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Microdroplet-enabled highly parallel co-cultivation of microbial communities.

Park J, Kerner A, Burns MA, Lin XN - PLoS ONE (2011)

Bottom Line: Conventional pure culture-oriented cultivation does not account for these interactions mediated by small molecules, which severely limits its utility in cultivating and studying "unculturable" microorganisms from synergistic communities.In this study, we developed a simple microfluidic device for highly parallel co-cultivation of symbiotic microbial communities and demonstrated its effectiveness in discovering synergistic interactions among microbes.Our device was able to detect a pair-wise symbiotic relationship when one partner accounted for as low as 1% of the total population or each symbiont was about 3% of the artificial community.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America.

ABSTRACT
Microbial interactions in natural microbiota are, in many cases, crucial for the sustenance of the communities, but the precise nature of these interactions remain largely unknown because of the inherent complexity and difficulties in laboratory cultivation. Conventional pure culture-oriented cultivation does not account for these interactions mediated by small molecules, which severely limits its utility in cultivating and studying "unculturable" microorganisms from synergistic communities. In this study, we developed a simple microfluidic device for highly parallel co-cultivation of symbiotic microbial communities and demonstrated its effectiveness in discovering synergistic interactions among microbes. Using aqueous micro-droplets dispersed in a continuous oil phase, the device could readily encapsulate and co-cultivate subsets of a community. A large number of droplets, up to ∼1,400 in a 10 mm × 5 mm chamber, were generated with a frequency of 500 droplets/sec. A synthetic model system consisting of cross-feeding E. coli mutants was used to mimic compositions of symbionts and other microbes in natural microbial communities. Our device was able to detect a pair-wise symbiotic relationship when one partner accounted for as low as 1% of the total population or each symbiont was about 3% of the artificial community.

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Comparisons between experiments and calculations for cell distribution in droplets.Calculations were based on the Poisson distribution. (A) Numbers of droplets carrying different numbers of cells. (B) Numbers of droplets carrying four different combinations of a two-strain system. (C) Numbers of droplets carrying eight different combinations of a three-strain system.
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pone-0017019-g002: Comparisons between experiments and calculations for cell distribution in droplets.Calculations were based on the Poisson distribution. (A) Numbers of droplets carrying different numbers of cells. (B) Numbers of droplets carrying four different combinations of a two-strain system. (C) Numbers of droplets carrying eight different combinations of a three-strain system.

Mentions: We hypothesized that compartmentalization of different microbial species in a community are independent events and for each species, the number of encapsulated cells in a droplet follows the Poisson distribution. For experimental validation of this hypothesis, a co-culture consisting of two differently labeled E. coli strains, named W- and Y-, was injected into the device and the distribution of cells was examined with fluorescence microscopy. As shown in Fig. 2a, for each strain, the experimentally measured distribution of droplets carrying various numbers of cells agreed very well with calculated values using the Poisson distribution. The average number of cells in each droplet, which corresponded to the λ parameter in the Poisson distribution, was dependent upon the cell density in the seed culture injected into the device and the droplet volume determined by the device configuration.


Microdroplet-enabled highly parallel co-cultivation of microbial communities.

Park J, Kerner A, Burns MA, Lin XN - PLoS ONE (2011)

Comparisons between experiments and calculations for cell distribution in droplets.Calculations were based on the Poisson distribution. (A) Numbers of droplets carrying different numbers of cells. (B) Numbers of droplets carrying four different combinations of a two-strain system. (C) Numbers of droplets carrying eight different combinations of a three-strain system.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3045426&req=5

pone-0017019-g002: Comparisons between experiments and calculations for cell distribution in droplets.Calculations were based on the Poisson distribution. (A) Numbers of droplets carrying different numbers of cells. (B) Numbers of droplets carrying four different combinations of a two-strain system. (C) Numbers of droplets carrying eight different combinations of a three-strain system.
Mentions: We hypothesized that compartmentalization of different microbial species in a community are independent events and for each species, the number of encapsulated cells in a droplet follows the Poisson distribution. For experimental validation of this hypothesis, a co-culture consisting of two differently labeled E. coli strains, named W- and Y-, was injected into the device and the distribution of cells was examined with fluorescence microscopy. As shown in Fig. 2a, for each strain, the experimentally measured distribution of droplets carrying various numbers of cells agreed very well with calculated values using the Poisson distribution. The average number of cells in each droplet, which corresponded to the λ parameter in the Poisson distribution, was dependent upon the cell density in the seed culture injected into the device and the droplet volume determined by the device configuration.

Bottom Line: Conventional pure culture-oriented cultivation does not account for these interactions mediated by small molecules, which severely limits its utility in cultivating and studying "unculturable" microorganisms from synergistic communities.In this study, we developed a simple microfluidic device for highly parallel co-cultivation of symbiotic microbial communities and demonstrated its effectiveness in discovering synergistic interactions among microbes.Our device was able to detect a pair-wise symbiotic relationship when one partner accounted for as low as 1% of the total population or each symbiont was about 3% of the artificial community.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America.

ABSTRACT
Microbial interactions in natural microbiota are, in many cases, crucial for the sustenance of the communities, but the precise nature of these interactions remain largely unknown because of the inherent complexity and difficulties in laboratory cultivation. Conventional pure culture-oriented cultivation does not account for these interactions mediated by small molecules, which severely limits its utility in cultivating and studying "unculturable" microorganisms from synergistic communities. In this study, we developed a simple microfluidic device for highly parallel co-cultivation of symbiotic microbial communities and demonstrated its effectiveness in discovering synergistic interactions among microbes. Using aqueous micro-droplets dispersed in a continuous oil phase, the device could readily encapsulate and co-cultivate subsets of a community. A large number of droplets, up to ∼1,400 in a 10 mm × 5 mm chamber, were generated with a frequency of 500 droplets/sec. A synthetic model system consisting of cross-feeding E. coli mutants was used to mimic compositions of symbionts and other microbes in natural microbial communities. Our device was able to detect a pair-wise symbiotic relationship when one partner accounted for as low as 1% of the total population or each symbiont was about 3% of the artificial community.

Show MeSH