Nanofabricated structures and microfluidic devices for bacterial communities

Bacteria commonly live in diverse and dense communities interacting through physical contact and through the exchange of biochemical metabolites. Studying these interactions is of paramount importance not only to harvest the full metabolic potential of the microbial world but also to deepen our understanding and treatment of infectious disease. While common co-culturing methods can be adapted to the study of bacterial interactions, they typically operate within bulk cultures and do not provide physical separation between different bacterial species. This limits the ability to study spatial and temporal differences in bacterial interactions at the single cell level, prevents the optimization of growth conditions for each species in the bacterial community and masks heterogeneity within the bacterial community. This thesis discusses the potential of microfluidic devices to study chemical interactions between different bacterial species individually cultured in independent growth chambers separated by hydrogel membranes. Two PDMS microfluidic platforms for culturing of individual bacterial species have been fabricated using Direct Laser Writing as lithography technique and tested by inoculating with Escherichia coli. Bacterial growth within the microfluidic device was monitored using optical microscopy and an image processing algorithm developed to quantify bacterial growth at the single cell level. Bacterial growth within the device was confirmed over a 12-hour period albeit at an extremely slow growth rate. It was observed that successful inoculation of the culture chamber was critically dependent on the geometry of the microfluidic device. Computational models were performed using COMSOL to better understand fluid flow within the devices and subsequently used to optimise the design of a double-layer PDMS microfluidic bacterial culture system. This double-layer microfluidic module could ultimately be fabricated in an array format in which adjacent chambers are connected via a permeable hydrogel to enable co culturing of mixed bacterial species.