UCSB members of the NSF ExFAB BioFoundry. From left to right: Oliver Vining, Elaine Kirschke, Jean-Marie Volland, Nathalie Elisabeth, Sherylle Mills Englander, Max Wilson, Michelle O’Malley, Joel Rothman, Niels Volkmann, Carolyn Mills.

An extensive collaborative project led by UC Santa Barbara studies unique and unusual microorganisms. Just like its name, the BioFoundry for Extreme & Exceptional Fungi, Archaea and Bacteria brings together distinguished professors from UCSB and collaborators from UC Riverside and California State Polytechnic University, Pomona, spanning departments such as bioengineering and geochemistry. This summer, the BioFoundry for Extreme & Exceptional Fungi, Archaea and Bacteria was one of five facilities awarded a $22 million grant from the National Science Foundation.

The National Science Foundation (NSF) grant will go into establishing an infrastructure accessible to the global research community, with staff dedicated to training both campus and external users on how to utilize the resources the biofoundry offers. It also provides fellowships for students to explore the equipment from the BioFoundry for Extreme & Exceptional Fungi, Archaea and Bacteria (ExFAB).

Biofoundries allow for the innovation of new technologies in the sectors of biology and manufacturing. UCSB chemical engineering professor and Principle Investigator for the ExFAB BioFoundry Michelle O’Malley describes the doors that the ExFab BioFoundry has the potential to open in the S.T.E.M. world.

“It’s a place where people can go to automate biology and biological experiments. In the past, these experiments would otherwise be done at the bench and be really time-consuming. The BioFoundry is really a facility where users can speed up engineering biology.” O’Malley said. “This new center that we we are building at UCSB is meant to develop novel instrumentation and workflows so that we can take unusual microorganisms from nature that are very difficult to grow and rapidly learn, engineer and template new biology into discoveries — these might be new enzymes, medicines and bioproduction platforms to make new biomaterials or sustainable products.”

Microbes are microscopic, single-celled organisms found in virtually every environment imaginable. The ExFAB BioFoundry’s goal is to harness microbes that have extraordinary traits, such as capturing nutrients or degrading forever chemicals — like those found in non-stick pans or waterproof fabrics — by developing improved prototyping and testing strategies.

The ExFAB BioFoundry plans to work with microbes of all kinds, including microorganisms found in the human body, the guts of animals, soil and the ocean. 

“We have projects where we are discovering enzymes that break down forever chemicals, microbes that degrade oil and microbes that produce synthetic fibers or fuel,” O’Malley shared.

The long-term goal of the ExFAB BioFoundry is to identify efficient and powerful enzymes that can enhance plant biomass deconstruction. O’Malley and her team aim to improve plastic conversion methods and develop oxygen-free production processes — an economically viable alternative to traditional biofermentation, which involves the conversion of organic material into other products through enzymatic activity and typically requires oxygen. The capabilities of these microbes can be harnessed for a wide range of bioproduction applications, from fuels and chemicals to materials and pharmaceuticals.

Each professor plays a different role in the BioFoundry and works on a specific component. While O’Malley and her lab study microbes that thrive in oxygen-free environments, such as anaerobes found in the gut or on the seafloor, Carolyn Mills, an assistant professor of bioengineering and one of many collaborators of ExFAB BioFoundry, specializes in the studies of proteins and protein engineering. 

“The fun thing I think about working on proteins, in particular, is that they exist in every single microbe. It turns out that these extreme and interesting microbes tend to have unique tools for surviving in their niche environment, and a lot of these tools come in the form of giant structures made of proteins,” Mills said. “I am excited to see what people find within the cell that I can take out and look at and offer my expertise through protein function characterization.”

Mills is currently working on a platform that can efficiently identify and test specific functions of microbes without the need for genetic tools. 

“Normally, the way you study [microbes] is you delete or make edits to the gene in the organism and then observe what happens to the functions — kind of like taking the wheels off a car and seeing if it still drives. We don’t have the tools for that for weird microbes.” 

Alongside UC Riverside’s work on genetic tool manipulation development, Mills is looking at cell-free protein synthesis systems, a method of examining a cell’s machinery and producing proteins without the use of living cells, reducing the process from days to just a few hours. According to Mills, her work is a complementary approach to the overall effort of protein cultivation and creating more hypotheses to test. 

O’Malley further highlighted the importance of multi-department and cross-campus collaboration that makes the ExFAB BioFoundry a hub of diverse research and ideas.

“Everybody who is part of ExFAB at UCSB, UC Riverside and Cal Poly Pomona are all people who work on microbes, just from a different perspective,” O’Malley said. “Some of us look at microbes as chemists, others as engineers and some view microbes as their own independent life forms just trying to survive in a tough world. You need all of those perspectives to enrich our biofoundry.”

“An opportunity we are really hoping to build up on campus is giving undergraduate students a chance to train on these automation techniques and software that will be really important going into the workforce,” Mills said. 

O’Malley looks forward to commercializing the ExFAB BioFoundry in a way that benefits the campus. She also hopes to develop a robust educational program in partnership with the California NanoSystems Institute, providing UCSB students with opportunities to get involved in the BioFoundry.

“We hope to develop intellectual property and provide the basis for spin-off companies and entrepreneurship at one level but also connect with established companies both local and worldwide who want to use our facilities, interact and hire our students.”