microbiology Flashcards
what proportion of the world’s biodiversity are bacteria
2/3
give 2 examples of industries that use microbes
pharmaceuticals - antibiotics
food and drink industry
what are the 2 most successful medical interventions for treating/preventing microbial infections
antibiotics
vaccines
what is an ecosystem
organisms and chemical/environmental factors that impact and create it
what is a habitat
part of the ecosystem most suited to a certain form of life - the place where an organism lives
what is a niche
small, specific area of habitat - the role of an organism in its environment
rapid change can induce feast or famine state
what is species abundance
the number of organisms in an environment
what is species richness
the diversity of species within an environment
what are the 4 different life strategies
photoautotroph
photoheterotroph
chemoautotroph
chemoheterotroph
what does chemo mean in terms of energy consumption
get energy by chemical oxidation of organic compounds
what does photo mean in terms of energy consumption
get energy from light
what does autotroph mean in terms of carbon consumption
get carbon from CO2
what does heterotroph mean in terms of carbon consumption
get carbon from preformed organic compounds
give an example of a photoautotroph
plants, algae
give an example of a photoheterotroph
purple/green non sulphur bacteria
give ab example of a chemoautotroph
extremophiles in hydrothermal vent
give an example of a chemoheterotroph
humans and animals
what proportion of the surface of the earth does the marine environment cover
2/3
list some physical parameters of our oceans
salinity temperature pressure nutrients pH
describe the neritic zone
mid temperature and low pressure
nutrient rich with diverse marine life
contains photosynthetic organisms
describe the oceanic zone
pressure increases with depth
more chemotrophs due to lack of light
large diversity of life
what is the salinity of the great salt lake
27%
explain the pink/blue sea
different colours caused by construction of a railroad which blocked of rivers and nutrient flow
this nutrient difference caused different microbes to inhabit different sides of the railroad resulting in the colour change
what is the only form of life found in the dead sea and especially which kinds
microscopic
especially photoheterotrophs and halophiles
why can we float on the surface of the dead sea
because the salt increases the density
what are the 4 different levels of slat tolerance
non-halophile - no salt tolerance - <0.3%
halotolerant - high tolerance for saline 0.3-3%
halophile - rely on salt for growth >3%
extreme halophile - e.g. great salt lake 30%
give 2 examples of halophilic fungi
hortaea werneckii
wallemia ichthyophaga
give an example of 2 halophilic archaea and how they can be used in human products
haloferax mediterranei
halobacterium
they can be used as health supplements and in some cooking sauces
how do organisms maintain their water-salt balance internally
they regulate the movement of water and ions across the membrane
what is the response if we have an organisms with high internal solute conc
we will get an influx of water to maintain osmotic balance between the cell and the environment
what is the response of a cell being placed in a solute rich environment
water is expelled from the cell and the cell will become dehydrated
how do halophiles stop flow of water from low internal salinity to high external salinity
they produce compatible solutes which increases the internal salinity preventing the outflow of water
this results in maintenance of the water salt balance in halophiles
are compatible solutes toxic to cellular processes
no
what did the sorcerer II global ocean sampling expedition find
- samples taken at 200 mile intervals and assessed using molecular methods
- SAR11 bacteria discovered - most abundant organism on the planet - newly discovered - very few had been cultured in the lab previously
- a number of new proteins and known proteins were identified
the most abundant families of bacteria are novel and ……..……..
