EDGE FGT: New approaches to rapidly domesticate non-model Clostridia for applications in sustainability and human health

Northeastern University, Boston MA

Investigators

Abstract

The Clostridia are a diverse group of bacteria that range from agents of human disease to industrial microbes used for renewable production of biofuels and biochemicals. Despite the importance of these bacteria, the majority cannot be genetically engineered, and even those that can are notoriously difficult to work with. This project develops fundamentally new approaches for genetically manipulating these bacteria, allowing scientists to study and control their unique physiology and metabolism at an accelerated pace, with far reaching impacts on sustainable biomanufacturing and human health. The research will provide interdisciplinary training for graduate students and a postdoctoral fellow. Additionally, aspects of the project will be incorporated into educational materials for K-12 and undergraduate students to expose them to career options in STEM fields. The tools developed will be disseminated to the broader community through conference workshops, online resources, and a new hands-on summer course. This project leverages state-of-the-art tools including CRISPR, phage recombinases, transposons, and directed evolution to develop new approaches to overcome the two main limitations in Clostridial engineering: i) low plasmid transformation efficiency; and ii) the reliance on plasmid-based homologous recombination for genome modification. The central premise of our team’s approach is that bringing together multiple labs with expertise in diverse Clostridia during the development and validation phases will result in more robust and portable functional genomics tools, maximizing their utility for the broader community. To ensure the broad dissemination of these tools and to democratize Clostridial genetics, we will create and maintain ClostridiaWiki, a community resource that will house detailed protocols and videos, as well as provide a forum for technical discussion between researchers. We will also run workshops at key conferences attended by Clostridia researchers. A new two week-long intensive Clostridial Genetics Short Courses at a state-of-the-art training lab at Northeastern will provide trainees and early career faculty lab-based instruction in Clostridial genetics, as well as seminars from leading local Clostridial researchers and professional development activities. Finally, in collaboration with the Northeastern and Tulane Centers for STEM Education, and the Tufts Pathway-to-the-PhD program, we will incorporate scientific aspects of this project into outreach activities aimed at broadening participation of URM K-12 and college students in STEM fields. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.