HTGAA 2021: Microbiome & Microfluidic

Guest Lecturer : David Kong (MIT), Mariana Matus (Biobots.io)

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

Background

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.

Homework

Part 1: Design a milli-fluidic device for microbial cell-culture

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.

Part 2: Design experimental conditions for...a microbial cross-feeding interaction?

Find a research or journal article where researchers cultivate 2 or more microbial strains. What technology are they utilizing? How scalable is this approach to more than 2 strains? How do they address issues related to requiring multiple media?
Propose a technology for culturing 2 or more strains. How might you innovate in this area given the paper you reviewed?
One of the great challenges in microbiology currently is culturing “unculturable” microbes. Propose a methodology for how you might explore this significant space of uncultured microbes.
Review an article on an artificial gut-on-a-chip technology. What scientific hypotheses are they testing with this in vitro tool? Could you propose an upgrade or innovation to their technique to enable the exploration of other scientific hypotheses? Provide an example of at least one hypothesis you would explore with your proposed system.
One of the biggest challenges in public health is quickly detecting new disease outbreaks. How would you go about adaptively responding to new outbreaks? Biobots is using qPCR, so you need to know what you are looking for. How might you develop a technology with a more general view? Some example approaches include microfluidics and point-of-care sequencing, but what else? In particular, are there ways to look for RNA viruses like the flu and SARS-CoV2?
Extra credit: In the hardware class you designed a fluidic device. Please either use this device as a starting point, or provide a sketch design of a fluidic device that could be used in the gut-on-a-chip system you are proposing in question 4.

Useful Resources

Readings on Microbiome

Microfluidics & Millifluidics

Gut-On-A-Chip

Living Therapeutics

Developing a new class of engineered live bacterialtherapeutics to treat human diseases

Swabbing Subways

Genetics of IBD

Jostins et al Host Microbiome have shaped the genetic architecture of Inflammatory Bowel Disease. Nature 491:119-24 2012

Microbiome therapeutics in IBD

Cohen et al. Genetic Factors and the Intestinal Microbiome Guide Development of Microbe Based Therapies for Inflammatory Bowel Diseases. Gastroenterology in press (accepted March 2, 2019)
Somineni and Kugathasan The Microbiome in Patients with Inflammatory Diseases. Clinical Gastroenterology and Hepatology 17:23-255, 2019

Healthy microbiome - Human Microbiome Project (HMP)

Human Microbiome Consortium: Structure, Function and Diversity of the Healthy Microbiome Nature 486:207-14
Human Microbiome Consortium: A Framework for Human Microbiome Research Nature 486:215-12
Glibert et al, Current Understanding of the human microbiome. Nature Medicine 24:392-400, 2018

Commensal Transmission and FMT

Browne et al. Transmission of gut microbiota: spreading of health. Nature Reviews Microbiology 9:531-543, 2017
Effect of fecal microbiota transplantation on 8-week remission in patients with Ulcerative Colitis: A Randomized Clinical Trial JAMA 321:156-164, 2109
Krajicek et al. Nuts and Bolts of Fecal Microbiota Transplantation Clin Gastro Hepatol 17:345-352, 2019

Dysbiosis and diseases

Frank et al Molecular-Phylogenetic characterization of Microbial Community imbalances in human inflammatory Bowel Diseases Proc Natl Acad Sci USA 104:13780-5, 2007
Yilmaz et al. Microbial Network Disturbances in relapsing refractory Crohn’s Disease. Nature Medicine March 7, 2019 Epub ahead of print

Host Microbe interactions

Dorrestein et al Finding the missing links among Metabolites, Microbes and the Host. Immunity 40:824-832, 2014
Yilmaz et al. Microbial Network Disturbances in relapsing refractory Crohn’s Disease. Nature Medicine March 7, 2019 Epub ahead of print
Blander et al Regulation of Inflammation by Microbiota interactions with the Host. Nature Immunology 18:851-860, 2017

Microbial Co-culture