unculturable
give examples of technology development that is allowing us to investigate deep ocean
submarines that are able to withstand high blood pressure
what are hydrothermal vents and why are they sometimes called black smokers
they are vents on the ocean floor that are found near volcanically active areas
black smokers - water rises and deposits iron sulphide
using submarines what have we discovered about hydrothermal vents
that even thought they are very hostile environments there is a high level of macroscopic life meaning that microbial life must also exist
at what depth are black smokers usually found
2000m
how many meters results in a gain of an atm
10m = 1atm
what is the deepest place on the earth
the mariana trench - 11000m = 1100atm
what are the 3 different levels of pressure tolerance
- piezotolerant - can grow at atmospheric pressure and can tolerate increased pressure
- piezophile - optimal growth is above atmospheric pressure
- extreme piezophile - requirement for high pressure for growth and survival - unable to survive at sea level
name 3 structural features that high pressure tolerant organisms require
compartmentalisation (integrity) interactive structure (functional) a level of fluidity
compare the membranes of extreme piezophile and piezotolerant organisms
EXTREME PIEZOPHILE
- membrane is as fluid as possible
- increase in the number of unsaturated lipids
- allows membrane to move around at high pressure
PIEZOTOLERANT
- membrane is as solid as possible
- increased number of saturated lipids
can humans withstand high pressure
no
what conditions are mines and caves associated with
high salt levels
mineral rich
extreme temperature
no light
how do organisms play a role in the formation of caves and mines
- acidification of water results in the sculpture of caves
- changing the composition of rock and precipitate out chemicals
- iron/sulphur oxidising minerals contain microbes that produce sulphuric acid. this removes sulphur from the minerals making the surrounding water very acidic - negative pH values
- acidophiles can turn water red when they remove sulphur from minerals
what alterations are made to membranes to tolerate pH and give an example
membranes contain glycerol ethers which are more tolerant to low pH - lactobacillus acidophiles
what happens to the spotted lake in Canada over summer
water in the lake evaporates over summer revealing large mineral spots
describe the growth of microbes at their minimum temperature
slow growth
enzymatic reactions reduced
membrane gelling
describe the growth of microbes at their optimal temperature
rapid growth
enzymes performing at their highest
describe the growth of microbes at their maximum temperature
loss of membrane stability protein denaturation cell death collapse of cytoplasmic membrane thermal lysis
what are the 4 different levels of temperature tolerance in microbes
psychrophile - optimum growth <15 C
thermophile - heat tolerant
hyperthermophile - extreme heat tolerance
mesophile - optimum growth at body temperature
give an example or use of a psychrophile
listeria monocytogenes
Chlamydomonas nivails
give an example or use of a thermophile
their spores are used as a biological indicator measuring sterilisation
give an example or use of a hyperthermophile
thermus aquaticus - PCR
give an example or use of a mesophile
E.coli and other human pathogens
compares membranes of psychrophiles and hyperthermophiles
PSYCHROPHILES - low temperature, membrane becomes too solid - need to keep interactive and fluid - increase unsaturated fatty acids HYPERTHERMOPHILES - high temperature, membrane becomes too liquid - to maintain integrity solidify fats - increase saturated fatty acids
what are the cryoprotectant heat shock proteins used for
they prevent proteins unfolding and denaturing
they maintain correct structure and activity of proteins
is there overlap between extremophiles
yes i.e. can be heat and salt tolerant
what does each earth strata in soil represent
a different microenvironment
stratification of soil = stratification of ………….
