Microbial Community Interactions on a Chip
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Abstract
Multispecies microbial communities drive most ecosystems on Earth. Chemical and biological interactions within these communities can affect survival of individual members and the entire community. However, the prohibitively high number of possible interactions within a microbial community has made the characterization of factors that influence community development challenging. Here we report a Microbial Community Interaction (μCI) device to advance the systematic study of chemical and biological interactions within a microbial community. The μCI creates a combinatorial landscape made up of an array of triangular wells interconnected with circular wells, which each contains either a different chemical or microbial strain, generating chemical gradients and revealing biological interactions. Bacillus cereus UW85 containing GFP provided the “target” readout in the triangular wells, and antibiotics or microorganisms in adjacent circular wells are designated the “variables”. The μCI device revealed that gentamicin and vancomycin are antagonistic to each other in inhibiting the target B. cereus UW85, displaying weaker inhibitory activity when used in combination than alone. We identified three-member communities constructed with isolates from the plant rhizosphere that increased or decreased growth of B. cereus . The μCI device enables both strain-level and community-level insight. The scalable geometric design of the μCI device enables experiments with high combinatorial efficiency, thereby providing a simple, scalable platform for systematic interrogation of three-factor interactions that influence microorganisms in solitary or community life.
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6 hours prior to the target strain
Have the authors considered or tried using spent supernatant from these 4 strains (instead of directly inoculating the strains)? It could be interesting to compare the effects of spent supernatant versus the presence of actual species to see if they mostly compare to the '6 hour prior to the target strain' or if they are pretty different.
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microbial community interactions
Eventually, if the authors want to measure/map the interactions within microbial communities using uCI, have the authors tested whether the effects of 3 species inoculated in 3 different variable wells connected to the same target strain are the same effect on the target strain than if 3 species were inoculated together in the same variable well. I believe that having the 3-species mixed together and associated interactions would lead to a different growth outcome for the target strain (and might be more representative of the original natural ecosystem). It is quite nice that the uCI platform offers the opportunity to explore such questions (whether community effects are the sum of more simple effects) and help decipher higher-order interactions.
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microbial community interactions
Eventually, if the authors want to measure/map the interactions within microbial communities using uCI, have the authors tested whether the effects of 3 species inoculated in 3 different variable wells connected to the same target strain are the same effect on the target strain than if 3 species were inoculated together in the same variable well. I believe that having the 3-species mixed together and associated interactions would lead to a different growth outcome for the target strain (and might be more representative of the original natural ecosystem). It is quite nice that the uCI platform offers the opportunity to explore such questions (whether community effects are the sum of more simple effects) and help decipher higher-order interactions.
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6 hours prior to the target strain
Have the authors considered or tried using spent supernatant from these 4 strains (instead of directly inoculating the strains)? It could be interesting to compare the effects of spent supernatant versus the presence of actual species to see if they mostly compare to the '6 hour prior to the target strain' or if they are pretty different.
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