PIMS Postdoctoral Fellow Eric Jones: On the far reach of the microbiome.
By Ruth A. Situma
Eric Jones’ research is interesting, actually, captivating! He is a physicist who enjoys studying ecological systems-specifically microbiomes. His current research involves microbiomes and how the composition of the gut microbiome can be controlled. What makes this research area fascinating, is that it affects all living things. In humans, gut microbiomes effect health, or disease. In fruit flies, they can determine the lifespan of the insect.
Eric received a Banting Fellowship and PIMS PDF award to focus on this area with Prof. David Sivak at Simon Fraser University. Not surprisingly, he has not yet stepped on campus. Until he can, he will be in Colorado with his parents, in his hometown of Fort Collins. Eric spent the last five years in sunny California (where he received his PhD in Physics from UC Santa Barbara in June 2020), so it is understandable that he has decided to re-experience a true winter in Colorado, and spend time with family. We checked in with Eric to see how he was doing and for a session on “all things microbiome”.
A lot of things changed in March 2020. You were at the tail- end of your PhD then, and moved home to Colorado right after graduating in June. How have you adjusted, and what are you doing to stay “sane”?
Last March I was a teaching assistant for an entirely virtual Complex Analysis class, which showcased to me the ways that COVID would impact people’s lives. I was impressed to see what was, all in all, an incredibly nimble transition to online teaching and learning over the course of three weeks. To compensate for the learning barriers associated with online teaching, I observed professors enacting “active learning” and other pedagogical methods to engage students. Above all, I was inspired to see students adapt to these incredibly difficult learning conditions.
Like many other academics, my professional life went entirely virtual a year ago — even my thesis defense was entirely virtual! I hope that one silver lining to come from the pandemic is the continued use of virtual infrastructure that allows for collaboration that is independent of physical proximity (for example, I currently attend and enjoy several seminar series that are organized by scientists across North America). For me the shift to working from home has been relatively smooth since all my research can be done either with pen and paper or on my computer. The many people with children that have managed both working from home and childcare have my full admiration and respect!
To stay sane I’ve depended on some combination of being outside, reading, playing music (guitar mostly), and staying in contact with friends. Last year in August I hiked the John Muir Trail with my brother, an incredible experience that offered a reprieve from COVID cabin fever and an opportunity to explore the Sierra Nevadas. I’ve tried to decorate my COVID lifestyle with regular outdoor activities — backpacking, skiing, or hiking — that can be done safely with a limited group of people. Now, with the rollout of the coronavirus vaccine I am hopeful that life will get back to normal sooner than later. All things considered, I’m doing well. I am fortunate that my research is entirely theoretical and computational and that I have a strong support network of friends and mentors.
Speaking of research, you are a physicist who works on biomes; what is the connection, and how did you get into this current research area?
When I started graduate school at UC Santa Barbara, my advisor Dr. Jean Carlson identified (with great foresight) the microbiome as a burgeoning field with abundant data but a dearth of models. In the last 20 years, the advent of high-throughput 16S rRNA sequencing has allowed scientists (at low cost and with high accuracy) to identify which bacteria are present in microbiome samples. I was initially intrigued by the microbiome’s complexity (trillions of bacteria interacting and competing for resources and space), and afterward became fascinated by its links to human health. In particular, the microbiome-altering therapy fecal microbiota transplantation (FMT) is a successful cure for most cases of C. difficile infection, an insufferable disease that antibiotics often fail to treat. The idea of “subtraction by addition” — that adding “healthy” microbes (via a fecal transplant) could dislodge a pathogenic bacteria — was curious to me, and I became interested in how tools from theoretical ecology could be used to explain the mechanism of action of FMT. Now, my theoretical research is motivated by the premise of “medicine for the microbiome,” and is directed at developing a general framework for transitioning from a generic diseased microbiome state (say, a microbiome suffering C. difficile infection) to a target healthy microbiome state.
