An Inexpensive Autonomous Colony Separator With Sub-Micrometer Repeability

Abstract

Recent advances in methods used to domesticate large numbers of unculturable microbes have opened new doors for drug discovery (Nichols, et al., 2010; Ling, et al., 2015). However, there remain challenges in handling these newly cultured samples. Many samples are so small that they can only be viewed via microscopy and are difficult to manipulate. This limits the number of downstream analysis that can be performed. One of which is the domestication of unculturable microbes in vitro. The ability to communicate with other cells has been implicated as a significant factor in the domestication of unculturable microbes (Donofrio, et al., 2010). To summarize, the easier it is for cells to communicate, the more robust they appear to become. What if these colonies recovered in diffusion chambers could be separated into parts that still enable bacteria to easily communicate with each other? The current state of the art to separate bacteria colonies from a diffusion chamber either increases the distance between cells and destroys extracellular structures that facilitate communication or is expensive and lacks automation for high throughput potential. Thus there exists a need to separate these colonies while preserving extracellular structures inexpensively and autonomously to study this microbial population. An inexpensive autonomous system with sub micrometer repeatability is realized in this thesis. The material cost to replicate the system is estimated at 4,000 USD in comparison to 150,000 USD commercially available solutions (Leica, 2018). The system has the ability to position itself with sub micrometer repeatability, reducing the amount of damage in theory to specimens during separation in the event of repeat cuts. Lastly, the system has the ability to position over multiple samples, identify the most likely bacteria colony candidate using machine vision, and generate a toolpath. Further work is needed to determine an effective machining method to separate the bacteria colonies from the agar.