Exploring the gut microbiome through mathematical modeling

I speak with Florence Bansept a Principal Investigator at CENTURI, based in LCB, Marseille. Florence shares with us her inspiring journey of perseverance and dedication towards becoming a PI (edited for ease of reading). Her work focuses on the group behaviors of microbes in the host gut using mathematical modeling.

What inspired you to pursue a career in science and how did you find yourself studying hosts and gut microbiomes starting from mathematics and statistical physics?

I have always been a curious student and my high school years were among the best years of my life. I developed an early fascination for Mathematics which I felt brought more logic and beauty to the world. After a rigorous training at the Math prep school, I joined the École Normale Supérieure (ENS) in Paris, majoring in statistical physics. Here, with the help of an excellent teacher and a great course, I rediscovered my passion for biology. I decided to pursue this passion through an internship, which eventually led to my Ph.D. I started studying infectious dynamics in the gut for my PhD and later, I moved on to explore the evolutionary aspects of microbial communities for my postdoc work.

Can you briefly describe the projects that excite you?

I am interested in exploring how a healthy individual maintains gut micro diversity. One possible mechanism is using the host immune system to distinguish between good and bad microbes in the gut but this can be challenging as similar-looking microbes may not behave the same. Sometimes, changes in the gut microbiome due to antibiotics or the acquisition of mutations could result in an initially harmless microbe evolving, replicating, and invading the host system. Gut perturbations can also lead to the translocation of a microbe to elsewhere in the body causing infections. Instead of distinguishing between good and bad microbes, I am interested in strategies that would not require this type of decision-making. With the help of my colleagues at the LCB who specializes in metabolism, I am eager to study how feeding and metabolism determine the composition of the gut microbiome.

My long-term goal is to classify hosts into different types, based on the characteristics of their gut microbiome dynamics. For example, in the worm C. elegans, which feeds directly on microbes and have a rapid turnover rate in the gut, the influx of new microbes from feeding may be more important than in humans, who tend to wash their food and for whom colonization at early life stages may be the key factor. Previously, I have collaborated with scientists working on mice, C.elegans, stickleback fish, moth larvae, and Drosophila. Depending on the model system employed, people tend to have strong opinions regarding the mechanisms of host-microbiome interactions. I think modeling can help overcome these apparent contradictions, by showing how the relative importance of shared mechanisms influences differently the microbiome composition. By performing similar experiments in multiple host systems, we will be able to check my models’ predictions.

Depending on the specific question I want to tackle with my model, I use either stochastic techniques (like agent-based simulations or branching processes), or deterministic systems of ODEs (ordinary differential equations) or PDEs (partial differential equations), which I study both numerically and analytically

Reflecting back on your academic career, what factors motivated you to remain in academia?

In my academic journey, my motivation has been the people I got to interact with. Meeting and learning from people has been extremely fulfilling for me. I really enjoy the aspect of teaching, engaging with students, and sharing knowledge. To me, the human aspect of academia is crucial. I am also extremely grateful to my Ph.D. and postdoc advisors, who played crucial roles in developing my career as a scientist. A pivotal moment in my academic journey was a discussion I had with my Brazilian master internship supervisor towards the end of my Ph.D. I was unsure about staying in academia and was considering a teaching career. He encouraged me to pursue a postdoc to avoid any “what if” regrets – I could always go back to teaching later! That advice was key.

Have you experienced gender-based discrimination in your academic career and what steps do you plan to take to promote diversity and inclusivity in your lab?

In short, I am a white woman from a relatively privileged background, I acknowledge that I have been lucky and not faced the same level of discrimination as many others in STEM. I initially got interested in feminism during my Ph.D. through Emma Clit’s comics. Her work helped me recognize discrimination as an insidious system of biases that exists in every aspect of our patriarchal society- including my own mind! Selecting candidates based on certain personality traits that are praised in men but often frowned upon in women highlights these double standards that hinder women’s progress. Recognizing your own biases and actively working to overcome them is the first necessary step, and I encourage individuals to embark on this journey!

