A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis.

Microbial ecologists are increasingly turning to small, synthesized ecosystems1-5 as a reductionist tool to probe the complexity of native microbiomes6,7. Concurrently, synthetic biologists have gone from single-cell gene circuits8-11 to controlling whole populations using intercellular signalling12-16. The intersection of these fields is giving rise to new approaches in waste recycling17, industrial fermentation18, bioremediation19 and human health16,20. These applications share a common challenge7 well-known in classical ecology21,22-stability of an ecosystem cannot arise without mechanisms that prohibit the faster-growing species from eliminating the slower. Here, we combine orthogonal quorum-sensing systems and a population control circuit with diverse self-limiting growth dynamics to engineer two 'ortholysis' circuits capable of maintaining a stable co-culture of metabolically competitive Salmonella typhimurium strains in microfluidic devices. Although no successful co-cultures are observed in a two-strain ecology without synthetic population control, the 'ortholysis' design dramatically increases the co-culture rate from 0% to approximately 80%. Agent-based and deterministic modelling reveal that our system can be adjusted to yield different dynamics, including phase-shifted, antiphase or synchronized oscillations, as well as stable steady-state population densities. The 'ortholysis' approach establishes a paradigm for constructing synthetic ecologies by developing stable communities of competitive microorganisms without the need for engineered co-dependency.

Quorum Sensing Communication Modules for Microbial Consortia.

The power of a single engineered organism is limited by its capacity for genetic modification. To circumvent the constraints of any singular microbe, a new frontier in synthetic biology is emerging: synthetic ecology, or the engineering of microbial consortia. Here we develop communication systems for such consortia in an effort to allow for complex social behavior across different members of a community. We posit that such communities will outpace monocultures in their ability to perform complicated tasks if communication among and between members of the community is well regulated. Quorum sensing was identified as the most promising candidate for precise control of engineered microbial ecosystems, due to its large diversity and established utility in synthetic biology. Through promoter and protein modification, we engineered two quorum sensing systems (rpa and tra) to add to the extensively used lux and las systems. By testing the cross-talk between all systems, we thoroughly characterized many new inducible systems for versatile control of engineered communities. Furthermore, we've identified several system pairs that exhibit useful types of orthogonality. Most notably, the tra and rpa systems were shown to have neither signal crosstalk nor promoter crosstalk for each other, making them completely orthogonal in operation. Overall, by characterizing the interactions between all four systems and their components, these circuits should lend themselves to higher-level genetic circuitry for use in microbial consortia.

Dynamic T cell-APC interactions sustain chronic inflammation in atherosclerosis.

Atherosclerosis is a chronic inflammatory disease of large and medium-sized arteries characterized by leukocyte accumulation in the vessel wall. Both innate and adaptive immune responses contribute to atherogenesis, but the identity of atherosclerosis-relevant antigens and the role of antigen presentation in this disease remain poorly characterized. We developed live-cell imaging of explanted aortas to compare the behavior and role of APCs in normal and atherosclerotic mice. We found that CD4+ T cells were capable of interacting with fluorescently labeled (CD11c-YFP+) APCs in the aortic wall in the presence, but not the absence, of cognate antigen. In atherosclerosis-prone Apoe-/-CD11c-YFP+ mice, APCs extensively interacted with CD4+ T cells in the aorta, leading to cell activation and proliferation as well as secretion of IFN-γ and TNF-α. These cytokines enhanced uptake of oxidized and minimally modified LDL by macrophages. We conclude that antigen presentation by APCs to CD4+ T cells in the arterial wall causes local T cell activation and production of proinflammatory cytokines, which promote atherosclerosis by maintaining chronic inflammation and inducing foam cell formation.