Microbiome: Engineering the Gut
April 4, 2019
The human body contains an enormous number of bacteria-in fact, we have more bacterial cells in us than we have "human" cells. This means much of our health is reliant not only on our genes, but also on our (hopefully) symbiotic relationship with the microbes living within us. However, there is still much we don't know about the microbiome's exact effects on our bodies, and it is an important area of modern research.
That being said, humans have engaged with manipulation and maintainance of the microbiome for a long time. Probiotics that we use and consume in yogurt, kefir, cheese, kombucha, and many others. These help maintain our gut ecosystems on a day to day basis, boosting variety within the microbiome and reducing the risk of specific species overwhelming our systems. Probiotics are bacteria that we commonly use in food, and we have for a long time, and so these microbiome interventions are not regulated. However, they are limited in scope, and are insufficient to treat more complex diseases of the microbiome.
One such disease is caused by the bacterium Clostridium difficile. This is an antibiotic resistant bacteria that often overruns the gut when on antibiotics for an extended period of time. Normally, C. diff is kept in check by other bacteria, but when the system is weakened, it can dominate. The current solution for this is using a fecal matter transplant, which allows healthy bacteria back in so that they can grow and control C. diff. However, this technique requires having a "healthy" donor (a term not always clearly defined) and transfers all of their bacteria rather than the ones that are strictly necessary.
Microbiome interventions need not solely be restricted to disease states. The microbiome has major effects on our mood and mental functioning-the gut is frequently referred to as our "second brain." One major function of the gut-brain axis is mood regulation. As our understanding of the mechanisms of this action increases, we may be able to create microbiome interventions that are able to control people's mood, by perhaps making them feel more satisfied and happy. With this interventions, there is always a potential for abuse-in this case, a microbe that decreased your fear response may make you more trusting and more willing to buy a product or sign a deal. As with all innovations, we must remember the potential for abuse inherent in the development of this technology.
In the experimental portion of this assignment, we sent in our bacteria for 16S ribosomal sequencing. I used BLAST to determine from the sequences what species they were. I determined the bacterium sampled from my oral microbiome was in the Lysinibacillus genus and the bacterium sampled from my skin microbiome was in the Acinetobacter genus. My skin bacterium had a high likelihood of being A. johnsonii, but my oral bacterium had very similar scores for many in its genus, but the closest from both forward and reverse sequencing was L. fusiformis. The company agreed with me on my skin bacterium, but thought my oral bacterium was L. mangiferihumi, which had a higher matching score using a slightly different metric.
We also used tape, coverslips, glass slides, and PDMS to make a small microfluidics device this week. Mine is below. The tape seal was slightly loose and it leaked a bit.
