The emergence of antibiotic resistance calls for discovering and researching microbial-origin natural products for antibiotic activity. Since nearly 99% of microbes are 'uncultivable' in standard laboratory conditions, developing cultivation methods for these microbes is of high importance to natural product discovery. This thesis explored the potential for growing 'uncultivable' microbes through the design of a microbial domestication pod (MD Pod). The MD Pod is a 3D printed device containing a cylindrical cavity in which the microbes are placed. Microbes are prevented from migrating across the MD Pod through two enclosing polycarbonate (PCTE) membranes. The PCTE membranes also allow for the diffusion of nutrients, chemicals, and wastes across the MD Pod, supplying the microbes with substances needed for their growth and survival. The MD Pod is different from other similar devices by providing a single cavity for the growth of diverse microbial samples at once, enabling better cell-to-cell communication and, therefore, better chances of growth through achieving quorum sensing.

This thesis also explored the effect of encapsulating microbial cells in agarose microbeads through the use of a 3D printed, 1000 µm cross-flow microfluidic device, in which the shear stress of a mineral oil phase (containing 4% v/v surfactant), caused droplet formation of an agarose/cell mixture. Single-cell encapsulation is targeted to provide each microbe with a separate microbead to grow, and the microbeads are expected to provide the growing microbes with nutrients. Several MD Pod in-situ incubation tests were implemented using marine sediment bacteria collected from North River and Brackley Beach, Prince Edward Island. Most of the tests showed contamination of the used MD Pod devices (confirmed using polymerase chain reactiondenaturing gradient gel electrophoresis (PCR-DGGE) analysis). However, devices showing no contamination led to observing that encapsulated microbes formed single colonies after in-situ incubation, which is expected to make downstream microbial isolation easier.

Three known marine sediment bacteria, M. polaris (Gram-negative), P. aquimaris (Gram-negative), and B. licheniformis (Gram-positive), were used as representative bacteria to examine the effect of encapsulation on their growth. It was observed that these species do not form colonies on agar plates from their encapsulated samples when their microbeads were suspended in 50% Instant Ocean®, but B. licheniformis grew into individual colonies when its microbeads were suspended in 10% Marine Broth. Moreover, better cell survival and viability were observed for the three representative species when their respective microbeads were suspended in 10% Marine Broth. This suggested that growth on plates from encapsulated samples might not be suitable for all types of bacteria and that their suspending solution must contain a dilute amount of nutrients (in addition to salts) for their continued growth. It was also found that higher temperatures (40ºC and 45ºC) decreased the survival of the three species, suggesting that exposure to the encapsulation temperature (45ºC) might limit the types of bacteria that could be cultivated after encapsulation.

This thesis also explored the design of a system that provided separation of the mineral oil (used in the encapsulation) from an aqueous phase. Two systems were designed and tested, with a cartridge filter-inspired separation column showing approximately 97% - 99% separation. The system was further tested for microbead transfer from the oil phase to the aqueous phase. Through imaging, microbeads were observed in the collected aqueous phase, indicating that this system could be coupled with the microbead generation system to achieve higher throughput.

Last but not the least, an alternative microfluidic chip fabrication method was proposed and developed. A scaffold (of the desired microfluidic channels) was 3D printed using acrylonitrile butadiene styrene (ABS), then it was dissoluted in acetone at controlled conditions. The resulting scaffold was then placed in liquid polydimethylsiloxane (PDMS) and cured. A microfluidic chip was obtained by dissolving the internal scaffold using acetone. A T-junction microfluidic chip was produced using this method and was tested for droplet generation, suggesting that such a chip could be used for encapsulating the marine sediment bacteria. Finally, the ability of this method to fabricate microfluidic chips with different geometries was confirmed by fabricating a bifurcation channel and a drug testing microfluidic chip.