Increasingly, realization is dawning that bacteria, micrometer-sized unicellular organisms, are an integral part of human health. Bacteria cause disease, a problem compounded by the alarming rise of antibiotic resistance. Conversely, bacteria are also central to our well-being, crowding numerous parts of the body such as our gut, mouth and skin, where they carry out essential physiological functions. To an important degree, our ability to detect and characterize disease-causing bacteria, and to understand and modulate beneficial bacteria, relies on cultivation of live microbes. It is surprising then, given the central role that bacteria play in our daily life, that we still depend on century-old classical microbiology techniques to cultivate, monitor and analyze bacterial growth, typically requiring an expansion to many billions of cells. The current PhD topic will focus on developing enabling technologies to cultivate, analyze and process bacteria at the single-cell level, obviating the need for batch growth and consequently speeding up downstream analysis and processing. Importantly, we anticipate not only the improvement and miniaturization of existing methodologies, but also to open up avenues towards the realization of groundbreaking innovations that may revolutionize healthcare and the emerging market of ‘health and wellness’.
Exploiting previous successful efforts to develop droplet microfluidics technology at imec, the platform will be adapted for single-cell level analysis of bacteria. In a first part of the research, the emphasis will be on developing a methodology to allow the massively parallel cultivation of bacteria, using picoliter droplets as discrete bioreactors. Individual encapsulation of bacteria avoids takeover of cultures by fast-awakening species when analyzing individual cells in a high-throughput manner. Different droplet generator architectures will be designed and experimentally evaluated to identify the most suitable approach, with special attention for configurations that maximize loading with single-cell droplet occupancy. Secondly, incubation of bacteria to allow for growth and cell division will preferentially occur off-chip. After sufficient time, the droplets are re-injected into the chip for quantification of growth. Different measurement modalities will be evaluated, e.g. based on fluorescence of dyes that selectively label the bacterial cell surface. In a final and third part, active microfluidic elements will be integrated into the chip to allow on-chip sorting of droplets of interest. Technological solutions for on-chip processing of droplet-contained bacteria will be explored depending on the downstream application that is envisaged, e.g. nucleic acid extraction for sequencing or PCR, visual inspection using lens-free imaging or recovery of viable cells for scaling up cultivation. Devices with various dedicated microfluidic structures will be designed and fabricated in imec’s cleanroom. The device will be thoroughly characterized and experimentally validated. This topic will be supervised and supported by a team of physicists, microbiologists and engineers in the imec life sciences department.
Required background: bio-engineering, physics
Type of work: 10% literature; 40% design, simulation and fabrication; 50% characterization and experimental validation
Supervisor: Liesbet Lagae
Daily advisor: Maarten Fauvart
The reference code for this PhD position is SE1712-27. Mention this reference code on your application form.