HTGAA 2021:  Microbiome & Microfluidic

Guest Lecturer : David Kong (MIT), Mariana Matus (

TA : Pat Pataranutaporn (MIT), M.S. Suryateja Jammalamadaka (MIT)


Gut Microbiome

The human gut microbiota is one of the most densely populated ecosystems of microorganisms on earth. With an estimated 100 trillion microorganisms, the gut is an extraordinarily complex system of microbe-microbe and microbe-host interactions. A growing body of research is beginning to elucidate the diverse impacts the gut microbiota plays in human health and development, from nutrition, to disease, and even cognition. Recently, with the success of fecal matter transplants (FMTs) to treat infectious disease, microbes are emerging as a unique therapeutic. Model systems to both prototype and study complex polymicrobial systems are a necessity for producing robust microbial communities that can be engineered at both the genetic level (subcellular) and population level (multicellular).

Microfluidic & Millifluidic Systems

Microfluidic & millifluidic, or lab-on-a-chip systems, have been used for several decades as a methodology for miniaturizing and automating biology and chemistry experimentation. Devices can be fabricated a variety of size schools using myriad materials depending upon the functional goals of the device. Active components can be fabricated using polymeric materials (e.g., poly-dimethyl-siloxane (PDMS)) or can be static and more easily fabricated using, for example, 3D printing.


In this homework, we will use Autodesk Fusion 360, a 3D CAD software, to design a 3D printed micro/milli fluidic device. Please install the software using the following instruction.

For inspiration, visit Metafluidic, an open repository for fluidic devices. Details on how to use software tools will be discussed in recitation on Wed 4/28 @5p ET.


Useful Resources

  • Readings on Microbiome
  • Microfluidics & Millifluidics
  • Gut-On-A-Chip
  • Living Therapeutics
  • Swabbing Subways
  • Genetics of IBD
  • Microbiome therapeutics in IBD
  • Healthy microbiome - Human Microbiome Project (HMP)
  • Commensal Transmission and FMT
  • Dysbiosis and diseases
  • Host Microbe interactions
  • Microbial Co-culture