How to Grow Almost Anything

Week 7: Microbiome and Microfluidics

Bacteria galore


Class protocol reference

Building a simple microfluidics device

We made a very simple two-inlet one-outlet microfluidics device with PDMS (a VERY strong silicone gel that is very clear (like a thick coverslip) and yet non-toxic), beneath it a thick double-sided tape with the channel lasercut, and a glass slide as the bottom of the channel beneath the tape. Three holes were punched into the PDMS according to the cutouts with biopsy punchers. Tubing is inserted in each hole (cut diagonally for easy insertion), and then a syringe inserted into the inlet tubes to add fluid.

At 10x magnification on a light microscope, we could see specks of bacteria (saturated, clumpy culture) flowing through the channel.

Microbiome ponderings

    Comparing gut microbiome intervention approaches:
  • Probiotics. Pros: The introduced microbiome composition is generally known and well-characterized, and can be introduced in very palatable manners (yogurt, kombucha, etc.) Cons: Effects on humans still not well-studied and varies greatly across microbiomes; probably not good as an acute treatment.
  • Fecal microbiota transplant (FMT). Pros: Very effective for treating C. difficile infection (CDI); screening methods and production pipelines are already in place. Cons: The introduced microbiome composition is highly complex and not completely characterized; doesn't really work on anything other than CDI.
  • Sterile Fecal Filtrate Transfer (FFT). Pros: Lower risk of introducing infectious microbial agent compared to FMT, since only contains sterilized microbial debris, DNA, proteins, etc. Cons: Can't introduce new bacteria for colonization.
  • Diet. Pros: Generally good for improving health; relatively cheap. Cons: Effects vary by person; insufficient for acute treatments.

Microbial human augmentation

I was thinking about superpowers, and while no amount of microbes would endow me with flight, I did think of something that's a stretch but nevertheless at least conceivable: poison immunity. By that I mean that we can find/engineer microbes to colonize everywhere in our body that would either break down toxins into non-harmful substituents, or sequester them and enter the digestive process for egestion with stool.

My Microbes

We plated skin and mouth swabs of ourselves and picked one bacterial colony from each location to send in for 16S rRNA sequencing. BLASTing both forward and reverse sequence reads gave the same result as Genewiz's own identification for the oral bacteria: Granulicatella adiacens, a typical oral commensal microbe. The skin microbe could only be identified as a species of Bacillus by Genewiz, but the sequence shares high sequence identity with Brevibacterium frigoritolerans, a soil microbe.