Miniaturizing Evolution: Adaptation of Whole-Cells Using a Microfluidic Chip

Introduction
Adaptive laboratory evolution (ALE) is a methodology used for the generation of novel optimized traits for bioproduction. Conventional ALE techniques involve axenic cultivation and do not consider that microorganisms preferably life in communities known as biofilms. Microfluidics have fundamentally changed the field of microbial ALE as it can mimic naturally occurring microenvironments promoting the growth of biofilms alongside planktonic cells.
Goals
The aim of the presented work was to develop a user-friendly and cost-effective microfluidic chip device to perform miniaturized, automated ALE experiments.
Materials and Methods
This poster introduces the microfluidic evo.S (evolution under stress) chip, which was designed to create tunable, spatially stable stressor concentration gradients across consecutive growth wells to adapt microbial cells to defined profiles of stressors such as antibiotics.
Results
The cultivation of microbial cells in the interconnected growth wells results in microenvironments within the chip creating mixed populations, ranging from planktonic cells over to stiff biofilms. The generation of controlled gradient profiles leads to the adaptation of Escherichia coli to antibiotics and revealed the chip’s ability to differentiate between persistence and resistance. ... mehrImportantly, this approach was effectively employed for the discovery of previously unknown mutations conferring resistance to nalidixic acid in E. coli. Recently, a customized chip setup was used to successfully adapt the thermophilic organism Thermus thermophilus to the antibiotic kanamycin, and also to the utilization of an alternative carbon source.
Summary
The microfluidic evo.S chip enables the cultivation of microbial cells under quasi-static conditions with tunable and spatially stable stressor profiles, enhancing the occurrence of mutations conferring resistance to antibiotics. This kind of chip-based ALE can be applied to adapt virtually any microorganism to desired environmental conditions and offers crucial insights into the mechanism of antibiotic resistance and biofilm formation.

References
Zoheir, A. E., Stolle, C., Rabe, K. S., Appl. Microbiol. Biotechnol. 2024, 108, 162.
Zoheir, A. E., Späth, G. P., Niemeyer, C. M., Rabe, K. S., Small 2021, 17, 2007166.