Spatiotemporal Dynamics of Synthetic Microbial Consortia in Microfluidic Devices

Abstract

Synthetic microbial consortia consist of two or more engineered strains that grow together and share the same resources. When intercellular signaling pathways are included in the engineered strains, close proximity of the microbes can generate complex dynamic behaviors that are difficult to obtain using a single strain. However, when a consortium is not cultured in a well-mixed environment the constituent strains passively compete for space as they grow and divide, complicating cell−cell signaling. Here, we explore the temporal dynamics of the spatial distribution of consortia cocultured in microfluidic devices. To do this, we grew two different strains of Escherichia coli in microfluidic devices with celltrapping regions (traps) of several different designs. We found that the size of the traps is a critical determinant of spatiotemporal dynamics. In small traps, cells can easily signal one another, but the relative proportion of each strain within the trap can fluctuate wildly. In large traps, the relative ratio of strains is stabilized, but intercellular signaling can be hindered by distances between cells. This presents a trade-off between the trap size and the effectiveness of intercellular signaling, which can be mitigated by increasing the initial seeding of cells in larger traps. We also built a mathematical model, which suggests that increasing the number of seed cells can also increase the strain ratio variability due to an increased number of strain interfaces in the trap. These results help elucidate the complex behaviors of synthetic microbial consortia in microfluidic traps and provide a means of analysis to help remedy the spatial heterogeneity inherent to different trap types.

Long-range temporal coordination of gene expression in synthetic microbial consortia

“…1d). As shown in previous theoretical work [19][20][21] and confirmed in a more extensive accompanying experimental study 22 , this design supports a stable distribution of strains once the trap was filled.…”

Majority sensing in synthetic microbial consortia

“…8 . This device has previously been demonstrated to result in fluctuations of strain ratios over time due to the small population size within the cell trapping region 38 . Microfluidic devices provide single-cell gene expression data by using fluorescence microscopy and continuous growth due to constant fresh media flow 39 .…”

“…Plasmids for all strains used were constructed using traditional restriction enzyme cloning and golden gate cloning methods. Plasmids for the 'control strains' are from Alnahhas et al 38 . The control strains are BW25113 ΔaraC ΔlacI E. coli cells 40 transformed with a single plasmid each.…”

Novel Tunable Spatio-Temporal Patterns From a Simple Genetic Oscillator Circuit

“…There are a vast number of experimental conditions which could be created to induce different spatio-temporal patterns in such microcolonies. Microfluidics has shown to be of particular help to control mechanical constraints (Ruprecht et al, 2017 ), substrate stiffness (Wang et al, 2018 ), nutrients (Alnahhas et al, 2019 ), chemical inducers (Danino et al, 2010 ), cell-cell signaling (Alnahhas et al, 2019 ), and pattern formation (Kantsler et al, 2020 ). As we showed in Figure 9 , controlling biophysical constraints using different channel layouts and mechanical properties of the substrate could produce different patterns of growth rate that give rise to structures that mimic different stages of the development of organisms (Johnson et al, 2017 ; Toda et al, 2018 ).…”