Lecture notes
Microbiology Lecture Notes
- Module
- Microbiology
- Institution
- University Of Exeter (UoEX)
Compilation of lecture notes from Microbiology module in first year Biochemistry
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History of Microbiology- Robert Hooke (1635-1704) – compound microscope + coined the terms cells looking a cork
- Antonie van Leeuwenhoek (1632-1723) = simple microscope, 1683 = wrote to Royal Society
about ‘animalcules’ (microbes) around 1um
- Abiogenesis – Aristotle 384-322BC = wrote about spontaneous generation of microbes
o First challenged by Francesco Kedi’s experiment = if you cover meat it doesn’t putrefy
- John Needham = argued for case of life force and vital atoms
- Lazzaro Spallanzani = refutes spontaneous generation in microscopic world
- Louis Pasteur – conclusively disproved spontaneous generation
Robert Koch (1843-1910)
Germ theory of disease = gave 4 postulates
1. The suspected pathogenic organism must always be present in animals suffering from the
disease and not present in healthy individuals
2. The organism must be cultivated in pure culture away from the animal body
3. Cells from a pure culture of the suspected organism should cause disease in a healthy animal
4. The organism should be reisolated and shown to be the same as the original
In action skills =
1. Microscope staining
2. Laboratory culture
3. Experimental animals
4. Laboratory reisolation + culture
These postulates still remain ‘gold standard’ in medical microbiology but not possible for all diseases
Alexander Fleming (1881-1955)
- Used Salvarsan i.v. for syphilis
- Penicillium notatum prevented growth of staphylococcus
- Won Nobel prize in 1945 with Chain + Flory
Edward Jenner (1749-1823)
In 1788 there was an epidemic of smallpox in Gloucestershire, but Jenner notices milkmaids with cowpox
didn’t get infected
- Therefore, he took material from the maids and inoculated into a child
- 1798 – An Inquiry into Causes + Effects of the Variolae Vaccinae
Modern Day Advances
- Advances in medicine has seen a change is death causes between low income and high income
countries
- ‘Tree of life’ is currently generated by 16s RNA sequences (present in all living things)
o Sequences are compared to generate phylogeny tree
1986 = Phylogenetic stains (Norman Pace)
1987 = Community sampling of ribosomal RNA genes shows diversity of bacteria (Norman Pace)
1992 = Discovery of marine Archaea (Jed Fuhrmant + Ed Delong)
1995 = First genome sequencer
2004 = First large scale metagenomic project (Craig Venter)
,Classification of Microorganisms
There had been little progress in 100 years from 1866-1969
- 16s RNA phylogenetics revolutionised classification
Prokaryotic taxonomic classification scheme is found in ‘Bergey’s Manual of Systematic
Bacteriology’
Gram Positive vs Gram Negative
Positive = simple cell wall with thick peptidoglycan
Negative = phospholayer = peptidoglycan + phospholipid bilayer (stains differently)
Classification
After 16s rRNA genes there are lots more groups of bacteria
Major phyla = proteobacteria, Bacteroidetes, firmicutes and actin bacteria
Gram Negative
- Proteobacteria = alpha, beta, gamma, delta + epsilon
- Stain pink in Gram stain
- Metabolically diverse (can get energy from chemical or light)
- Different environmental habitats
1. Symbionts
2. Nitrogen fixers
3. Aquatic environments
Alpha/Rhizobiales
Genus
- Agrobacterium = plant pathogen
- Bradyrhizobium = symbiotic nitrogen fixer
- Nitrobacter = nitrifying
- Rhizobium = symbiotic nitrogen fixer
Symbiotic = form symbiosis with plants and fix nitrogen to ammonia
Beta/Neisseriales
Neisseria = human pathogens
- Characteristic = diplococci
- Medically important species
o e.g., N. meningitidis = meningitis
o Carried in 95% of population
o Or N. gonorrhoeae
Gamma/Enterobacteriales
1. Shigella = human pathogen (food poisoning)
2. Escherichia = human commensal, some pathogenic (common inhabitant of intestinal
tract) E. coli = v important search tool
3. Salmonella = human pathogen (food poisoning)
Largest subgroup of proteobacteria + have the most pathogenic species
,Delta/Spirilla
- Bdellovibrio = uses other bacteria as a host, curved shape + potential antimicrobial
