Microfluidics for creating and controlling spatially structured ...
Microfluidics for creating and controlling spatially structured environments for single cells and multi-species communities applied to anaerobic microorganisms Meghan Vincent Rustem Ismagilov Lab: James Boedicker, Hyun Jung Kim, Weishan Liu, and Wenbin Du Support: NIH
Microbial Communities -- the least understood biosphere
Mixed microbial communities in lichen The ISME Journal 2009, 3, 1105-1115
Bacterial communities are spatially structured, and do interesting chemistry everywhere-- plants, soils, humans...
We don’t fully understand who does what and how many functions are performed
Challenges include: •Isolating interesting microbes that we see from metagenomic databases • Cultivating new species • Understanding heterogeneity and confinement in natural environment • Understanding community stability • Utilizing microbial communities
Microfluidic tools can allow us to probe functions of microorganisms by controlling the spatial environment
Aqueous droplets in tubes
Aqueous droplets in arrays on glass
Controlled spatial structure on small scale
Controlled spatial structure on large scale
We use quorum sensing in Pseudomonas aeruginosa to ask if confinement can activate high density behavior in single cells
Boedicker, JQ et al, Angew. Chem. Int. Ed. 2009 48: 5908-5911
One is a quorum
200 fL of media cell at ~1010 CFU/mL Boedicker, JQ et al, Angew. Chem. Int. Ed. 2009 48: 5908-5911
1) Creating high density environment a) Induce behavior b) Analyze function
2) Building spatially structured functional communities a) Synthetic b) Large scale c) Anaerobic
Functional significance of QS induced by confinement: QS-dependent growth from single cells Growth with adenosine as carbon source; a QS-dependent growth condition
Boedicker, JQ et al. Angew. Chem. Int. Ed. 2009 48: 5908-5911
Small volumes can be used to separate single cells from a mixture for cultivation and analysis
Liu, W et al. Lab Chip Lab Chip 2009 9: 2153-2162
High density environment can be used for running functional assays on small numbers of cells
Liu, W et al. Lab Chip Lab Chip 2009 9: 2153-2162
Building functional communities using microfluidics
Synthetic community with syntropic interactions
Kim, HJ et al. PNAS 2008 105:18188- 18193
The community is unstable in a traditional well-mixed culture system – winner takes all
Kim, HJ et al. PNAS 2008 105:18188- 18193
A simple microfluidic device to control spatial structure and chemical communication
Kim, HJ et al. PNAS 2008 105:18188- 18193
With spatial structure, the community is stable even under starvation conditions
Kim, HJ et al. PNAS 2008 105:18188- 18193
Community stability only at intermediate separations (fences make good neighbors)
Kim, HJ et al. PNAS 2008 105:18188- 18193
Scaling-up spatially structured communities
Synthetic communities produced in a scalable fashion
Kim, HJ et al. Integrative Biology 2011 3: 126-133
Synthetic Biology without Genetic Engineering: new functions by spatially structured synthetic microbial communities
Kim, HJ et al. Integrative Biology 2011 3: 126-133
In Conclusion 1) Creating high density environment a) Induce behavior in single cells Study heterogeneity Potential for cultivating unculturable? b) Analyze function pull out microbes of interest 2) Building functional communities a) Synthetic Understand what makes communities stable b) Large scale Utilizing communities to perform a function c) Anaerobic Goal: build and understand the functions of microbial communities in the gut
Microbial Communities -- the least understood biosphere Microfluidics enables us to control single cells, the physical environment around cells, and spatial structure of microbial communities.
Mixed microbial communities in lichen The ISME Journal 2009, 3, 1105-1115
Microbial Communities -- the least understood biosphere
Mixed microbial communities in lichen The ISME Journal 2009, 3, 1105-1115
Bacterial communities are spatially structured, and do interesting chemistry everywhere-- plants, soils, humans...
We don’t fully understand who does what and how many functions are performed
Challenges include: •Isolating interesting microbes that we see from metagenomic databases • Cultivating new species • Understanding heterogeneity and confinement in natural environment • Understanding community stability • Utilizing microbial communities
Microfluidic tools can allow us to probe functions of microorganisms by controlling the spatial environment
Aqueous droplets in tubes
Aqueous droplets in arrays on glass
Controlled spatial structure on small scale
Controlled spatial structure on large scale
We use quorum sensing in Pseudomonas aeruginosa to ask if confinement can activate high density behavior in single cells
Boedicker, JQ et al, Angew. Chem. Int. Ed. 2009 48: 5908-5911
One is a quorum
200 fL of media cell at ~1010 CFU/mL Boedicker, JQ et al, Angew. Chem. Int. Ed. 2009 48: 5908-5911
1) Creating high density environment a) Induce behavior b) Analyze function
2) Building spatially structured functional communities a) Synthetic b) Large scale c) Anaerobic
Functional significance of QS induced by confinement: QS-dependent growth from single cells Growth with adenosine as carbon source; a QS-dependent growth condition
Boedicker, JQ et al. Angew. Chem. Int. Ed. 2009 48: 5908-5911
Small volumes can be used to separate single cells from a mixture for cultivation and analysis
Liu, W et al. Lab Chip Lab Chip 2009 9: 2153-2162
High density environment can be used for running functional assays on small numbers of cells
Liu, W et al. Lab Chip Lab Chip 2009 9: 2153-2162
Building functional communities using microfluidics
Synthetic community with syntropic interactions
Kim, HJ et al. PNAS 2008 105:18188- 18193
The community is unstable in a traditional well-mixed culture system – winner takes all
Kim, HJ et al. PNAS 2008 105:18188- 18193
A simple microfluidic device to control spatial structure and chemical communication
Kim, HJ et al. PNAS 2008 105:18188- 18193
With spatial structure, the community is stable even under starvation conditions
Kim, HJ et al. PNAS 2008 105:18188- 18193
Community stability only at intermediate separations (fences make good neighbors)
Kim, HJ et al. PNAS 2008 105:18188- 18193
Scaling-up spatially structured communities
Synthetic communities produced in a scalable fashion
Kim, HJ et al. Integrative Biology 2011 3: 126-133
Synthetic Biology without Genetic Engineering: new functions by spatially structured synthetic microbial communities
Kim, HJ et al. Integrative Biology 2011 3: 126-133
In Conclusion 1) Creating high density environment a) Induce behavior in single cells Study heterogeneity Potential for cultivating unculturable? b) Analyze function pull out microbes of interest 2) Building functional communities a) Synthetic Understand what makes communities stable b) Large scale Utilizing communities to perform a function c) Anaerobic Goal: build and understand the functions of microbial communities in the gut
Microbial Communities -- the least understood biosphere Microfluidics enables us to control single cells, the physical environment around cells, and spatial structure of microbial communities.
Mixed microbial communities in lichen The ISME Journal 2009, 3, 1105-1115
