5um
Yeast 5 – 10um
Eukaryotes 5-100um
Algae 10-100um
Protists 50-1000um
Smaller cells = faster rate of nutrient exchange = faster growth = faster mutation rate = greater
evolutionary possibilities
Bacterial Cell Membrane:
• Positive inside cell
➔ Protein anchor
➔ Prevents bursting
➔ Respiration + photosynthesis
Bacterial Cell Wall:
• Coccus, rod, spirillum, librio, spirochete, filamentous, stalk, hypha
• Diplococci/streptococci
➔ Prevents osmotic lysis
1. Gram +ve: thick peptidoglycan, lipoteichoic + teichoic acid, wall associated proteins
Retains dye -> purple
2. Gram -ve: thin peptidoglycan, outer membrane = lipids, proteins, lipopolysaccharides
, Dye washed out -> pink
3. Mycobacterial: thin peptidoglycan, mycolic acid
4. Archaeal: pseudopeptidoglycan, S-layer = proteins + glycoproteins
Gram staining: crystal violet stain -> add iodine -> wash with ethanol -> counter stain with
safranin
Peptidoglycan structure: GM polymer linked via peptide bridges
G (N-Acetylglucosamine) + M (N-Acetylmuramic acid
G + M are alternating
Lysozymes -> break peptide bond -> cell wall loses structure -> kills bacteria
Capsule: made of polysaccharides
➔ Increases size -> protect from phagocytisus
➔ Protects from desiccation
➔ Surface attachment
Fimbriae: short, thin, hair-like appendages
➔ Recognition + surface attachment
Flagella: made of flagellin protein
1. Monotrichous: 1 polar flagellum
2. Amphitrichous: 1 flagellum at each pole
3. Lophotrichous: cluster of flagellum at 1 or both poles
4. Peritrichous: flagella spread out over entire cell surface
Pili: long, thick + less numerous hair-like appendages made of pili protein
➔ Surface attachment
➔ Sex pili: pass genetic material
Bacterial Cytoplasm: gelatinous material = ribosomes, nucleoid, cellular inclusions, macromolecules,
organic molecules, inorganic ions
Nucleoid: irregularly shaped region containing genophore
Plasmid: small circles of DNA + replicate independently of nucleoid
➔ Transfer DNA between species
Cellular inclusions: granules of organic + inorganic material reserved for the future e.g. glycogen,
sulphur + polyphosphate granules
Magnetosomes: store Fe in magnetite form in some pecialist bacteria
➔ Orients cells in magnetic fields
Gas Vesicles: arranged in bundles -> buoyancy e.g. cyanobacteria
Endospores: produced by some gram-ve bacteria -> survival mechanism
Cell differentiates -> spores -> chromosome + other survival apparatus migrates into spore ->
spore attaches to surface + waits for adverse conditions to end
+ Survive long time
+ Stores sulphur
+ Resistance to drying, radiation + chemicals
+ Specialised proteins protect DNA
+ Contain calcium carbonate CaCO3 -> binds to H2O molecules -> dehydrates endospore ->
stabilises DNA
Prokaryote Eukaryote
Cell size < 5um >5um
Number of chromosomes 1-2 >1
, Cell wall Thin + peptidoglycan Thick (plant cells) or absent
Ribosomes in cytoplasm 70S 80S
Ribosomes within organelles No 70S
Cilia No Yes
Flagella Helical arrangement 9:2 Fibril arrangement
Cell division Binary Fission Mitosis
Nutrients: provide all elements involved in cell membrane synthesis
Macroelements: required in large amounts in all cells
C, O, H, N, P -> amino acids, DNA, carbohydrates
S (cysteine, methionine), K (enzyme activity), Ca (cell wall stability), Mg (ribosomes, membrane), Fe
(ET proteins)
Microelements: required in small amounts by some organisms e.g. Cu, Zn, Ni
Bacterial Sampling:
Culture media: nutrient solutions containing all elements required for growth
Chemically defined media: exact chemical composition known
Complex media: digests of complex material – exact chemical composition not known
Batch culture: grown in closed system
Bacterial growth: increase in cell numbers by binary fission
Streaking: produces isolated colonies of bacteria on agar plate
➔ Purification + allows biochemical tests + obtain appropriate colony numbers
Sterilise inoculating loop -> scrape some bacteria off colony -> spread it over agar plate = parallel
lines -> sterilise loop + repeat -> areas of high to low bacterial concentrations
Bacterial Growth:
Binary fission: DNA replication -< cell elongation -> septum formation -> cell separation
Generation time = doubling time
Ideal conditions = constant doubling time = exponential growth
Growth Curve: lag phase -> Log phase -> Stationary phase -> Death phase
VBNC = viable but not culturable -> still cause disease + have low metabolic activity due to stress
Direct microscopic count: uses species microscope counting slide -> count live + dead
1. Total count: stains all bacteria using non-specific dye
2. Viable count: counts active bacteria using fluorescent dye
3. Culturable count: counts cells that form colonies on solid media/ increase turbidity in liquid
media
Culturable count < viable count < direct count
Turbidity: cells scatter light passing through suspension
Antibiotics:
1. Bacteriostatic: stops growth
2. Bactericidal: kills bacteria -> cells still present
3. Bacteriolytic: bursts cells -> releases contents
Nutrient Types:
1. Heterotrophs: organic molecules from other organisms
2. Autotrophs: CO2 carbon source
3. Phototrophs: light -> ATP
4. Chemoorganotrophs: oxidises organic compounds -> ATP
, 5. Chemolithotrophs: oxidises inorganic compounds -> ATP
Oxygen:
1. Obligate aerobes: need O2
2. Obligate anaerobes: O2 = toxic
3. Facultative anaerobes: prefer O2 but don’t need it
4. Aerotolerant anaerobes: O2 has no effect
5. Microaerophilic: need O2 at low concentrations
Temperature:
1. Psychrophiles: 0-20
2. Mesophiles: 20-40
3. Thermophiles: 45-80
4. Hyperthermophiles: >80
pH: acidophiles, neutral zone, alkaliphiles
Osmolarity: solute concentration
1. Mild 1-6%
2. Moderate 7-15%
3. Extreme 15-30% = Halophiles (salt)
Bacterial Disease:
Pathogenicity; ability to cause disease
Virulence: degree of pathogenicity = invasiveness + toxicity = adhesins, invasins, toxins
Infection: bacteria persist in host
Disease: overt damage to host
Primary pathogens: cause disease in absence of immune defects
Opportunistic pathogen: only causes disease when host defences are impaired e.g. Clostridium
difficile (colon infection)
Kochs Postulates:
1. Microorganisms isolated from diseased animal
2. Grown in pure culture
3. Identified under microscope
4. Injected into healthy lab animal
5. Disease reproduces
6. Microorganisms isolated + grown in culture
7. Microorganism identified
Infection Cycle: reservoir -> host -> adherence -> colonisation -> tissue invasion -> tissue damage ->
reservoir/host
1. Reservoir: Pathogens must have 1+ reservoirs
2. Transmission:
a. Direct host-to-host transmission; aerosols, touching kissing
b. Indirect host-to-host transmission: vector borne (living) or vehicle (non-living)
transmission
3. Adherence: stick quickly to host cell surfaces
Streptococci -> adhere to teeth surfaces
Staphylococci -> adhere to shunts + plastic catheters
Non-specific forces -> bacterial adhesins + host receptors acts as anchor -> bacterial aggregation
produces biofilm -> biofilm disperses -> seed new infection sites
