Microbes and Immune System Flashcards
What are 4 life strategies?
Photoautotrophism
- Sunlight
- Carbon Dioxide
- Organisms that use this strategy are plants, algae and cyanobaccteria
Photoheterotroph
- Sunlight
- Pre-formed organic compounds
- Purple/green non-sulphur bacteria
Chemoautotroph
- Chemical oxidation
- Carbon dioxide
- Extremophiles
Chemoheterotroph
- Chemical oxidation
- Pre-formed organic compounds
- Humans, animals
Give a brief overview of the Marine environmnet
It’s dominant!
- Covers 2/3 of the surface
- Several km deep
Highly diverse
- Various environments within marine environment
- Habitat to bacteria, fungi and algae
Physical parameters
- Salinity
- temperature
- Pressure
- Nutrients
Describe the different zones within the marine environement
Neritic zone
- Mild temp, low pressure, nutrient rich
- Diverse marine life
- Photosynthetic organisms
Oceanic zone
- Pressure increases with depth
- Chemotrophs
- Not as unstable as once thought
What organisms do the dead sea house due to its salinity?
The Dead Sea
- Microscopic life only
- Photoheterotrophs
- Halophiles
How do halophiles stop the flow of water from low internal salinity?
- Halophiles need to stop flow of water from low internal salinity
- Production of compatible solutes increase internal salinity, preventing outflow of water
- Maintenance of the water-salt balance in halophiles
What are compatible solutes?
Osmoprotectants or compatible solutes are small molecules that act as osmolytes and help organisms survive extreme osmotic stress. Examples include betaines, amino acids, and the sugar trehalose. These molecules accumulate in cells and balance the osmotic difference between the cell’s surroundings and the cytosol.
What are Piezophiles and the different types?
Piezophiles (barophiles) are organisms whose survival and reproduction is optimized to high pressures, such as those in deep sea environments.
Piezotolerant
- Grow at atmospheric pressure but can also tolerate increased pressure.
Piezophile
- Optimal growth above atmospheric pressure.
Extreme piezophile
- Need high pressure for survival. Unable to survive at sea level.
What is the difference between extreme piezophile and piezotolerant membranes?
The membrane of the extreme piezophilic organism is highly unsaturated making it extremely fluid.
As opposed to the membrane of the piezotolerant organisms which have highly saturated membranes making them as rigid as possible.
Why are humans anomolous when it comes to withsatnding high oressures compared to other eukaryotes?
Humans are anomolous because we are not able to withstand high pressures like most other eukaryotes.
Why would extremophiles be found in caves despite them being a relativley stable enviornment?
Extremophiles also inhabit caves and mines which is associated with high level of salts, mineral-rich, extreme temperatures and no light.
How do organisms play a role in shaping mines and caves?
Organisms often play a role in the formation of these structures through:
- Acidification of water, resulting in sculpture of caves
- Changing the composition of rock and precipitate out chemicals:
- Iron/sulphur oxidising minerals
- Produces sulphuric acid
- Removes sulphur from minerals
- Negative pH values!
Different tyoes of thermophiles
Psychrophile
- Optimum growth <15ºC
- 90% ocean is <5ºC
- Chlamydomonas nivalis, Listeria monocytogenes
Thermophile
- Spores used as a biological indicator, measuring sterilisation
Hyperthermophile
- Survival at >70ºC
- Not only tolerate, but require for survival
- Thermus aquaticus
Mesophile
- Optimum growth at body temperature
- Human pathogens
How do Psychrophiles and Hyperthermophiles survive their respective environments?
Psychrophiles
- Low temperature, membrane is too solid
- Keep interactive and fluid
- Increase unsaturated fats
Good fat = liquid
Hyperthermophiles
- High temperature, membrane becoming too liquid
- To maintain integrity, solidify fats
- Increase saturated fat content
Bad fat = solid
What are the Oxygen requirements of different organisms?
Aerobes
- Growth in oxygen
- Rhizobium spp - soil
- Neisseria spp
- Meningitis, gonorrhoea
Anaerobes
- Death in oxygen
- Clostridium spp - HAI
- Actinomyces spp – soil
Facultative Anaerobes
- Survive +/- oxygen
- Staphylococcus spp.
