Fiona is a computational biologist focused on the relationship of the microbiome to human health. She received her BS in Biochemistry from Boston College in 2014 and is currently a fifth-year PhD student in Ami Bhatt’s lab.
Can you tell us a bit about yourself, personally and professionally?
I grew up in Connecticut and attended Boston College, so New England has a special place in my heart. Here at Stanford, I’m a fifth-year PhD student in Ami Bhatt’s lab in the Genetics department. I’m interested in the relationship of the gut microbiome to both infectious disease and noncommunicable disease, and most of my work focuses on computational analysis of microbial genomes and gut microbiome sequence data.
How did you end up here? How did you first become interested in genetics and science?
I was aware of the concept of genetics as far back as I can remember because I have always looked a lot like my mom, and it’s something people have invoked my whole life (“You look just like your mother, wow genetics!”). So that was always on my radar. And my father is a biochemist by training and worked in drug discovery for years and really hyped that career choice, which I, as an impressionable young kid, totally bought into. I was utterly brainwashed honestly, and I was devoted to the idea of becoming a scientist from a young age, but, interestingly enough, my mom (not a scientist but a smart lady) was the one who actually suggested that I explore genetics. She follows the lay science press closely and I remember talking to her on the phone during my first year of college, and she said something to the effect of “You know, I really think you’d like this genetics thing.” I joined a genetics research lab at Boston College shortly thereafter.
As a child growing up in the era of the Human Genomic project, I had always envisioned working in human genomics. I only developed an intense interest in bacteria and the microbiome after I had already arrived at Stanford. My advisor, Ami Bhatt, started her lab the same year I began graduate school, and I heard her give a talk at our department retreat, which utterly blew me away. Right around this time, I was also reading a book that my uncle gave me and there was a chapter on microbes that was so compelling, there’s one quote that I love — “Bacteria may not build cities or have interesting social lives, but they will be here when the Sun explodes. This is their planet, and we are on it only because they allow us to be.” And you know, after studying the gut microbial community for a few years, I think bacteria might have more interesting social lives than we give them credit for. 🙂
Can you tell us about your current research and what you hope to achieve with it?
A major goal of our lab is leveraging the microbiome to improve the health of patients. In particular, we study individuals who have undergone hematopoietic cell transplant as a treatment for hematological malignancy. As you might imagine, these patients are immunocompromised and therefore very susceptible to infection – and we frequently don’t know where infectious organisms are coming from. We sought to identify whether organisms causing bloodstream infection may have originated from the gut, and found some interesting cases of infectious organisms thought to arise from the skin or environment actually colonizing the gut.
I think this work is important because it challenges the clinical dogma that infections microbes originate from a stereotypical source. The next step is to perform a larger prospective study to try to assess the relative frequency of BSIs from the gut. For a given organism, how often do we expect this to happen? And if this could be replicated at other centers that would be informative. And then we can think about how we might intervene – whether we can better manage gut health to prevent gut-derived infections, for instance.
The project that I’m spending most of my time on right now focuses on describing the gut microbiome composition of individuals living in two populations in South Africa, in collaboration with researchers from the University of the Witwatersrand in Johannesburg.
We are seeing increasingly that the microbiome is intertwined with – and may even drive – disease, yet we are largely in the dark as to whether the results of research studies carried out in the west are generalizable to other populations. What we’re seeing is that our methods and reference databases are incomplete for non-western individuals. These study participants have sequences in their gut microbiome that originate from genomes we haven’t described and are therefore not present in our reference collections. We are working to leverage recent improvements in metagenome assembly to better describe the gut microbiomes of these individuals.
Briefly, what’s the coolest thing about your work?
There are multiple reasons why studying the microbiome is cool — one big thing is that it’s a “hot” area of research right now and talked about a lot in the lay press. So it’s a subject that’s on peoples’ radar and that people are really interested in talking about. It’s generally easy to talk to non-scientists about my research and get them excited about the microbiome.
