Fluidics For Synthetic Biology: Prototyping Microbial Communities

MIT IAP 2015 | 20.S952 Biological Engineering Graduate Course

The human gut is an astonishing ecosystem of trillions of micro-organisms that live in a remarkable harmony with us, the human host. In this intensive graduate course, students developed 3D design and fabrication skills and constructed fluidic "artificial guts." Students utilized these structures to culture a variety of gut-based micro-organisms, both in mono- and co-cultures, to prototype and construct from scratch their own microbial communities.


Dr. David Sun Kong with students and mentors at MIT Lincoln Laboratory Beaver Works




class1: introduction

Course overview, Talks "Synthetic Biology," Dr. Peter Carr (MIT Lincoln Laboratory); "Microfluidics," Dr. Todd Thorsen (MIT Lincoln Laboratory)

class 2: 3D Design

3D design workshop by Brian Chan, Talk "3D Printed Hardware for DNA Assembly," Will Patrick (MIT Media Lab)

class 3: fluidics & fabrication

High-throughput microfluidics and sequencing the "dark matter" of microbes. 3D stereolithography printing workshop by Formlabs. Talk "Microfluidics for Microbial Genomics," Professor Paul Blainey (MIT Broad Institute)

class 4: engineering the human microbiota

Process first prints, biology lab (68-074) safety training. Talk "Making the Microbiota - how microbes colonize the gut," Sean Kearney (MIT Human Microbiome Center) Talk "Engineering the human microbiome: Designing personal analytics technology," Mariana Matus and Yaniv Turgeman (MIT Human Microbiome Center).


Process prints, start microbial cell culture, Talk "Open Biome," Mark Smith (President & Co-Founder, www.openbiome.org)


Talk: "Little Devices," Jose Gomez-Marquez (Principal, Little Devices)


Talk: "Multi-material 3D Valves," Steven Keating & Will Patrick (MIT Media Lab)





student course comments

"Amazing 9 days! I was blown away by how much we and other groups were able to accomplish. Thanks for this awesomely MIT-flavored experience!"

-Charlie Shih, Graduate Student, Biology

"Content and overall structure were great! It felt well thought out and executed. The curation of a fantastic group of people both to speak and to work was notable. The facilities and resources were perfect. Generally awesome!!"

-Yaniv Turgeman, Graduate Student, Human Microbiome Center

"The course exceeded my every expectation! I appreciated the safe environment that David created where I felt completely free to explore my questions and take creative risks. This inviting space seeped into the wet lab and the fabrication lab. The connection between the lectures, design, and investigation pieces of the class tied the material together to create a fantastic education experience. I am so glad to have been a part of such a supportive community of brilliant individuals who were so willing and ready to help me."

-Noa Machover, Pre-Frosh

"I loved the rapid pace at which we could design, get results, evaluate, and redesign, get results again, evaluate, over and over. It was super exciting!

-Guan Rong Tan, MIT-Singapore Alliance

student comments regarding instructor

"David's enthusiasm for the course material was nothing short of inspiring. He was also incredibly thoughtful and supportive of everyone in the class. He was able to create a community of collaborators and friends out of strangers."

-Noa Machover, Pre-Frosh

"David was great across the board, but I think his particular strengh is in bringing people and ideas together and encouraging mental connections. I felt like he ran the course in a way that maximized our intellectual freedom."

-Charlie Shih, Graduate Student, Biology

"Energy, charisma, knowledge, insight, pedagogy, the complete package, boom!"

-Yaniv Turgeman, Graduate Student, Human Microbiome Center

"Thanks for being super encouraging :) You really helped make all of us with all different kinds of skill sets and expertise feel comfortable with whatever we were doing!"

-Guan Rong Tan, MIT-Singapore Alliance

"Very good in explaining every step of the course to beginners and pros at the same time...very motivating. Very patient."

-Helene Steiner, Visiting Researcher, Media Laboratory