- E. coli
Aerotolerant
- Can survive in oxygen but metabolise anaerobically
- Rhizobium spp.
- Streptococcus spp.
Microaerophile
- Prefer reduced oxygen, can’t respire anaerobically
- Lactobacillus spp.
- Campylobacter spp.
What is the Rhizosphere?
Rhizosphere is an area of soil containing a diverse population of microorganisms that utilise plant secretions e.g. proteins and sugars. Microbes consume the minerals and feed them back to the plant, promoting growth
Give a brief overview of P. syringae
- P. syringae allows ice formation at higher temperatures
- Plants normally survive at -2°C to -8°C through internal proteins, changing freezing temp of water
- Bacteria produce ice nucleation active (INA) proteins, increasing freezing temp
- Punctures plants cells, allowing bacteria to penetrate
Define symbiosis, parasitism, mutualism and commensalism.
Hawaiian Bobtail Squid and the Aliivibrio fischeri have a mutualist relationship, describe how this is the case.
The Hawaiian Bobtail Squid provides a selective environment exclusively for A. fischeri. The A. fischeri produce fluorescent light which casts a light shadow from the squid. This is beneficial to the squid because it is nocturnal and the moon above the squid would cause a night shadow to be cast by the squid which would alert predators below of its presence and subsequently kill them. The light from the A. fischeri cancels out the moon shadow and shields the squid from predators.
How does the Hawaiian Bobtail Squid utilise the A. fischeri?
- Light is omitted specifically from the light organ within the mantle of the squid.
- The light organ has epithelial cells which form a ciliated surface on its structure, beating water into the light organ.
- Water passes over tiny, microscopic pores in the light organ.
- A. fischeri accumulates in the deep crypts on the squid.
How does the Hawaiian Bobtail Squid specifically accumalate A. fischeri?
- Water passes through the anterior appendage (ciliated cells) and over the pores.
- Bacteria travel down the light organs and colonise the deep crypts.
- This is where we see specific colonisation of A. fischeri.
How does the the Hawaiian Bobtail Squid specifically allow A. fischeri to colonise?
- Peptidoglycan is a structure specific to bacteria and acts as a signal to epithelial cells.
- Ciliated cells secrete mucus, trapping bacteria from passing freely.
- Squid produces compounds which have an antibiotic effect against Gram +ve
- A. fischeri is Gram –ve
- A. fischeri outcompete other microbes and becomes dominant by activating chitinolytic enzyme within the squid, digesting chitin in the environment.
- Broken down chitin (chitobiose) acts as an attracted for A. fischeri, specifically.
- Acts as an attractant for more A. fischeri to more over the pores.
- Only A. fischeri left, colonising the deep crypts of the squid. A. fischeri becomes non-motile, induces host-epithelial cell swelling and eventually releases light.
Diagram showing the stages of colonisation of a newborn Hawaiian bobtail squid’s deep cysts
- Sterille - The crypts of a newborn squid are sterile within the first 30 min.
- Permissive - Initial mixed bacterial population in the crypt. Mucus is shed to attract bacteria.
- Restrictive - Antibiotic production to inhibit certain types of bacteria. A. fischeri has immunity to these mechanisms.
- Specific - Specific A. fischeri colonisation due to chitobiose secretion
Diagram detailing squid and A. fischeri stages of colonisation
What is the Diel Cycle?
Cycle of colonisation of A. fischeri every day and night in the squid.
DAY
- Nocturnal squid buries in the sand, doesn’t need to omit light.
- Removal of most A. fischeri from the light organ into the environment.
- Remaining bacteria begin to replicate throughout the day, to reach peak density.
NIGHT
- Light organ is full of fresh A. fischeri.
- Bioluminescence enables hunting.
- Removal of bacteria from squid.
Fresh population of A. fischeri generated.
Seeding of the environment with A. fischeri for the next generation of squid.
What is Quorum sensing? And how is it useful to the Hawaiian Bobtail Squid and the A. fischeri?