bacteria
what is a winogradsky column used for
it is an enclosed system allowing the study of microbial communities
describe aerobes and give an example
growth in oxygen
e.g. Neisseria spp - meningitis, gonorrhoea
describe anaerobes and give an example
death in oxygen
e.g. actinomyees spp - soil
describe facultative anaerobes and give an example
can survive with or without oxygen
e.g. E.Coli
describe aerotolerant organisms and give an example
can grow in oxygen but metabolise anaerobically
e.g. rhizobium spp
describe microaerophiles and give an example
prefer reduced oxygen
can’t respire anaerobically
e.g. lactobacillus spp, campylobacter spp
what does spp mean
2 or more species of the genus
what is a rhizosphere
area of soil around plants containing a diverse population of microbes that utilise plant secretions e.g. proteins and sugars
what is microbial presence in soil essential for
proper root formation
how do the microbes in the rhizosphere act
microbes consume minerals and feed them back into the plant, promoting growth
how are microbes associated with the atmosphere
microbes have been associated with clouds, impacting out weather systems
how does precipitation occur and how is this useful for microbes
precipitation occurs through ice particles forming in clouds
- ice forms around nucleation particles (bacteria)
- particles are taken up into the atmosphere
this allows for widespread dispersal of microbes
……..…………. allows ice formation at higher temperatures
p.syringae
how does p.syringae allow ice formation at higher temperatures
the bacteria produce ice nucleation active proteins which increase freezing temperature
this punctures plant cells, allowing bacteria to penetrate
p.syringae is presented in snowfall, proving their role in precipitation - bacteria use this as their mode of transport
what is Vibrio fischeri
a gram negative bacteria that produces fluorescent light
describe the mutualistic relationships between V fischeri and the Hawaiian bobtail squid
the moon above the ocean casts a shadow from the squid and the v fischeri colonise the squid and release light to counteract this. this helps the squid hunt and helps it evade predators
the squid provides a selective environment exclusively for v fischeri and the v fischeri provide the bioluminescence advantage to the squid
what is the hawaiian bobtail squid
a nocturnal squid that uses moonlight hunting and employs v fischeri in a symbiotic relationship to aid its hunting
describe vibrio colonisation
- peptidoglycan signals epithelial cells to secrete mucous trapping bacteria
- v fischeri accumulate deep into the crypts of the squid after travelling down the light organ
- squid produces antibiotic against gram +ve bacteria which causes v fischeri to outcompete other microbes
- v fischeri activate the chitinolytic enzyme in the squid which digests chitin the environment
- chitinobiose attracts VF and more VF move over the pores and colonise
- VF becomes non motile and induces host epithelial cell swelling and release light
describe the light organ of the squid and how it is used
- light is emitted from the light organ in the squid mantle. the light organ has epithelial cells which form a ciliated surface on it structure beating water into the light organ
- water is passed through the ciliated cells and over the pores before travelling down the light organ and
describe newborn squid VF colonisation
- sterile - crypts are sterile in the first 30 mins
- permissive - initial mixed bacterial population in the crypt and mucous is shed by epithelial cells to attract the bacteria
- restrictive - antibiotic production to inhibit certain bacteria and VF is immune to this
- specific - specific VF colonisation due to chitinobiose secretion and an antibiotic compound against bacteria
VF are colonised within 2 hrs of birth
what happens when the VF threshold is reached in squid
- pores close and prevent microbe entry
- the process is controlled by LPS which acts as a signal to stop VF attraction by squid
- squid growth ceases, appendages regress, mucous production stops
- apoptosis of area around epithelial cells is induced to stop water beating across pores
- the squid gets a fresh influx and efflux of microbes every day
what is LPS
lipopolysaccharide which is found on the cells surface of bacteria
describe the diel cycles of the squid and VF
DAY
- squid buries in sand
- remaining bacteria replicate throughout the day to reach peak
NIGHT
- light organ full of VF and bioluminescence enables hunting
- going into day, bacteria are removed seeding the environment with VF for the next squid generation
describe quorum sensing in bioluminescence - the Lux operon
- Lux L synthesises AHL which binds to Lux R which produces a TF
- the TF activates bioluminescence genes
- increased activation of Lux L results from Lux R activating its gene
- we get amplification
what is quorum sensing
when bacteria sense their population size and coordinate their behaviour
give 3 examples where we see quorum sensing
biofilm formation
virulence
antibiotics
why doesn’t bioluminescence occur at low VF densities
