ISB News

Dr. Sean Gibbons joins ISB faculty as WRF Distinguished Investigator

Dr. Sean Gibbons has joined Institute for Systems Biology (ISB) as Washington Research Foundation Distinguished Investigator and assistant professor, and is our newest faculty member.

Gibbons’ new position brings a number of changes, including relocating to the Pacific Northwest from the Northeast.

Following is a Q&A with Gibbons that sheds light on his research career to date, his areas of study, where he sees research going, and even a hidden talent.

ISB: As the Washington Research Foundation Distinguished Investigator, you are ISB’s newest faculty member. Welcome! What does this appointment mean to you?

Sean Gibbons: I’ve been chasing the dream of running my own lab for more than a decade and I’m honored that ISB and the WRF have put their faith in me. I’m excited to have the opportunity to start my independent career in such a supportive, cross-disciplinary environment. I am looking forward to tackling challenging scientific questions at the interface between microbial ecology, evolution and human health.

ISB: Prior to ISB, you completed your postdoc training in the Department of Biological Engineering at MIT. You’re moving from the Northeast to the Northwest. What will you miss about Boston, and what are you looking forward to in Seattle?

Gibbons: The scientific ecosystem in Boston is incredible and I feel like I’ve learned so much during my time there. I will miss the amazing friends and colleagues that I met in Boston.  Luckily, because this is academia, I will see them all regularly at academic conferences or during seminar visits.

I’m happy to be back in the West. I’m from western Montana. I miss the people, culture and the natural beauty. The Pacific Northwest is particularly stunning. I visited Seattle a lot growing up. The idea of living here has always been attractive to me. I’m looking forward to drinking a Victrola Coffee and eating a Top Pot Doughnut while I browse the shelves at Elliot Bay Books.

ISB: Your areas of expertise include microbial ecology, evolution, complex adaptive systems, bioinformatics and the human microbiome. Are there common threads that unify these fields?

Gibbons: Yes, I believe “complex adaptive systems” represent the nexus of these fields. Ecology is the study of interactions between species and their environment, which can be highly complex. Evolution adds another layer of complexity over ecology by continually generating phenotypic diversity. This evolutionary diversification produces novel traits that are more or less adaptive, which can result in a reshuffling of ecological networks. The interplay between ecology and evolution gives rise to the rich biotic world we observe around us, be it a rainforest or a multicellular organism. The human gut microbiome is just one example of a complex adaptive system. The microbiome is largely invisible, which makes it challenging to study. Galileo developed a telescope to accurately track the movement of imperceptible celestial bodies. Similarly, microbial ecologists take advantage of molecular biology and genetics to follow the comings and goings of microbes. Our “microbial telescope” is a DNA sequencer, which produces a deluge of data that allow us to count and categorize millions of bacteria at a time. In order to process these data, we develop bioinformatic algorithms, which act like lenses to focus these data into an image of what is happening in the system. Thus, to answer your question more succinctly, my lab employs theory from complex adaptive systems (i.e. eco-evolutionary systems), molecular biology (i.e. meta-omics), and computational methods (i.e. bioinformatics) to uncover the rules governing the form and function of the microbiome in health and disease.

ISB: How will working at a research organization focused on systems thinking change your research approach? What attracted you to ISB?

Gibbons: I have always loved thinking at a systems-level. I started off my research career looking at how gene expression within a single bacterial population can alter overall ecosystem function. I find it fascinating how simple interactions at the molecular- or organismal-scale can yield unexpected emergent behaviors at an ecosystem-scale. My systems perspective was further cemented in 2014 when I attended the Santa Fe Institute’s Complex Systems Summer School. I saw how insights at this high level could be applied to a wide variety of unrelated systems, which reveals a deep truth for how these systems work.

There were many things that attracted me to ISB. First, the lack of departmental structure and the breadth of research impressed me. My biophysics Ph.D. program was interdisciplinary, with biologists, chemists and physicists working together to address difficult problems. Often, the best science happens at the fringes of fields and I think it is wise to structure a research institution in this way. Second, I was really impressed by the people and research being carried out at ISB during my visits. In addition, my postdoctoral adviser, Eric Alm, has a high regard for ISB and several of his friends and colleagues have moved through ISB at some point during their careers. Third, I saw enormous opportunity at ISB for achieving a lot of progress in both basic and translational research. The recent partnership between ISB and Providence opens up many paths to obtaining high quality clinical samples, which is absolutely crucial for understanding how the gut microbiome influences wellness. In particular, I’m looking forward to establishing long-term clinical partnerships in order to look at how within-host microbial evolution affects human health. Finally, I was excited to live in Seattle and be near family again. The Northwest affords a really great lifestyle.

