Droplet microfluidics for microbiology: techniques, applications and challenges

Abstract

Droplet microfluidics has rapidly emerged as one of the key technologies opening up new experimental possibilities in microbiology. The ability to generate, manipulate and monitor droplets carrying single cells or small populations of bacteria in a highly parallel and high throughput manner creates new approaches for solving problems in diagnostics and for research on bacterial evolution. This review presents applications of droplet microfluidics in various fields of microbiology: i) detection and identification of pathogens, ii) antibiotic susceptibility testing, iii) studies of microbial physiology and iv) biotechnological selection and improvement of strains. We also list the challenges in the dynamically developing field and new potential uses of droplets in microbiology.

Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms

“…Single-cell analysis is attracting great interests in many frontiers of microbiological research, as single-cell imaging, isolation and sequencing techniques are providing the possibility to monitor phenotypic and genetic heterogeneity among isogenic populations during cell growth, stress resistance, metabolites accumulation and other bioprocesses1, and to select individual cells with desired properties for biotechnology applications2. On the other hand, as the majority of microbes on earth are yet to be cultured, single-cell isolation in combination with single-cell sequencing can help identification of unknown species from environmental samples or clinical specimens and investigation of microbial community structure and functions3.…”

“…Recently, microfluidics-based methodology has shown great potential in single-cell isolation with facile automation, accuracy and high efficiency29. Single-cell trapping systems based on on-chip valves and microchambers were demonstrated for individual environmental bacterial cells and combined with on-line digital PCR10 or whole genome amplification1112.…”

Detection of antibiotics synthetized in microfluidic picolitre-droplets by various actinobacteria

“…Droplet microfluidics has the potential to revive the golden era of natural product discovery, as it combines miniaturization of reaction vessels and high-throughput on an unprecedented level 1–4 . In stable compartments of volumes down to a few picoliter or even femtoliter, functional tests are carried out in a highly parallelized manner at rates often exceeding 1000/s.…”

Accelerating bacterial growth detection and antimicrobial susceptibility assessment in integrated picoliter droplet platform

“…Furthermore, these devices frequently rely on additional materials (e.g., cellulose membranes (Balaban et al, 2004; Wakamoto et al, 2013) and agarose gels (Choi et al, 2013; Eun et al, 2011; Li et al, 2014)) or external forces (e.g., electric force (Lu et al, 2013)) to trap bacteria, which increase the complexity of device fabrication and operation. In part to address such challenges, droplet microfluidics recently emerged as an approach for single-cell isolation, detection, and analysis (Kaminski et al, 2016; Yan et al, 2016). Similar to microchambers and microchannels, microfluidic droplets enable volume reduction, high local signal-to-background ratio, and accelerated time to detection (Boedicker et al, 2008; Ng et al, 2016; Tushar D. Rane et al, 2012).…”