I have personally witnessed biases in action and it’s frustrating that despite the goodwill towards hiring women, a man is very often chosen for the position. While quotas can create new problems, such as legitimacy questioning and increased workloads for women, I believe affirmative action is a transitory ‘necessary evil’ to ensure representation at all levels. Creating role models is also crucial for establishing a more equitable and inclusive workspace

In my limited role as a PI, I am aware of the need for gender balance and diversity in my own hiring practice. But, achieving this balance can be challenging since we usually recruit only one person at a time. I often discuss this topic with more experienced colleagues and although finding the perfect solution seems challenging, I will try my best.

What strategies did you use to overcome self-doubt and build confidence while navigating the competitive academic journey?

Yes, I have indeed experienced self-doubt throughout my academic journey. Initially, I tried to ignore those feelings while making decisions. However, after joining Twitter, I found that humor helped alleviate these common feelings. I recall a meme that suggested embracing imposter syndrome, implying if you made it this far, you must be a great imposter!

Starting my master internship was daunting. The vast literature, unknown scientists, lab hierarchies, and acronyms overwhelmed me. But with time and help from my mentors, I learned to overcome my shyness and gained confidence. I also realized that most scientists were open to discussing their work even with inexperienced students. As a “first-generation academic”, I also recognized that many academics had prior exposure to academia through their family background. Familiarity takes time so it’s important to be kind to yourself during the process.

 Science can be competitive, but solely focusing on competition is not productive. Networking with experts in the field provides unique opportunities to learn and work together. I firmly believe that the best scientific breakthroughs have come from collaborations, so I would prioritize collaboration over competition.

What advice do you have for students who plan to embark on this academic journey?

Get a website! It helps to centralize all your information, including your CV and publications for hiring committees. It’s an effective way to highlight your research and achievements when someone searches for your name.

When applying for positions or grants, connect with scientists in similar positions and ask them if they would be willing to share their applications with you. In this way, you can understand the process and improve your own applications.

Applying for positions and facing rejections are inevitable in academia, what insights can you offer to young PhDs and researchers?

In academia, having a backup plan is normal. It’s ok to pursue something new and exciting when things don’t work. Don’t burden yourself with unrealistic expectations of perfection.

As you start applying for positions and envision yourself in your new role, rejection can be hard to bare. But on Twitter, I found support and solidarity with others facing similar struggles.

It’s important to recognize the role of luck in academic selection. With the number of academic positions decreasing and grant applications becoming highly competitive., many qualified candidates are not being hired or funded. Thus many scientists believe that after an initial screening, a partially random selection process could ensure fairness and efficiency. Some grant agencies have also been exploring this alternative. So you should view rejection not necessarily as a reflection of the quality of your application but rather as a decision taken based on context. Academic hiring decisions can be complicated. Sometimes, you are hired for skills that are different from what the lab does to push its research boundaries. My advice is to apply for positions or grants even if they don’t seem like a perfect fit. You never know, it could lead to exciting results!

Can you share your strategies to prioritize mental health while keeping up with the demands of academic life?

During my prep-school days, I struggled with my mental well-being, but I found a better balance during my Ph.D. years by joining a choir, which brought me a lot of joy! Engaging in activities outside of academia has always been key for me. While we are passionate about our research it is sometimes necessary to remind ourselves that life doesn’t have to be solely about it. During my postdoc, I joined a peer-mentoring program for women where we talked about our career plans and future aspirations. Although I found this topic stressful, the program’s supportive and nurturing environment helped me navigate through the challenges of an early career in academia. I’m also fortunate to have a strong support system of close friends and a supportive family outside academia. Finally, taking breaks after big deadlines is a good way to recharge!

What plans do you have for your lab management and what are your priorities regarding mentoring your students and postdocs?

As a mentor, I aim to create a positive environment in my lab, similar to the ones I experienced during my Ph.D. and especially my postdoc. I believe that most productive collaborations occur when people are content and motivated to come to work and I will prioritize fostering these conditions within my lab as much as possible. I do not intend to manage a large lab and want to maintain regular communication with my lab members. I also envision lots of collaborative work within the lab to encourage a supportive growing environment where everyone feels valued and respected. While committing to pursue high-quality science is of course the key, I also want my lab members to have positive memories of their time in the lab.

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