because it is an energy expensive process and an small colony size would have a very small effect so it is not worth the cost
what does quorum sensing rely on to sense the population size
autoinducers
what do AIs do when the threshold has been reached
they activate cellular processes to respond
when density increases AI feed back into the cell and bind to transcription activators which results in transcription of genes for the desired response
what is the response of AHL at low densities
AHL diffuses out of the cell at low conc
no light is produced
what is the response of AHL at high cell density
AHL binds to Lux R
increased activation of Lux L
increased expression of Lux genes
light produced
give examples of other quorum sensing operons
agr operon controls virulence in S aureus
P. aeruginosa has 2 quorum sensing sytems - las and rhl
what is a biofilm
microbes adherent to each other or a surface, contained within an extracellular matrix
the majority of microbes prefer to be in a ………… state
sessile
what are the steps in biofilm formation
- cells colonise surface and easily detach
- quorum sensing promotes rapid growth
- extracellular matrix production
- mature biofilm formation
- quorum sensing detects growth slowing and aids biofilm dispersal
- nutrients inside the biofilm deplete when it gets large
what is biofouling
fouling of underwater structures with micro/microorganisms
what can biofouling lead to (disadvantages)
complete loss of functionality
detrimental economic impact due to increased energy and fuel costs and reduced speed
……… ………… are essential for biofouling
microbial biofilms
what are the steps in biofouling
- conditioning film
- multispecies microbial biofilm
- chemical signals attract secondary colonisers - unicellular algae
- invertebrate larvae and sponge colonisation
- algae and invertebrates grow a large community
give examples of how biofilms can form in medicine
prosthetic hip breast implant dentures urinary catheter voice prosthetics
what is the problem with biofilms in medicine
they are difficult to treat and they make devices difficult to remove
why are drugs becoming more inactive for
due to antimicrobial resistance
what stage of a biofilm is more dangerous, when it is intact or when it starts to disperse
dispersal - the cells are more pathogenic and highly virulent
give an example of a space biofilm
biofilm in Russian space shuttle caused corrosion and blocked water purification systems
how do biofilms change with changes in gravity
normal gravity - flat biofilm
microgravity - column and canopy shaped biofilms
why does classical microbiology restrict growth
because it does not cater for organisms found in all environments
the lab conditions are far form reality
classical microbiology is time consuming what other techniques are we using now
using DNA for identification
microarray
what are the steps in DNA identification of a microbe
- extract DNA and digest it
- clone into plasmid vectors before sequencing
- analysis to ID
what are the different types of omics
genomics
proteomics
transcriptomics
metabolomics
what are the steps in microarray analysis
- insert ss DNA into each square of the grid –> target gene
- extract mRNA and synthesise cDNA
- combine samples and add to microarray
- measure fluorescence
what is a microbiome
a large and mixed population of microbes coexisting together under many circumstances
what is the aim of the human microbiome project
to characterise the human microbiota to further out understanding of how the microbiome impacts human health and disease
give an example of how different areas of the body have different microbial environments
all areas of the mouth have similar microbiota but this is very different to the microbiota of the nose even though these structures are in close proximity - perhaps to do with temperature differences
gut bacteria is a big area of study - what areas have been looked into
research into IBS
obesity is associated with increased firmicutes and 90% less Bacteroidetes than a lean person
how can the microbiome be influenced
it changes with age changes depending on birth type changes depending on if breast fed changes depending on exposure to antibiotics changes depending on nourishment
what is symbiosis
close and usually obligatory association of 2 organisms of different species living together
what is mutualism
symbiosis where both organisms benefit
what is commensalism
symbiosis where one organism benefits and the other is neither hindered or benefited q
what is parasitism
symbiosis where the parasite benefits at the expense of causing detriment to the host
are microbes found in isolation or pure culture
very rarely
what is a commensal
lives in or on the host without injuring or benefitting the host
give examples of gut microbes that are commensals
- remodel VitB12 from diet to allow absorption
- involved production of thiamine, riboflavin and VitK
- metabolism of bile salts to allow reabsorption and recirculation
what is a pathogen
an organism that causes damage and disease to the host
what are Robert kochs postulates
