Module 3

Lecture 18: Microbiology and the ‘One Health’ Concept

Define the five major types of microbes (viruses, bacteria, fungi, protists, algae)
- Viruses
- The smallest and simplest biological entities
- Depend on host cell for replication & metabolism
- Don’t have own metabolism
- Have ability to evolve
- Bacteria
- Unicellular, smallest free-living organisms
- Have own metabolism and replication
- Fungi
- Large complex cells (eukaryotes), have nucleus, mitochondria
- Can be unicellular (e.g. yeasts) or multicellular (e.g. moulds)
- Can have both macroscopic (fruiting bodies) and microscopic parts (spores of
mushroom)
- Protists
- Large complex cells (eukaryotes), have nucleus, mitochondria
- Protozoa: protists that are animal-like (predatory)
- Algae
- Large complex cells (eukaryotes), have nucleus, mitochondria
- Plant-like protists
- Photosynthetic (have chloroplast)

Describe key inventions and ideas in microbiology: microscopy, agar plates,

spontaneous generation, germ theory, Koch’s postulates, penicillin
- Microscopy
- Robert Hooke 1664: Hooke’s microscope allowed up to 30x magnification
- The idea of ‘cells’
- Antonie van Leeuwenhoek 1684: powerful (300x mag) microscope
- First evidence of bacteria and protists
- Spontaneous generation → Louis Pasteur 1861 debunks the theory of spontaneous
generation
- The idea that non-living objects can give rise to living organisms (thought that
germs just appear spontaneously)
- When flask is sealed, microbes did not re-appear; swan-necked flasks which
allowed entry of air but not microbes
- Germ theory & Agar plates → Robert Koch
- Germ theory of disease: proof that microbes cause disease
- Koch’s postulates
- An organism that causes a disease must:
- Be found in all cases of the disease
- Be isolated from the diseased host in pure culture
 - Produce the same disease in experimentally-infected host
- Be re-isolated from the experimentally-infected host
- Penicillin → Alexander Fleming 1928
- Found mould growing on a petri dish that killed the bacteria around it
- Work by Florey and Chain: purified penicillin & mass produced

Discuss difference between normal flora & pathogens

- Normal flora: microbes that live in us and on us
- Found at specific sites, different body site has different microbes
- Acquired at birth, from diet, and from the environment
- Primes the immune system, provide nutritional benefits (help breakdown complex
molecules) and compete with pathogens
- Can cause disease if moved to wrong location (wound infection) or even in
normal habitat (tooth decay)
- Pathogen: a disease-causing microorganism
- Some pathogens are always harmful (viruses)
- Others are opportunistic, depending on:
- Numbers → too many can cause host damage
- Location → get into the wrong place
- Host health → immune system compromised
- Virulence factors → some bacteria can pick up new genes for
toxins/become drug-resistant

Explain the concept of One Health

- One Health: a unifying principle in infectious disease microbiology
- Need to consider animals, plants, and the environment when we are trying to manage
human diseases
- Many diseases originate in either the environment or in animals
- Disease is influenced by urbanisation, globalisation, climate change and pollution

Describe one major problematic infectious disease

- Emerging infections due to new pathogens
- Human: HIV, Ebola, Covid-19
- Animal: Chytrid fungus (frogs), Varroa mites (bees)
- New problems with old pathogens
- Human: malaria, tuberculosis
- Animals: Koala Chlamydia
- Plant: Panama disease (banana)
- Tuberculosis
- Caused by a bacterium: Mycobacterium tuberculosis
- Spread person-to-person by airborne droplets (coughin)
- Infects lungs → cough, chest pain, weight loss, death
- New strands of TB are resistant to antibiotic treatment
- ‘MDR-TB’: multidrug resistant TB
 - ‘XDR-TB’: extensively drug-resistant → very bad
- Hard to treat and treatment is expensive