ISB: There are a lot of unknowns surrounding the human microbiome. What excites you about the field of study?

Gibbons: Perhaps the most exhilarating thing about the microbiome field is that the pace of discovery has not yet slowed. This is a rapidly expanding field that many predicted would collapse under its own weight within a few years. However, there continue to be major results every couple of months that upend how we think about the gut and human health. We seem to have identified a heretofore-unrecognized organ of the human body. It’s not an essential organ, like the heart or liver. We could probably survive without it. However, it is becoming clear that long-term health and wellness are strongly tied to our commensal microbes. Disruptions of our microbiome can lead to autoimmune disorders, chronic inflammation, cancer, and even depression. I’m particularly interested in how we can leverage our knowledge of the microbiome to develop personalized treatments and nutrition.

ISB: Do you have any advice for people inundated with questionable marketing and messaging about what the microbiome is, how it can be “optimized,” etc.?

Gibbons: The pre- and pro-biotic market is currently not well regulated. It’s the Wild West. Probiotics that can be purchased at the grocery store are often not the same species as what is marked on the label. Few of these products have been shown to be generally effective. The only disease that appears to be reliably treated by certain over-the-counter probiotics is mild diarrhea. In most cases, efficacy is very patchy – it works for some people and not for others (perhaps due to differences in their endogenous microbiota). Part of the problem is lax regulation and poor quality control, but another part of the problem is that effective pre- and pro-biotic treatments should probably be tailored to individuals. It is unlikely that they will work uniformly across most people, like an aspirin (except in a few cases: e.g. fecal transplants for recurrent Clostridium difficile infections). The bottom line: There is a lot of snake oil out there. Try to buy more expensive products that have stricter quality controls. And stay tuned over the next few years. There are many companies (e.g. Finch Therapeutics, Vedanta, etc.) pushing “microbial therapeutics” through phase 1-3 clinical trials for a number of diseases. In addition to microbial therapeutics, I anticipate a boom of higher-grade pre- and pro-biotics targeting specific wellness metrics based on better science. Finally, a lot of progress has been made recently in designing personalized nutrition based on microbiome composition. Together, these advances should eventually allow people to “optimize” their gut ecology.

ISB: Look into your crystal ball: What will the research landscape look like in 10 years?

Gibbons: In 10 years, I anticipate major advances in single-cell technologies and long-read sequencing that will make short-read sequencing more-or-less obsolete. In a perfect world, we would assess a microbial community by running long-read sequencing (or some combination of long- and short-read sequencing) on millions of single cells, combining the power of both whole-genome sequencing and shotgun metagenomics. This culture-free methodology would make it easier to study both the ecology (i.e. track changes in species and gene contents across samples) and evolution (i.e. track mutations and horizontal transfer of genetic material) of bacterial communities from a single sample.

ISB: What do you do when you’re not in the lab?

Gibbons: Although I haven’t had as much time over the past few years to dedicate to my non-scientific interests, I like to engage in the arts. I see a connection between art and science in that both require a creative spark. I find that exposure to art makes me a more thoughtful scientist. I love film and television. My partner is a filmmaker and actor. I’ve acted in a few of his short movies and I acted in a couple plays in college. My postdoc lab gave me a year pass to Seattle Film Institute events as a going away present, which I’m looking forward to using. I also enjoy reading. I try to read a novel or two each month, in English or in French. My father is a poet, and when I was in college I translated a collection of his work into French. I’ll occasionally dabble in writing myself.

In addition to the arts, I like to stay physically active. I’m a runner. When I lived in Montana, I liked to go camping, hiking, biking, rock climbing, and whitewater rafting. I hope to get back into outdoor recreation in Seattle!

ISB: What is the last book you read?

Gibbons: The last book I read was called “The Uncommon Reader” by Alan Bennett, which was a realistic fiction piece about Queen Elizabeth (of England) falling in love with reading late in life. It was short and sweet. Before that, I read “The Logic of Scientific Discovery” by Karl Popper, which is a philosophical exploration of how we come to know things in science (highly recommended, especially for early-career folks).

ISB: Any hidden skills or talents you want to share?

Gibbons: I’m very flexible. My mother is a yoga teacher and I grew up doing yoga. If there is a limbo competition at ISB, I am likely to win – and would relish some competition!

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