Abstract
With the emergence of inexpensive 3D printing technology, open-source platforms for electronic prototyping and single-board computers, “Do it Yourself” (DIY) approaches to the cultivation of microbial cultures are becoming more feasible, user-friendly, and thus wider spread. In this perspective, we survey some of these approaches, as well as add-on solutions to commercial instruments for synthetic and system biology applications. We discuss different cultivation designs, including capabilities and limitations. Our intention is to encourage the reader to consider the DIY solutions. Overall, custom cultivation devices offer controlled growth environments with in-line monitoring of, for example, optical density, fluorescence, pH, and dissolved oxygen, all at affordable prices. Moreover, they offer a great degree of flexibility for different applications and requirements and are fun to design and construct. We include several illustrative examples, such as gaining optogenetic control and adaptive laboratory evolution experiments.
Highlights
Microbiology is experiencing a renaissance driven by several applied and basic research fields, e.g., combating antimicrobial resistance and using microbes in industrial biotechnology relies on successes of systems and synthetic biology that strive to understand and engineer microorganisms
To decipher complex interactions of biological systems and identify mathematical models that best depict their behavior, systems biology benefits from large datasets, “Do It Yourself” Microbial Cultivation which are often captured working with small culture volumes that require experiment-specific control of growth environments
The high accuracy of bacterial cell density measurements achieved with the bioluminescence method enabled, for example, functional classification of antimicrobial drugs according to their pairwise interactions (Yeh et al, 2006)
Summary
Microbiology is experiencing a renaissance driven by several applied and basic research fields, e.g., combating antimicrobial resistance and using microbes in industrial biotechnology relies on successes of systems and synthetic biology that strive to understand and engineer microorganisms. “Do It Yourself” Microbial Cultivation which are often captured working with small culture volumes that require experiment-specific control of growth environments. Small volumes at the start that can later be scaled up, very specific environmental control of growing cultures, and an increasing range of microbes that are of great interest, make it almost impossible to purchase a microbial cultivation unit that will “do it all.”. Two most frequent small-volume microbial cultivation units are a bioreactor and a plate-reader. A bioreactor is a vessel that allows controlled growth of a microbial culture, for example, through the supply of fresh media and fixed environmental oxygen levels. Problems that can benefit most from DIY culturing technology require a great degree of flexibility or levels of control that are not readily available commercially. We discuss examples of custom build bioreactors (Toprak et al, 2013; Takahashi et al, 2014; Wang and Yang, 2017) (Figures 1a–c) and microplate readers (Chen et al, 2012; Heo et al, 2015; Richter et al, 2015) (Figures 2a–c), all of which needed to satisfy few common requirements
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