Intellectual Adventures in the Poop Squad

Contributed by Carson Ingold

It’s Carson, with more updates from the poop squad and a few late-night philosophical thoughts sprinkled in. As the great Sam Cooke said, “a change is gonna come”, and change indeed has come. Since my last post, I developed and executed experiments based on the founding data of the poop squad. That founding experiment, and the squad’s namesake, investigated the effects of fecal microbiota transplants (FMT) on the gut microbiota composition of a mouse model of inflammatory bowel disorder. The data produced, however, had much more potential for investigation than simply the FMT experiment. We noticed that the inflammatory indexes of the dysbiotic mice showed outcomes comparable to the control mice, in association with high detections of members of the Lachnospiraceae family. This highlighted the potential importance of this family and piqued our research interest. Upon analysis of metagenome-assembled genomes resolving to Lachnospiraceae, we identified genes relating to glutathione metabolism. Glutathione, as an antioxidant, holds a critical role in the inflamed gut. However, the literature did not reflect this function with any specificity. A research question was then formed. We then sought to characterize the potential of Lachnospiraceae and bacterially-derived glutathione metabolism to relieve oxidative stress in the gut. What followed was a barrage of experiments, continually tried and retried to form a body of evidence in support of the anti-inflammatory potential of Lachnospiraceae. Many of these experiments were a version of the Caco-2 co-culture experiments mentioned in my previous blog post. Other experiments involved simple bacterial culture and growth curves. What resulted was a paper that, while it does not prove the anti-inflammatory potential of Lachnospiraceae, it certainly provides another piece in the puzzle of host-microbe interaction in the gut. For more info on Lachnospiraceae and bacterially-derived glutathione, check out the pre-print version of the paper here: Eubacterium rectale detoxification mechanism increases resilience of the gut environment | bioRxiv.

Now, my experiments in Lachnospiraceae have occupied amount of my time and energy in the past year and a half. However, even more personally influential are the thoughts I had surrounding this excursion into scientific investigation. I am confident that I could have had no better opportunity for life learning than the opportunity presented to me as a Lee Lab undergraduate. The Lachnospiraceae project didn’t just teach me protocols about analyzing metagenomic data and bacterial metabolism, though I certainly gleaned some of that information. In daily life as an undergraduate researcher, there was much time spent waiting for the centrifuge to stop spinning or waiting for the anaerobic chamber to finish its cycle. It was in those moments that I learned the most. It’s in the days that I asked “what the hell am I doing here”, that learning happened.

It was at such a time when I learned to view science as an artistic pursuit. Where I once regarded science as an objective field of people with specialized knowledge seeking to apply that knowledge to specific questions, I learned it to be completely reliant on the intuitions and curiosity of the human brain (which is often more intuitive first and logical second) to seek answers to questions exploding with beauty and insight. Then, to share that beauty and insight with others. As strange as it may be, I learned more about art and beauty in the lab than I ever did looking at a painting or listening to a piece of music. Any application of attention to a curious thing, really, could be viewed as artistic. I suppose this way of thinking about scientific investigation was partly informed by the work of the philosopher, Simone Veil, in her work Reflections on the Right Use of School Studies. Attention allows the space for a scientist to let curiosity guide the direction of a project, and desire to drive it forward. This cross-application of knowledge, from one discipline to another, is how understanding and innovation are formed. In the Lachnospriaceae project, much of the inspiration was biochemically motivated, rather than a true expression of pure microbiology. It was born out of true curiosity. This view of science, along with a healthy understanding of attention, now critically informs my intellectual process. Really, from my time in the lab, I had more self-discovery than scientific discovery. I found that my passion, and what I suspect is also true for other scientists, is in finding questions of a truly curious nature and applying true attention to those questions, regardless of the discipline the question could be categorized under. This is an artistic process in that it isn’t a way to create a perfect world, but a way to deal with the fundamentally ambiguous state we live in, and to feed our curious nature.

The Carson that entered college as an 18 year old couldn’t have imagined a better foundation on which to build a meaningful life. My plan is to continue to follow the path that curiosity and the desire for exploration and understanding have laid out for me. I hope you all find something of a curious nature to seek for yourself.