- B. bacterivorus = predator of Gram-negative bacteria, found is soils and aquatic
environments
o Grows in periplasmic space + feeds off nutrient
Epsilon
- Campylobacter = highly motile bacillus, curved, C. jejuni = food borne disease
- Helicobacter = has multiple flagella, causes stomach ulcers (H. pylori)
Bacteroidetes = human biome responsible
Gram Positive Bacteria
Divided into ‘low G+C’ and high ‘G+C’ based on GC content in the genome
Low G+C = Firmicutes
High G+C = Actinobacteria
Firmicutes
Lactobacillales = lactic acid bacteria + tolerant to low pH
- Lactobacillus = lactic acid producers, human commensal
- Streptococcus = human pathogens + commensal
Bacillales
- Staphylococcus = human pathogens
- Bacillus = endospores + some human pathogens
Clostridiales
- Clostridium = anaerobes, endospores + human pathogens
Staphylococcus, Bacillus and Clostridium produce other acidic by-products e.g., acetic acid
or butyric acid
Lactobacillus - variable size, used in fermented products, important in gut flora? L. caseii =
cheese
Streptococcus – medically relevant, subdivided by haemolysis (rupture of blood cells)
Staphylococcus – some medically important. S. aureus = boils + produces toxins, MRSA =
major hospital acquired infection
Bacillus – endospore-forming which enables survival during extreme environments e.g.,
heat, desiccation. Medically important e.g., anthrax + B. cereus = contaminates cereals from
soil
Clostridium – also endospore, location of spore helps identify species e.g., tetani = lockjaw,
botulinum in Botox, difficile = hospital diarrhoea
High G+C = similar to fungi
- Actinomyces = filamentous branching + some human pathogens. Facultative
anaerobe, looks like fungal hyphae, important in soil ecology
- Frankia = symbiotic nitrogen fixers. Filamentous + carry out nitrogen fixation in soil
(into ammonia)
, - Streptomyces = filamentous + produce antibiotics. Form mycelium + produces psores
called conidia. Important producers of antibiotics, occurs during nutrient depletion
therefore a survival mechanism for competition
Bacterial Diversity
Y-proteobacteria = most common subdivision containing lots of human bacteria + easily
culturable and lab grown therefore lots is known about them. But how do you study non-
culturable bacteria?
Culture Independent Analyses
- Take specific 16s rRNA, label + probe to see structure (using fluorescent
oligonucleotides)
- Called fluorescent in situ hybridisation (FISH), can see proportions etc.
Ecosystems = sum of organisms and abiotic factors in a particular environment
- Symbiosis = mutualism (both benefit) and commensalism (one benefits, other
neutral)
- Syntropy = 2+ organisms catabolising a nutrient that can’t be catabolised by one on
its own
- Some bacteria in our large intestine give us vitamin K
- Species richness = total no. of species present in an ecosystem
- Species abundance = proportion of each species
- Interactions with plants = e.g., legume-root nodule symbiosis (nitrogen fixing)
- Interaction with mammals = microbiome
- Colon composition = 64% Firmicutes 23% Bacteroidetes
Phylogenies + Trees
- Evolution by natural selection led to the idea of descent with modification
- Tree of life = logical extension of the idea of descent with modification
- Organisms are ultimately related to each other
- Trees help us understand processes like extinction, speciation and relations between
species
- Until 1962, prokaryotes were classified due to their biochemistry, morphology,
metabolism then division into eukaryotes + prokaryotes occurs
Bacteria Eukaryotes
Circular chromosomes Linear chromosomes wrapped around histones
Peptidoglycan cell wall Sometimes chitin/cellulose cell wall
DNA free in cell DNA in nucleus, mitochondria (sometimes plasmids)
No sub-cellular compartments Subcellular compartments (organelles)
Smaller ribosomes Larger ribosomes
No cytoskeleton Cytoskeleton w/ motor proteins
How do you calculate a universal tree of life?
1. DNA sequence in formation
2. Need universal gene for comparison
3. Mixture of evolutionary rates to determine relationships
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