Team:MichiganState/Human Practices


Human Practices

Human Practices

This year, Michigan State iGEM set out to develop a biocontainment strategy that could be used by the synthetic biology community in a variety of applications to ensure safety and security in their engineered solutions. Therefore, gaining a better understanding of the needs of the SynBio community was integral to the design of our project. To understand the needs of the community, we spoke with representatives from various SynBio startups as well as members of the synthetic biology research community.

Our project was conceptualized as a result of conversations with judges, mentors, and past MichiganState iGEM team members in response to the growing need for improved biocontainment strategies within iGEM. MichiganState’s 2020 iGEM team worked to develop an engineered gut symbiont for bees in order to break down neonicotinoid pesticides. However, the implementation of such an uncontrollable transgenic microbe would be challenging from a biosafety standpoint. This was noted by iGEM Safety committee members as well as the iGEM judges, and while MSU’s 2020 team worked towards developing some physical containment measures, we were unable to identify a pre-existing robust mechanism to prevent horizontal gene transfer.

Furthermore, our 2020 work identified several key concerns of the public at large concerning biosafety of synthetic biology solutions. For example, the survey we administered to the general public indicated that many individuals were concerned about the safety of GMOs and their impact on both human health and the environment. Dr. Laurie Thorp at Michigan State University also stressed that rigorous biosafety measures and testing would be critical in both gaining public trust and ensuring public safety if a transgenic microbe were to be implemented in a relatively uncontrolled environment.

Summary of Interviews

Interviewee Takeaways Project Integration
Finn Stirling

Finn Stirling completed his PhD in Pamela Silver’s lab at Harvard. His research focused on the design and implementation of microbial kill switches, so we wanted to talk with him to gain insight about biocontainment in general and receive feedback on the design of our toxin/antitoxin layer. Dr. Stirling advised us to pay close attention to the evolutionary stability of the toxin component of our system in order to ensure that it would be effective as a security measure for many generations. He also noted the lack of a sufficiently sensitive assay to detect horizontal gene transfer. Our conversation with Dr. Stirling informed our toxin/antitoxin system design. He advised us to pay attention to the evolutionary stability of the toxin component of our system.

After speaking with Dr. Stirling, we decided to pay particular attention to attributes of our TA system that could decrease burden and increase evolutionary stability. For these reasons, we decided to chromosomally integrate the antitoxin gene in the final design to increase its evolutionary stability and decrease the odds of transfer to non-target organisms. We also decided to minimize the burden placed on the cell by the TA components, as excess burden would select for mutations that render the TA system nonfunctional [citation]. For this reason, in our initial experiments, we planned to place both the toxin and antitoxin under inducible promoters and characterize by adjusting respective inducer concentrations to find the minimal expression rates needed to lyse and rescue the cell, respectively. Reducing expression levels should reduce burden, reducing the strength of selection against the TA system. We also chose a TA system we believed would pose a relatively low burden (link to Design page).

Zach Abbott ZBiotics, CEO

Zach Abbott was the first individual from industry that we spoke with, and our conversation with him was integral to our understanding of the biocontainment needs of SynBio startups. He confirmed that horizontal gene transfer will become a critical consideration in engineered probiotics going forward. He suggested that we consider which bacterial strains our intended audience uses most frequently. He also informed us that E. coli is unlikely to be used in commercialized engineered probiotics due to public concerns.

Because we want our system to be adaptable to multiple applications, we chose to first implement our system in E. coli, but to be mindful of the ways in which we could simplify adaptation of our system to other microbial chassis (see Proposed Implementation).

Lauralynn Kourtz Allied Microbiota, CEO

Allied Microbiota is a SynBio startup dedicated to utilizing natural pathways for environmental cleanup purposes. Dr. Kourtz spoke with us at length about biocontainment needs in the industry and the criteria that would need to be met for a company to consider implementing a novel biocontainment strategy. Dr. Kourtz placed a heavy emphasis on rigorous testing, including extensive field testing, before a biocontainment system could be widely implemented by industry professionals.

For this reason, we emphasized education and outreach in our project (link to education and outreach page). We held webinars with iGEM teams as well as students from our university on biocontainment and its role in synthetic biology research. Our conversations with Dr. Kourtz and Dr. Stirling (see above) motivated our team to focus heavily on quantifying horizontal gene transfer with our HGT assay.

Kelly Smith and Tammy Zimmer JoynBio Represenative

We spoke with representatives from JoynBio, an agricultural biotechnology company, about regulations and steps companies can take to mitigate risks associated with their engineered solutions. They confirmed that horizontal gene transfer is an area of concern for those working on agricultural synthetic biology projects.

Our team was mindful of this when approaching implementation strategies. We also conducted literature reviews to assess the discrepencies from our results in lab to an agricultural environment. This was additionally important for understanding the accuracy of the comprehensive biocontainment strategy as a whole and how it could be modeled beyond in vitro results.

Todd Kuiken iGEM Safety & Security

We met with Dr. Kuiken to gain insight into the ways in which the iGEM community approaches biocontainment. He brought our attention to the issue of the potential negative impact of synthetic toxin/antitoxin systems as a biocontainment measure on native microbial ecosystems. He also noted that although biocontainment is a critical concern in synthetic biology, organisms are unpredictable, and it may not be feasible to entirely prevent horizontal gene transfer.

Although we did not have time this summer to assess the potential impacts of our TA system components on other microbes, we suggest that future teams making use of a TA system as part of their biocontainment mechanism attempt to purify their toxin and ensure it does not inhibit growth in any non-target microbes that may be found in a native microbiome. We also urge teams to consider the overall safety of their engineered constructs, regardless of the efficacy of their biocontainment mechanisms.