Growing microbes in millifluidic droplets

Microbiology has continuously pushed efforts towards understanding microbial diversity. Technologies and methods have also evolved, from plating, and use of microscopes and cytometers, towards micro-well handling robots and, finally, fluidic-based devices. The aim of this review was to bring microbiologists attention to the outstanding analytical and handling power of millifluidic droplet technologies for analysing and sorting phenotypic diversity in the microbial world. This new format overcomes many limitations of previous approaches. It provides outstanding reproducible growth conditions over droplet reservoirs allowing unprecedented sensitive read-out over thousands of colonies over time. The confinement of the millifluidic train within tubes and the implementation of a three phases format excludes any contamination issues. The automation and handling of reservoir droplets is inherently facilitated. We show as a proof of principle the efficiency of capturing phenotypic diversity within a bacterial sample submitted to a sub-minimum inhibitory concentration of antibiotic. The precision offered by the millifluidic format allows the detection of a variety of resistance strategies that compete and coexist. The review finally explores the potential of this approach to address new challenges such as community-based growth of multiple-strain systems.