Bioengineering artificial microfluidic habitats for microbial single-cell analysis

IBG-1 at Forschungszentrum Jülich has been successfully pioneering the development of microfluidics for applied and basic research in microbiology and biotechnology since 2010. Innovative bottom-up concepts for microbial single-cell analysis enable researchers to address questions that cannot be answered by conventional laboratory-scale approaches. In highly interdisciplinary projects, microstructures at the femto- to picoliter scale are used to grow microorganisms with diverse requirements, providing new insights into mixed cultures, population heterogeneity, cellular interactions, single-cell physiology and more. Fluids behave differently at the micrometer scale. Laminar flow and diffusion governed mass transport can be precisely controlled, allowing precise spatial and temporal control of the microenvironment. Recent focus has been on advanced chip functionality and the development of more complex microfluidic landscapes to mimic natural, structured and dynamic environments. Deep learning algorithms are also being developed to efficiently analyze large image data stacks obtained by automated live-cell microscopy. The resulting software tools now enable nearly automated cell segmentation, cell tracking in dense populations, and discrimination between different organisms and fluorescently labelled strains.