Quorum – specific/minimum number
Quorum sensing
- Bacteria sensing their population size and coordinating their behaviour (biofilms formation, virulence, antibiotics)
- Behaviour changes depending on low or high cell density
In the A. fischeri emitting light is an energy expensive process and only emit it when the bacteria use qurorum sensing to decide whether there’s enough of them for the light to impact the host (Hawaiian Bobtail Squid).
The Individual behaviour is different from group of organisms - multicellular
What does Quorum sensing rely on?
Quorum sensing relies on autoinducers (AI) to sense the environment population.
Once a threshold has been reached, AI’s activate cellular process to respond to the environment – luminescence within the A. fischeri
What controls the ptoduction of light in A. fischeri?
The lux operon controls the production of light in A. fischeri.
- LuxI – synthesises AHL. At low A. fischeri densities, the AHL diffuses out of the cell and no light is produced.
- However, at high A.fischeri concentrations, there are also higher concentrations of AHL which can then re-enter the bacterial cell and bind to luxR.
- The binding of AHL to LuxR activated transcription of luxC, luxD, luxA, luxB and luxE.
- LuxA and luxB genes produce proteins which form luciferase. Luciferase then catalyses a redox reaction which produces light.
Which gene is the regulatory gene in the lux operon?
LuxR is the regulatory gene which produces transcription activator
What is a Biofilm?
A biofilm is a growth of organisms within a mucous bound film either in a substrate or on a surface.
Majority of microbes to be in a sessile state.
- They usually begin by colonising a surface. Here they can be easily detached.
- At this point an Extracellular matrix has been produced (like sugars and peptides).
- When the biofilm is fully formed. Quorum sensing detects growth slowing and aids biofilm dispersal and the cycle starts again,
What is Biofouling?
Biofouling – fouling of underwater structures with micro/macroorganisms
Can cause loss pf functionality in pipes, chains and bottoms of ships etc.
The biofilming of microbes onto these surfaces allow for other higher lifeforms to latch on like barnacles etc.
What are the stages of biofouling?
What is different in the disperesed cells from a biofilm than the original microorganisms?
They are usually more toxic to their environment.
How do Biofilms cause issues in Medicine?
What are the issues with culturing microbes in a lab?
Restricts growth
- Does not cater for organisms found in all environments
- Laboratory environment is far removed from reality
Time consuming
- Some organisms can take weeks to grow (Mycobacterium spp.)
Therefore, it is approximated that we only know of 1% of all microbes that exist.
How do we idenitfy different species of microbes within an interspecies biofilm?
- Extract all DNA from the population and digested into smaller fragments.
- Cloned in to plasmid vectors before sequencing.
- Data analysis to identify organisms.
What are 4 omic studies?
How is Transcriptome tech used?
What is a Microbiome?
Large and mixed population of microorganisms coexisting together under many circumstances.
How are microbes found in the wild?
Although we tend to consider study these organisms in pure culture, in nature they are infrequently found in isolation, but rather as dynamic communities, which compete for resources but frequently depend on each other for survival.
What is a commensal relationship within communities?
Commensal: on or in host without injuring or benefiting the host
What is commensalism?
- Commensalism: when a product produced by one organism can be used beneficially by another
What is the definition of a pathogen?
- Definition: an organism that causes damage and disease to the host
- Much smaller group of organisms
What does Koch postulate a pathogen to be?
- He said that to be a pathogen, the microbe must be absent in all healthy individuals but present in all diseased hosts.
- It should be possible to isolate and grow the microbe in pure culture from all diseased patients and that if this microbe was then used to inoculate a healthy host, it should cause the same disease in that host.
- And that finally it should be possible to reisolate the pathogen from the inoculated host.
- These postulates are still valid today although recovery of the genetic material rather than the organism is now sufficient and resulted in renaming these as Kochs molecular postulates
What is the definition of pathogenicity?
The capacity of a microbe to cause damage in a host
What is the definiton of virulence?
- Virulence refers to the degree of damage caused by the microbe
What are Virulence Factors?