Lecture 19: Microbes, Food and Nutrition

Describe the role of microbes in each stage in the food production and consumption
chain:
- Soil, plants, animals
- Soil
- Transforms and releases important elements (nitrogen, phosphorus, iron,
sulphur, etc.)
- Breaking down organic wastes into inorganic nutrients (decomposition)
- Suppresses microbes that can cause plant and animal disease
- Breaks down toxins (pesticides)
- Animals
- Enable animals to digest cellulose which is abundant in plants
- Animals rely on rumen microbes to break down cellulose
- Cellulose → sugars → organic acids, CO2, CH4
- Organic acids and microbial cells are digested by animals as nutrients
- Plants
- Promote plant growth via mutualism
- Mycorrhizal fungi: enhance water + inorganic nutrient uptake while
receiving sugars from plant
- Increase surface area of root network
- Rhizobium bacteria (legume roots): fix nitrogen and receive sugars in
return
- Fermentation & food processing
- Fermentation: anaerobic metabolisms of sugars
- Yeast and bacteria are good for fermentation (make beer, wine, bread,
cheese, kimchi, yogurt, etc.)
- Food spoilage
- Spoilage is due to the growth of fungi/bacteria, and/or due to enzymes that these
microbes make and secrete
- Enzymes break down food into undesirable products making it less safe &
palatable to eat
- Food poisoning
- Poor hygiene can cause food poisoning
- Can occur from spoiled food or fresh food (different sets of microbes are
responsible for spoilage vs poisoning)
- Food-borne infection: microbes grow in gut (grow in the body)
- Food-borne intoxication: microbes make toxins in food (grow in food)
- Not all microbes are killed by cooking the food, some are activated by cooking

Provide examples of microbial pathogens in the food supply chain that affect crops,
livestock, and human health microbiome in health and disease
 - Plant pathogens
- Tobacco mosaic virus (simple but can infect many crops)
- Sigatoka fungi: threaten the survival of bananas globally
- Bananas are all clones so they’re all equally susceptible
- Fungus rapidly evolving resistance to fungicides
- Animals pathogens
- Foot and mouth disease
- Animals that are infected must be killed, meat unsafe for human
consumption
- Zoonosis: human infection arising from animals
- Salmonella → normal flora for the animal
- Animal is a ‘vector’ for disease → ticks carry lyme disease
- Covid-19 → original host is bat
- Gut microbiome
- Depends on diet
- High fibre (healthy) diet: high in Bacteriodetes
- High protein & fat diet: high in Firmicutes

Lecture 20: Planetary Health: Microbes and Ecosystems

Appreciate that the majority of life’s diversity is microbes
- The vast majority of all biodiversity is microbes

Describe the role of microbes in the carbon cycle

- Biogeochemistry → biological processes that impact chemistry at global scale
- Most reactions are done by microbes

Define an autotroph and a heterotroph, and give microbial examples of each

- Autotroph
- Use either light (photoautotrophs) or chemical (chemoautotrophs) energy sources
- Algae perform ~50% of global photosynthesis
- “self-feeder” → uses CO2 as carbon source
- Convert inorganic C to organic C (CO2, to other forms of C)
 - Methanogens → consume CO2 and H2 to produce CH4
- Chemoautotrophs: CO2 is carbon source, H2 is (chemical) energy source
- Overall bad for climate change because CH4 is a worse greenhouse gas
- Anaerobic → killed by oxygen
- Heterotrophs (“other-feeder”) → needs to eat other organisms/organic carbon sources,
also supply energy
- Methanotrophs → consume methane, produce CO2
- Methane both as carbon and energy source
- Overall good for climate change because sinks CH4
- Decomposers → recycle dead cells into CO2
- “other-feeder” → eat other organisms that also supply energy
- Predators
- Protists → predators of other microbes
- Ciliates: tiny hairs/cilia all over surface to help move
- Flagellates: have large hair (flagellum)
- Amoebae: like a blob & drags itself to move around
- Not all protists are predators, some are ‘detritivores’ or photosynthetic
- Detritivores: eat dead, decomposing matter, don’t hunt prey
- Pollutant degraders
- Hydrocarbon-degrading bacteria → specialise in eating ancient fossilised
organic carbon

Explain the impact of microbes on global climate change as sources and sinks of CO2
and CH4
- Autotrophs → fix carbon into organic materials (sink CO2)
- Good for climate change (algae)
- Methanogens → produce CH4 so bad for environment
- Heterotrophs → source of CO2
- Bad for climate change (decomposers)
- Methanotrophs → consume CH4 so not as bad (sink CH4)

Provide examples of the importance of microbes in:

- Marine ecology (coral-algal symbiosis)
- Corals depend on symbiotic microscopic algae to supply them with food
- Corals → host animal, heterotroph, sugars → CO2
- Algae → photoautotroph, CO2 + light → sugars
- Terrestrial ecology (lichen symbiosis)
- Lichens are primary producers in some terrestrial habitats (photosynthetic but not
plants)
- Symbiosis between 2 microbes: heterotrophic fungus and an autotrophic algae
- Fungus attach to rock and feed algae with inorganic nutrients & moisture
needed for algae to grow
- Pollution cleanup (bioremediation) → cleanup of pollution by microbes
- Hydrocarbon-degrading bacteria are useful for bioremediation
 - Heterotrophs (including methanotrophs)
- Eats ancient fossilised organic carbon

Lecture 21: Cell Factories and Biotechnology

Explain why microbes are useful for biotechnology, using examples of specific fungi
(S.cerevisiae) and bacteria (E.coli)
- Viruses → carry genes into new hosts
- Sources of enzymes, e.g. T4 ligase infects E.coli
- Archea → sources of thermostable polymerase enzymes (for copying DNA sequences)
- Many live in extreme environments → enzymes & proteins are thermostable
- Bacteria → hosts for cloning DNA and expressing proteins
- E.coli useful as host for cloning genes and expressing proteins
- Very easy to extract/add plasmid DNA
- Fast growth and simple nutrient requirements
- Algae → convert CO2 + light into biofuels (ethanol & H2)
- Fungi
- Yeasts → host for cloning and gene expression
- Saccharomyces cerevisiae (S.cerevisiae) for expressing eukaryotic gene
- GRAS: generally recognised as safe
- Moulds → antibiotic synthesis, e.g. penicillium

Explain what a plasmid is, and define the roles of different kinds of plasmids in nature
and in biotechnology
- Host cell → contains machinery for biosynthesis of high-value products from simple raw
materials
- Needs instructions/blueprint to twll which products to make (add DNA)
- Plasmids → circular DNA elements found in microbes, replicate independently of the
chromosomes
- Most commonly used vector for delivery of foreign DNA into a target host cell
- ‘Wild’ plasmids found in nature allow microbes to swap useful genes
- For biotech, take the ‘wild’ plasmids and take out everything we don’t
need
- Features of plasmids
- Selectable marker (amp) → enable us to force cells to take up
plasmid
- Cloning site (polylinker) → add foreign genes here
- Replication functions (ori) → ensures persistence in host

Define the terms “DNA cloning”, “recombinant DNA”, “GMO”

- DNA cloning → making copies of a piece of DNA by adding it into a plasmid, then
replicating the plasmid
- Cloning in vitro using polymerase chain reaction
- or put DNA into a plasmid & replicate plasmid inside a host cell
 - Recombinant DNA → DNA that contain bits of foreign DNA

- GMO → genetically-modified organism

- The final product

Explain how recombinant DNA and GMOs are made, and especially which enzymes do
which jobs in this process
- Thermostable polymerase → copying DNA
- Restriction enzyme → cutting DNA
- T4 ligase → joining DNA
- Recombinant DNA
- Isolate DNA strands and ligate with plasmids to create recombinant DNA
- In the ligation mixture (recombinant DNA, starting plasmid, other parts of the
DNA that is not ligated)
- GMO → recombinant microbe carrying gene of interest, the final product
- Add ligation mixture into the cloning host
- Transformation = uptake of DNA
- Select plasmid-containing cells
- If not then all the host cells will grow and not only the ones that take the
plasmid (some grows on plate and others don’t??)
- Look for gene of interest by:
- Phenotypic screen → look for effect of gene on host, e.g. jellyfish gene
will glow in the dark
- Sequence-based screen → look for DNA directly

Discuss why vaccines are important, and how recombinant DNA methods can be used to
make them
- Promoter drives the expression of gene of interest, it causes transcription and then
translation to get the protein
- Promoter: a DNA element that recruits RNA polymerase and allows transcription
to take place
- Protein will be purified and then:
- Protein may be the end-product → vaccine
- Use protein to make the end-product
- Vaccine: a primary defence against infectious disease
- Lead to ‘herd immunity’: protecting not only yourself but also the people around
- Work by ‘training’ the immune system to recognise antigens associated with an
invader