Week 11: Engineering the gut microbiome

Engineering the gut microbiome

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?

The research I have chosen was published in 2016 by Han et al., where they cultivated microalgae with bacteria strains. The bacteria Muricauda sp. were co-cultured with microalga Tetraselmis chuii, Cylindrotheca fusiformis and Nannochloropsis gaditana in extra organic carbon containing medium To solve the media problem, the bacteria reduce the dissolved oxygen concentration and consume the organic material excreted by microalgae. In turn they produce biotin, cobalt amine and thiamine Many microalgae can grow on light and chemical energy. Although it would be reasonable to think that the bacteria and microalgae will compete for nutrients if they’re grown in the same cultivation system, the competition can be abated by adding excessive nutrients or continuously adding nutrients. .

Photo credit: Han et al., 2016

Propose a technology for culturing 2 or more strains. How might you innovate in this area given the paper you reviewed?

I would be curious to automate the selection of organism to co-culture. If for example we had a chip where we could culture different combinations of microbes (eg. a chip with 1,000 options), we would be able to select the more “symbiotic combinations” of 2,3 or even tenths of organisms

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.

I guess that most unculturable microbes are those that live in very specific conditions that we cannot replicate. By giving them the media we think they need, we might be promoting the growth of certain microbes instead of others within the sample. Therefore, playing with low concentration of certain substrates might be enough to allow the growth of those microbes while containing the growth from the others. We might even be able to use a micromanipulator to separate the different cells and then do a high screening on culture conditions for each of them.

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.

I have selected this article by Poceviciute et al, 2019 They created an oxygen gradient across the endothelium-epithelum-lumen axis to culture human endothelial and epithelial cells with a diverse microbiota The chip has 2 channels separated by a permeable membrane. Endothelial cells grew in the lower channel and epithelial cells in the upper one, where they got in contact with the microbiota. They co-cultured two established cell lines (human intestinal microvascular endothelial cells, and Caco2 epithelial cells) and a model anaerobe (Bacteroides fragilis) on the chip. On the left hand side of the image are the hypothesis they were testing and on the right one, the follow-on hypothesis they want to test. Below is the chip design

Photo credit: Poceviciute et al, 2019

I would want to understand how the digestion process affects the microbiota. For example we know that bile acids produced by the liver are secreted into the gut and affect the microbiota composition. Those microbes can metabolize them and some of them will get re-absorbed. If we could insert a pump that adds bile acids at specific times, simulating digestion, we could check how the microbe composition changes over time.

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?

Virus encode proteases, so if we were able to design a protein that can be cleaved by different viral proteases, similar to a backbone vector with different restriction sites we might be able to detect many different viruses no matter what their specific sequence is since I would expect that there would be some commonalities between cleavage sites. The actual detection after the cut would happen because our peptide would be bound by specific aminoacids modified to have a quencher and reporter compounds so once the peptide is cut, we would expect to see fluorescence.