- A product made by the organism that contributes to overall virulence (eg toxin)
Describe the Virulence factor:
Tetanus toxin
Tetanus toxin
Released by C. tetani, following its growth within the anaerobic environment of a deep puncture wound. On release from the organism, the toxin binds to the peripheral neuronal axons and undergoes retrograde transport to the inhibitory interneuron, where it prevents the release of inhibitory neurotransmittors such as glycine and g-aminobuytric acid (GABA).
How does the tetanus toxins’ actions impact animals?
This prevents the deactivation of the neurone resulting in contraction in both agonist and antagonist muscles.
This causes tetanic muscle spasm, an extreme example of which is shown here.
The vaccine that is given to prevent disease results in antibody production that binds to the toxin, preventing its interaction with nerve endings. However, in the absence of such antibodies, mortality is high.
What are oppurtunistic pathogens?
The capacity of these organisms to cause disease depends upon the opportunity they are given to cause disease hence the term ‘opportunistic pathogens.
This may include the age the patient (with the very young and very old often being immunocompromised, antibiotic treatment that may reduce the presence of protective organisms, the prevalence of exposure, how much and in what form you are exposed to that pathogen, your host genetics and factors that influence your immune system including nutrition and stress
What are many of the oppurtunistic infections also classed as?
Many of the opportunistic infections on man are also zoonotic organisms in that these are diseases transmitted to man from animals
Interestingly many of these microbes are commensals in the animals – only causing disease when they cross the species barrier.
These include Campylobacter jejuni which is a common cause of diarrhoea in man, enterohemmorhagic E.coli or EHEC which causes kidney failure in children and rabies in bats, which is always lethal in man but can be carried without symptoms in bats.
Why is the rate of evolution much more rapid in microbes compared to humans?
Evolution in microbes is much more rapid than humans due to their high rate of multiplication. Under optimal growth conditions in a lab, there growth is rapid, with doubling times as short as 25 min under optimal conditions. This means that 1 organism can replicate to 100 million within 8h
How do bacteria mutate?
- Alter sensitivity to particular drugs
- Alter receptor recognition (of tissue)
- Alter recognition by the host (immunity)
However, this type of mutation does not explain how much larger pieces of DNA that encode specific virulence traits such as toxins are acquired.
What are the three types of horizontal gene transfer in bacteria?
- In natural transformation, bacteria take up DNA from the environment, which depending on regions of homology between the DNA and the bacterial DNA may recombine and replace exitsing regions of the chromosome.
- In conjugation, DNA is exchanged between bacteria through the formation of a conjugative pilus
- And in transduction, genetic exchange is the result of predation by bacteriophage, small viruses of bacteria, which inject DNA into the cells as part of the infection process.
When does transformation occur?
And what is the probable reason for it?
Occurs in bacteria that are naturally ‘Competent’. Occurs when ssDNA is released when bacteria die and lyse. The uptake of DNA and incorporation into genome of ‘competent’ bacteria is done through homologous recombination.
Some become competent in response to quorum sensing compounds – released by bacteria – competency factors
But if gene associated with antibiotic resistance – transformed bacteria will now be resistant
How do competency factors change incompetent bacteria and how has thi sled to issues regarding antibiotic treatment?
These competency factors modify the membrane to enhance uptake of single strand pieces of DNA, which due to the homology found in closely related species, allows rapid recombination into the bacterial chromosome.
If the piece of acquired DNA encodes something like an antibiotic resistance gene, the clone with the acquired DNA will outgrow those bacteria that are not naturally competent.
What is conjugation?
- Conjugation in contrast to transformation is an active process that requires the generation of a conjugative link between two bacteria that allows the direct transfer of Dna from one bacteria to another. Conjugative plasmids found in bacteria, are self replicating pieces of DNA that encode tra genes, which are essential for the transfer of DNA.
- Once of the best described systems of conjugation if the transfer of the F pilus in E.coli.
- Exchange of DNA occurs when an F +ve organism carrying the plasmid meets an F- organism that does not have this plasmid. The F pilus encoded on the plasmid and expressed on the surface of the F+ bacteria, is used to initiate contact with the F- cell. On contact, a structure is formed between the two cells, through which the plasmid DNA is able to pass.
What are the tra genes?
The tra genes found on the conjugative plasmid encode all the proteins necessary to make the the relaxasome, which is the structure through which the DNA passes.