1 - pathogen must be absent in all healthy individuals and present in all diseased
2 - pathogen must be isolated form diseased and grown on pure culture
3 - pathogen must cause same disease in inoculated host
4 - pathogen must be re-isolated from inoculated host
what are primary pathogens
organisms that always cause disease in a healthy individual
what is pathogenicity
the ability to cause disease
what is virulence
the degree or magnitude of capacity to cause disease
what are virulence factors
a product made by an organism that contributes to overall virulence
describe tetanus
- tetanus toxin is released by C tetani following growth of the organism in anaerobic environments of a deep punctured wound
- on release the toxin binds to peripheral neuronal axons and undergoes retrograde transport to the inhibitory interneuron where it prevents the release of inhibitory neurotransmitters such as glycine and GABA
- the neuron continues to be activated resulting in muscle contraction in both agonist and antagonist musculature - results in tetanic spasm
what does the tetanus vaccine do
it prevents disease by inhibiting binding of the toxin to the nerve endings
the vaccine is made from chemically detoxified tetanus toxin
what is an opportunistic pathogen
the capacity of these organisms to cause disease is dependent on the opportunity present e.g. geography, antibiotic, stress, age, genetics, nutrition
what is Neisseria meningitidis
- organisms found in the community at the back of the throat and generally do not cause disease
- sometimes colonisation with a new strain which we have no immunity to can result in disease and this frequently occurs in new uni students
- this causes meningitis
what is the vaccine for meningitis
protection mechanism is mediated by immunity to the capsule
what does staph aureus cause
- it is a skin organism that the majority of people are colonised with
- on the skin alone it is not dangerous but if it enters the blood it can cause significant disease
- access to the blood (bacteraemia) may be after surgery or via catheters
what is zoonosis
when a disease is transmitted from animals to man
give 3 examples of zoonosis
- campylobacter jejuni - most common cause of gastroenteritis in man and comes from poultry
- enterohaemorrhagic E.coli - can cause haemolytic uremic syndrome in man, especially children and is transmitted from cattle
- rabdoviridiae causes rabies in man and is transmitted from bats
susceptibility to infection is ………………., what are some of the factors that it is dependent on
multifactorial
factors: susceptibility, agent, exposure, dose, virulence
most mutations are lethal but what happens if one is advantageous
the resulting organism proliferates rapidly and becomes dominant, outgrowing its competitors
why is microbial evolution so rapid
it is rapid because unlike humans, their growth is rapid
what can mutations in microbes cause
altered sensitivity to drugs
altered receptor recognition (of tissue)
altering recognition by the host (immunity)
name two examples of virulence associated traits
toxins and adhesins
how are new trait acquired in a bacterial population
by horizontal gene transfer and rapid growth ensures spread within a population
what are the 3 types of horizontal gene transfer
natural transformation - uptake of naked DNA
conjugation - genetic exchange between bacteria
transduction - exchange due to phage predation
what are the stages of bacterial growth
lag
log
stationary
death
what are the steps of transformation
- ss DNA released when bacteria lyse and die
- uptake of DNA and incorporation into the genome of other bacteria through homologous recombination into chromosomes
(competency factor increase uptake and are produced in response to quorum sensing)
it is thought that it evolved as a mechanism of bacterial repair
what are conjugative plasmids
plasmids that encode the genes that are required for the transfer pilus - self replicating pieces of DNA
what are the steps in conjugation (bacterial sex) - E.coli
- DNA exchange occurs when an F +ve strain carrying the plasmid meets an F -ve strain with no plasmid
- the F pilus makes contact with the cell pulling them closer together
- a relaxosome forms through which ss DNA passes and the double helix is regenerated by DNA pol
what is the relaxosome made of
several proteins that are able to recognise a specific site on the conjugation plasmid
what do some of the other genes on the conjugative plasmid encode for
virulence factors
what are HFr strains
strains in which plasmids integrate into chromosomes at high frequency
what are the steps that lead to transduction
it is dependent on infection by phages which are capable of both the lytic and lysogenic cycle
- lytic - virus uses host to replicate DNA an dproteins an produce new particles and burst out of the cell killing it
- lysogenic - viral DNA integrated to bacterial chromosome where it is replicated - reversion to lytic cycle if bacteria are under threat
what are the 2 types of transduction
generalised and specialised
what is generalised transduction
bacterial chromosome part wrongly packaged into phage head
