Week 12: Engineering the Human Gut Microbiome


This class was taught by David Kong with guest lecturers: Sean Kearney from Alm Lab at MIT & Professor Neri Oxman from MIT Media Lab. We discussed about the human gut microbiota, which 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).

Fig. 1: David, Sean and Neri at EMW Streetbio during the lecture!

Lab Homework Assignments

1. 3D print a 14 mL culture tube in at least one material. Culture a bacterial strain of your choice in this tube and compare the growth rate (optical density) over time versus a polystyrene control tube. Ideally use a strain featuring antibiotic resistance and culture in the presence of an antibiotic.

We 3D printed the design in 4 different materials. Here you can find their MSDS:

The three first were printed with an Objet Eden260VS from Stratasys which has a large pool of possible materials that we can print. The last one was printed with a MakerBot Replicator 2, however it was impeded by low-resolution fabrication which made it pourous and leaky.

Fig. 2: Planned protocol by Rachel and initial colony preparation.

The next day, we prepared each candidate test tubes with 3mL LB-Ampicillin and inoculated them simultaneously with 3uL stock (1:1000 ratio). We put the tubes in the shaking incubator at 37 degrees.

Fig. 3: Pipetting growth media, antibiotic and bacteria into each tube and incubating!

At given time points, we loaded a fraction of each tube’s culture sample into a cuvette, and measured the absorbance in the spectrophotometer. This number, the O.D. (Optical Density), is measurement of light shown through the side of the square cuvette. It is a common indices of how densely populated the bacterial culture is.

Fig. 4: At regular intervals, we performed optical density measurements using a spectrophotometer.

Growth Curves typically have an S-shape, an exponential growth phase from around OD 4.0 – 8.0. The lag phase prior shows accelerating growth, while the stationary phase after occurs when growth slows (due to space and energy resource limitations). Below are the resulting growth curves for our different materials.

Fig. 5: The resulting growth curves for the different materials.

2. a) Design a milli- or micro-fluidic 'artificial gut' or other 'organ-on-a-chip' device to be utilized, at a minimum, for cell culture.


2. b) Fabricate your device, or at least one component of your device.


2. c) Culture the organism from (1) in your milli- or micro-fluidic device.


3. Share your 'final' device designs on 'Metafluidics' www.metafluidics.com