On the experimental side, at the beginning of my PhD I was introduced to Dr. Will Ludington (Carnegie Institute for Science, Department of Embryology), a close collaborator and eventual postdoctoral employer of mine, that runs a fruit fly microbiome lab. His intricate experiments allow for flies to be born without a microbiome, then exposed to specific sets of bacteria. These experiments quantitatively reveal that microbiome composition influences fly physiology, including significant differences in fly lifespan and the number of eggs females lay per day depending on the fly’s microbiome composition. Even the simple and well-controlled fly microbiomes (which consist of ~5 bacterial species, compared to ~1000 species in the human microbiome) exhibit rich behaviors that are ripe for modeling. With his experimental data I have studied how the combinatorial complexity of fly microbiomes can be reduced, for example by examining how the lifespan of flies with multi-species microbiomes can be predicted based on the lifespans of flies with single-species microbiomes. Another aspect of my research studies probabilistic community assembly of the fly microbiome, which occurs since exposing a fly to a particular bacteria doesn’t necessarily mean that it will colonize. Model organisms like the fruit fly allow us to better understand these colonization processes, and might improve our ability to characterize the great microbiome diversity observed across individuals.
My research is wonderfully interdisciplinary, and I would feel at home in an applied mathematics or ecology department just as easily as I do in a physics department. That said, my training as a physicist undoubtedly affects my research approach. Mathematically, I have developed a dimensionality-reduction technique that permits the analytic investigation of complex multi-species ecosystems. Experimentally, my work in the fly microbiome features a “bottom-up” approach that seeks to model ecological behaviors from first principles. In both cases, I attempt to reduce ecological systems to the simplest possible form that retains the ecological behavior of interest.
You will be speaking at the PIMS Emergent Research Seminar, on Stochasticity in an ecological model of the microbiome influences the efficacy of simulated bacteriotherapies. This brings to mind a recent NYT article on gut microbiomes. Why do you think this research area is important and does it change the way we perceive microbiomes?
I think the article linked does a great job of demonstrating why microbiome research is important. What stands out to me is the sheer number of microbiome-associated diseases that exist: people suffering diseases as disparate as ulcerative colitis, type-2 diabetes, autism spectrum disorder, and depression often possess so-called “dysbiotic” microbiomes that differ from the microbiomes of healthy people. To me, the pivotal question (which is not yet resolved) is the extent to which the human microbiome can be used as a vehicle for microbiome-based therapies. Fecal microbiota transplantation has already shown great promise. Might “medicine for the microbiome” be a new paradigm for disease treatment? (Along these lines, I recently won the SFU Postdoc Research Day “Writing for the Public” contest where I speculated about the SmartToilet, a futuristic device that provides personalized healthcare recommendations; you can read my submission on my website here.)
My theoretical research — how to deliberately drive a microbiome towards a target state — has not yet been tested experimentally. Nonetheless, personalized microbiome-based therapies will require models that predict how a person’s microbiome will change in response to interventions, and my research provides a framework for studying these therapies in theoretical ecology models. Furthermore, my work on modeling the fly microbiome allows for the inference of ecological insights from raw microbial abundance data (which is available in great quantity); currently I am working to extend some of these methods to infer ecological interactions between microbial species in the human microbiome. In the future I hope to apply my theoretical research to experimental systems, starting with the fruit fly microbiome, to better understand how an individual’s microbiome composition may be engineered.
Has there been any new /updated research as a result of the pandemic?
One neat application of microbiome research (unrelated to my work) has been testing for coronavirus at wastewater treatment centers (link). People with COVID shed the virus in their stool which travels as sewage to wastewater plants. The amount of COVID that scientists detect in the sewage can then be used to predict COVID prevalence 1–3 weeks in advance. (For example, this technique has been used to preempt/react quickly to coronavirus outbreaks in university dormitories.)
Eric Jones will be speaking at the PIMS Emergent Research Seminar Series, April 28, 2021 at 9:30AM Pacific. Details on his talk (Stochasticity in an ecological model of the microbiome influences the efficacy of simulated bacteriotherapies) can be found here.