DNA then injected into the new cell which may integrate into the chromosome
what is specialised transduction
sometimes phages take DNA that lies adjacent to bacterial DNA resulting in chimeric phage with a mix of viral and bacterial genes
what are some scars of DNA transfer
change in codons
remnants of phage proteins etc
what are pathogenicity islands
when large pieces of DNA are integrated - frequently encode structures with virulence traits
does transferred DNA always persist
no - maybe because of:
- restriction enzyme of CRISPR recognises DNA
- endonuclease activity
what happens if transferred DNA does persist
it may multiple within the chromosome and produce a toxin
elements can excise - what is clean excision
when excised element is identical to the inserted element
elements can excise - what is inefficient excision
excised DNA contains genes from the host chromosome
how was penicillin discovered
by accident - alexander flemming was a messy scientist
he found some bacteria that had grown overnight and saw that something (penicillin) was being produced by mould and was killing the bacteria
what are the 5 types of antibiotics
- inhibition of bacterial cell wall synthesis or destruction of synthesis enzymes
- inhibition of protein synthesis by bacteria - binding to ribosome
- disruption of microbial cell membranes
- inhibition of reproduction by interfering with nucleic acid synthesis
- inhibition of cell metabolism and growth
what are the common uses of antibiotics clinically
- treatment of infection
- post surgery recovery - breaking skin allows bacteria in
- chemotherapy - immune system suppressed
- chronic diseases
what is streptomycin effective against
M tuberculosis
what is the second leading cause of death worldwide
infectious diseases
drug resistance in which diseases is predicted to have the largest impact
E.coli
malaria
TB
what are some causes of resistance
- over prescribing antibiotics
- not finishing treatment course
- overuse of antibiotics in livestock
- poor infection control in hospitals
- lack of hygiene and poor sanitation
- lack of new antibiotics being developed
what is intrinsic resistance
the innate ability of bacteria to resist activity of a particular antibiotic due to structural and functional characteristics
what is acquired resistance
microbe obtains resistance to antibiotic which it was previously susceptible to sue to mutation or acquisition of foreign resistance genes
why are gram -ve bacteria more resistant to antibiotics
because the antibiotics can’t cross the membrane very easily
what is triclosan effective against
gram -+ve and some gram -ve but does not inhibit pseudomonas because they carry a gene that makes a protein that is insensitive to the antibiotic
what are some ways that microbes acquire resistance
- minimising antibiotic entry
- mutating the target of the antibiotic - changing chemical groups - can change affinity or block site
- inactivate the antibiotic by hydrolysis
resistance is inevitable
why is less money being spent on antimicrobial resistance compared to other areas of health
because pharma companies are profit making organisations and are trying to make as much money as possible for share holders
antibiotics are cheap and effective so don’t make so much money as drugs for chronic long term conditions
how does resistance happen
- bacteria susceptible to antibiotic but bacterial genomes are subject to mutation
- they acquire additional genes via horizontal transfer
- natural selection occurs and resistant population is favoured
what 2 factors mean resistance can occur very quickly
horizontal gene transfer
short generation time
mutations that increase resistance often come at a cost of what
reduced growth which is subsequently regained by additional compensatory mutations
……..….. ………. plays a role in resistance development
spatial location
how do B lactam become resistant
they have sites for enzymatic degradation of penicillin and caohaloporins
what are potential solutions to AMR
- reduce demand
- increase the number of effective antimicrobial drugs
- a global coalition for action on AMR
- global public awareness
- improved hygiene
- reduced unnecessary use of antimicrobials in agriculture
- promote new diagnostics to reduce misdiagnosis
- promote vaccines and other alternatives
- improve working rewards of people working on infectious diseases
- improve global surveillance of AMR
what are new diagnostic techniques for infectious disease
molecular diagnostic techniques - e.g. sequencing
what are alternatives too antibiotics
protein based bacteriophage use photoexcited quantum dots for killing multidrug resistant bacteria alligators bdellovibrio
how are American alligators alternatives for antibiotics
their wounds heal rapidly and without infection
they produce cationic antimicrobial peptides with antimicrobial properties
how are bdellovibrio alternatives for antibiotics
they are gram -ve bacteria and members parasitize other bacteria by entering their periplasmic space and feeding on biopolymers
they prey on other bacteria so could be used as antibiotics
