Microbiome Flashcards
What is the microbiome?
how prevalent are microbes in these systems:
immune digestive dental health nervous reproductive other
what are the 3 main parts to studying the microbiome?
collection microorganisms in a particular environmental niche- including bacteria, archaea, fungi etc
microbes colonise as infant
break food, release nutrients & disease
protect surface of teeth but some can degrade enamel
chemicals interact with
microbes to exchange info & lead development sleep, happiness etc
vagina colonised by bacteria- connection with bacteria & outcome of pregnancy
skin, body odor, bad breath, cancer & chemotherapy types that works
culturing
imagine
sequencing
How can you use GFP to label bacteria?
why is it good?
what does it require?
why is it limited?
how can you use bioluminescence to label bacteria?
what are the pros?
cons?
what do these techniques allow you to do?
engineering to express GFP with protein of interest
labels living cells & parts of cells
excitation light (hard for deeper tissues) & oxygen to mature (anaerobic bacteria hard to label)
only culturalable bacteria & limited number of colours - only 2-3 species at 1 time
engineering to express enzyme that emits light
doesn’t require excitation light- can be seen in deeper tissue
labels living cells
only 1 colour- only track 1 species of bacteria at a time
limited to only culturable bacteria
visually see & locate living bacteria in an organism
what is ex-vivo imaging?
pros?
cons?
what is FISH?
what is it used for?
pros?
cons?
how do you prepare for it?
what does it allow?
imaging by cutting open the organism & pulling out individual samples & cutting into thin sections
greater sensitivity- access to locations
cut open sample = hard to tell what looking at & might be different than when you prepared it
fluorescent compounds linked to single stranded DNA which is complementary to specific bacterial species
track species with known DNA
track multiple species at once (up to 20 different colours)
requires fixed & permeabilised cells so no dynamic/living systems
take piece single strand DNA complimentary to piece you want to find in specific bacterial species- attach probe & fluorophore to the probe
visualise & see all bacterial species & their interactions with eachother
How are biofilms formed?
what happens when communities become large?
what is bacterial invasion?
how does the biofilm stay together?
what does it contain?
what is unique about biofilm?
what happens at the core of the biofilm? (gases)
what else is in high concentration at the core?
what is at high conc towards outside?
by motile bacteria that replicate & forms communities when adhere to a surface
genes involved that signal bacteria to disperse from biofilm & become motile again
bacteria can’t naturally colonise directly with biofilm but can attach & grow to the bacteria already on it (antagonistic)
macromolecules
bacteria, extracellular DNA, proteins/polysaccharides (backbone), fatty acids/lipids, amyloid fibres & filamentous phages
not uniform throughout
centre = less oxygen so more anerobic bacteria which produce NO which diffuse out
communication signals, bacterial waste
oxygen, food & nutrients
what are biofilms used for?
what are the 5 different mechanisms?
because biofilms enable colonisation on surfaces bacteria normally don’t grow on, what can this affect in humans?
protect bacteria against antibiotics & antibacterials
- antibiotics cannot enter/penetrate the biofilm
- nutrient gradients mean bacteria towards outside grow slower so are more resistant to antibiotics
- the individuals that produce antibacterial resistance genes can protect whole community
- differentiation can lead to persister state
- resistant mutants can be collected
organ transplants, implanted devices, piercings, open wounds, tooth decay & genetic diseases (cystic fibrosis prevents clearing of bacteria out of lungs)
how can you identify what species are present in a population?
what can be done with 16S ribosome gene sequences?
what are commensal microbes? what are the 2 categories and types within those?
what is CDI and how is it caused?
how can you induce species diversity into the human microbiome?
isolate DNA, amplify genes of interest with PCR & readout different genes expressed at one time
amplify- identify what species is present
microbes that reside on surfaces (humans) but don’t harm health
indirect = immune induction & metabolic products direct = nutrient competition & direct toxicity
Clostridium difficile infection CDI- caused when take antibiotics & bad pathogens take over- can be treated with antibiotics but produces spores & allow CDI to take over again
fecal transplant- take sample, process, filter & inject via endoscopy
