challenges in the measurement of the microbiome emma allen-vercoe
Post on 08-Jan-2018
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Challenges in the measurement of the microbiome
Emma Allen-Vercoe
Model microbiomes
• Important to study a microbial ecosystem as an ecosystem– It is more than the sum of its parts
• For the gut (and oral) communities, continuous culture (chemostat) systems have been developed– Have plans for a vaginal chemostat
Chemostats
Pros• Ethically acceptable• Can run for several weeks or
more• Cheaper than animal
studies • Controllable • Metabolites not absorbed• Sample all you need, when
you want to
Cons• No host side to the
equation • Some components of the
ecosystems may be lost• Liquid phase necessary
Our “Roboguts”
•Seeded with fresh feces and set to model the distal gut ecosystem•Host-free system•Can be used to support growth of fastidious gut anaerobes
Simplified (defined) communities
• Human gut ecosystems display functional redundancy– Can we therefore create simplified, defined
communities?• Working on this…
– Defined ecosystems are highly reproducible (fecal ecosystems are not (between donations))
– Currently using iPath to indicate functional redundancy in order to rationally design ecosystems
– Can test them for e.g. function and stability in chemostats
Mathematical modeling of ecosystems
• Collaborations with theoretical biologists– Can we create model microbial ecosystems in silico?
• Very early days – only 2 or 3 strain ecosystems can be modeled at one time (processing constraints? Programming constraints?)
• Need more communication between mathematics and biology
• Start process early for maximum benefit!
A shout out for metabolomics
• It’s not what’s there, it’s what they are doing that’s important!– Profiling small molecules is like eavesdropping on
microbial conversations• Powerful when combined with in vitro modeling
– Best methods? MS? NMR? Both?• Need better predictive tools to get from
metagenomes to small molecules– What’s the pathway?
“Liquid gold”
Allows us to eavesdrop on microbial conversations!
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