Evolution on a microscale: Empowering adaptation and selection through a microfluidic chip

Introduction

Adaptive laboratory evolution (ALE) is a key tool to investigate fundamental questions about the processes underlying the evolution of life and how microbial populations adapt to their environments, such as the emergence of antibiotic resistance. Microfluidics have fundamentally changed the field of microbial ALE as it can mimic naturally occurring microenvironments promoting the growth of biofilms alongside planktonic cells.[1]

Goals

A microfluidic ALE chip device that features adjustable, spatially defined physico-chemical stressor gradients should be developed employing an in-flow gradient aligned parallel to the flow direction to enhance the robustness of ALE process including the efficient on-chip screening of the complete entire cell population.

Materials & Methods

The evo.S (evolution under stress) microfluidic chip was designed using CAD and fabricated from PDMS (polydimethylsiloxane) and used for the adaptation of microbial cells to stressors in a customizable stressor concentration gradient.[2]

Results

The controlled generation of different gradient profiles across the interconnected compartments leads to adaptation of Escherichia coli to the presence of antibiotics and revealed the chip's capacity to differentiate between persistence and resistance. Importantly, this approach was effectively employed for the discovery of previously unknown mutations conferring resistance to nalidixic acid in E. coli. Recently, the chip was modified to successfully adapt the thermophilic organism Thermus thermophilus to kanamycin.

Summary

The evo.S chip enhances the occurrence of mutations, resulting in the generation of stress-resistant strains. This kind of miniaturized chip-based ALE offers crucial insights into the mechanism of antibiotic resistance and can be applied to adapt virtually any microorganism.

References

[1] Zoheir, A. E., Stolle, C., Rabe, K. S., Appl. Microbiol. Biotechnol. 2024, 108, 162.

[2] Zoheir, A. E., Späth, G. P., Niemeyer, C. M., Rabe, K. S., Small 2021, 17, 2007166.