Another thing I love about my work is that it’s so immediately relatable to one’s daily habits. There’s a powerful relationship between diet and exposures and the microbiome – the average person can probably recall a time when they ate something out of the ordinary and felt differently! Of course, I can’t give medical advice, but it’s neat to be able to talk to people about how various sources of fiber can change their microbiome. That said, I’ve changed my habits surprisingly little given what I know about the microbiome. Knowing what I know, I should probably eat more cruciferous vegetables and fewer Reese’s’ peanut butter cups on a daily basis but here we are!
Were there people (or one person) in particular to whom you would attribute your professional success?
I certainly owe any success I’ve had to all of the advisors and mentors that I’ve worked with so far. I’ve been fortunate to have a series of nurturing mentors throughout my training – at Boston College, at a summer internship at UCONN Health Center, and here at Stanford. In particular my current advisor, Ami Bhatt, has pushed me to grow in my ability to posit a hypothesis and interpret results, but also equally importantly, she has encouraged me to conduct myself with confidence as a strong female leader in bioscience.
What advice would you offer to other grad students or postdocs who are considering pursuing a similar educational and career path as you?
My advice is generally to follow your passion and your interests, but also find a supportive advisor whose mentorship style is compatible with your interests and goals. If you have an open mind and an inquisitive attitude, one can cultivate an interest in nearly any subject.
I would also emphasize the importance of grit and willingness to figure things out on your own. Coursework can be important to build foundational knowledge, but almost all of the skills that I employ on a daily basis in my work are self-taught and empirical. I think that there’s this myth that you need to take a bunch of classes to learn how to program or do computational biology, for instance, but I haven’t found that to be necessary personally. I think it’s better to have a research question and some data and hack it together and learn by doing and by asking questions!
What are your future plans? Where do you see yourself professionally in the next 5 or 10 years?
I think that I’m driven mostly by interesting research questions, so I’ll see where the exciting opportunities are as I embark on the next step of my career, and go from there. Ideally, I’d like to work toward improving infectious outcomes for patients. A major unmet need is the ability to identify a pathogen and its antimicrobial susceptibility in real time so that doctors can utilize that information to make decisions about patient care including central line maintenance and antibiotic selection, and innovations in DNA sequencing hold great promise in that area.
CEHG’s core values include “interdisciplinary research” and “collaboration.” Can you speak to the ways your work has embodied these values or to their importance to your future work or past experience?
Studying the microbiome in a clinical context requires expertise from many areas – including but not limited to genomics, microbiology, biochemistry, and medicine. I’m fortunate enough that our lab is incredibly interdisciplinary and I have worked closely with colleagues on every project I’ve been a part of at Stanford. That includes working with a clinical fellow in my lab on clinical trial data, collaborating with the clinical microbiology labs at Stanford Hospital, and working with researchers in the Microbiology and Immunology department.
In an ideal collaboration, each party comes away with a bit of an enhanced knowledge of the other’s domain, and I have been fortunate to learn so much from collaborations here at Stanford. I have also had the incredible opportunity to collaborate with researchers at the University of the Witwatersrand, from whom I have learned so much about how to handle a collaboration across great distance (and time zones!), as well as how to conduct human subjects research in an equitable and respectful manner.
Tell us what you do when you aren’t working on research and why. Do you have hobbies? Special talents? Other passions besides science?
I got more involved in distance running in graduate school (I’ve run two marathons and am training for a third, yikes!) – there’s definitely a parallel there to the PhD experience in the sense that both are a long grind. I’ve also gotten into mountain biking lately. I’m not a super hardcore biker but I love that it allows me to cover more ground than I would be able to on foot. I also fall off my bike a lot — I’d like to think that builds resilience. Lest I fool anyone into believing I’m athletic, I am also very much into knitting and crochet. I always have one too many yarn-based projects ongoing (this is also an apt metaphor for my PhD). Finally, California is a pretty neat place so I’ve gotten into photography in my time here so that I can document all the beautiful West Coast sights.