In conjugation what is the process used to transfer DNA?
DNA is transferred in a process known as rolling circle, with the DNA cut at a site close to the original of replication of the plasmid. The DNA is then drawn through the relaxasome, with DNA polymerase activity required in both cells to generate a second strand of plasmid DNA. Both cells now contain the plasmid and are capable of producing an F pilus and transferring their plasmids to other strains.
What is Hfr transfer in the rolling circle process?
In some cases the plasmid may have regions that are homologous with the bacterial chromosome allowing direct integration of the plasmid through recombination. In this situation the integrated DNA can remain in the chromosome or can excise. Sometimes when they do excise, they do so imprecisely taking some adjacent bacterial chromosome DNA with them. The presence of this DNA means they are more likely to integrate at Higher frequency than normal conjugation. This is known as High frequency or Hfr transfer.
What is transduction?
Transduction, a process of genetic recombination in bacteria in which genes from a host cell (a bacterium) are incorporated into the genome of a bacterial virus (bacteriophage) and then carried to another host cell when the bacteriophage initiates another cycle of infection.
What are the two life cycles of bacteriophages?
They have 2 life cycles
- The lytic cycle in which the virus binds to a receptor on the surface of the bacteria and injects in its genome. Like mammalian viruses, It then hijacks the cellular machinery of the bacteria to produce multiple copies of its genome that are packaging inside structural proteins also made by the bacteria. It then escapes from its host by lysis of its bacteria membrane
- Bacteriophage are also also to undergo lysogeny, which occurs when the injected phage genome integrates into the host chromosome. In this form, it is replicated as part of the natural lifeccyle of the bacteria and is transferred from mother to daughter.
However, if the bacteria becomes stressed or under threat, the intact phage can excise from the chromosome and reinitiate the lytic cycle that results in the production of intact and infectious phage.
How does generalised transduction accidentally occur in bacteriaphages sometimes?
Although the infection process, including the packing of the viral DNA into the structural heads of the phage is largely efficient, occasionally a piece of bacterial chromosomal is packaged into a phage head by mistake. These defective phage will be released from the bacteria during lysis.
However, as the structure of the virus is unchanged, the defective phages are able to bind to any susceptible bacteria and the DNA inside the head injected into the bacteria by this molecular syringe. Once inside the cell, the DNA may or may not integrate into the bacterial chromosome. This type of transduction is known as generalised transduction
What is specialised transduction?
In contrast specialised transduction is linked to the lysogenic lifestyle that follows the integration of phage DNA into the bacterial chromosome and follows imprecise excision form the bacterial chromosome, that means that some of the DNA adjucaent to the site of integration is also excised and packaged, These chimeric phage that carry both viral and host DNA can transfer these genes to a new host.
As a phage head can package up to 40kb of DNA, this offers a significant opportunity for DNA exchange
How can microbes acquire virulence?
The best example of how acquiring DNA using these mechanisms can enhance virulence can be demonstrated using E.coli.
E.Coli is considered as a commensal organism that lives in the gut.
However, some strans of E.coli have acquired a plasmid that encodes 2 toxins, that cause toxin mediated diarrhoeal disease in humans
Other strains have acquired a plasmid that encodes an adhesin that allows successful adhesion and mediates invasion into the epithelial tissues
Enterohemmorahgic E.coli has acquired both the capacity to intimately adhere to the gut surface through gene found on an integrative plasmid and produce a toxin that was acquired through phage transduction.
Similarly enteropathogenic strains cause damage and diarrhoeal disease through acquisition on mechanisms that allow increased adhesion by this organism
What is a pathogenicity island?
When large pieces if DNA are integrated they are known as pathogenicity islands and frequently encode structures such as the very elegant type 3 secretion injector that is important in the attachment of several medically important gut bacteria including Salmonella and Shidella.
What can be problematic for the implementation of DNA into bacteria?
- DNA introduced may not persist
- Restriction systems, such as phage encoded CrispR/Cas recognise foreign DNA
- Endonuclease activity
- If persist may integrate and multiply within the chromosome
- Many toxins – cholera toxin, diphtheria toxin (phage encoded)