“Investigating the Relationship Between the Female Genital Reproductive System and the Microbiome and Metabolism." by Aaron Abai '22

Aaron Abai HeadshotSenior Thesis Spotlight with Aaron Abai ‘22

Interview conducted by Cody Chou '25

Aaron Abai (he/him) is a first-generation Ethiopian-American born in Las Vegas, Nevada and raised in Littleton, Colorado. A senior in Mather House, Aaron studies Molecular and Cellular Biology with a secondary in African-American studies. For his senior thesis, he is studying the chemistry of the vaginal microbiome in a cohort of Black, South African women. He is interested in the intersection of science, medicine, and social justice. Outside of school, he loves to run, hike, take photos, and spend time with his friends and family. 


Aaron: My name is Aaron. I live in Mather House. My major is Molecular & Cellular Biology, and my thesis title is “Investigating the Relationship Between the Female Genital Reproductive System and the Microbiome and Metabolism."

Cody: So why did you pursue this topic as your thesis?

Aaron: So, I joined the Quan lab the semester before the first semester of my sophomore year. And I was really interested in understanding why young women were more at risk of contracting HIV. So I spent the summer before sophomore year in South Africa, which was the center of the HIV epidemic. While I was there, I learned that young women, who were not much older than I was, were at 3-4x higher risk of contracting HIV when compared to men of the same age. So, I was really interested, also really disturbed, by that disparity. Also, while in South Africa, I learned that the microbiome of the female genital tract is a major risk factor in contracting HIV. So microbiomes that are more diverse lead to higher HIV risk so I came back to Cambridge interested in learning how the microbiome and the female gential tract may be increasing risk and mediating impact on health outcomes. So I joined the lab to research that and, three years later, that led to my senior thesis project! 

Cody: Focusing on your project, what were the main findings and source of inspiration for your project? 

Aaron: Yeah! So to share a little more about the project, I was looking at the microbiome’s relationship with the metabolome. So the metabolome is essentially all the small chemicals that are present in some samples. So I was looking at what bacteria comprises the microbiome and what material comprises the metabolome. And I was looking at the relationship between the two. The key parts of my project were showing that, yes, there is a really strong relationship between the microbiome and all the small chemicals which is a challenging thing to do with experimental studies because the microbiome is so complicated and there are so many players in it. And there are also so many chemicals that comprise the metabolome so a big part of my project was looking at samples from young women in South Africa and establishing this strong relationship between the microbiome and metabolome. And from there, I also worked at looking at what key chemicals were present in key microbial communities. So the purpose of that work is to identify biomarkers that can be used to characterize the microbiome. So if you have a microbiome composed of bacteria “x”, the question I asked is what chemicals might be used to identify that microbiome. So it is looking at a more chemical-focused approach at looking at microbiomes. So all of that is important because we don’t know how the microbiome affects health. We don’t know how the microbiome and the female genital tract leads to higher HIV risk so by looking at the chemicals, we are able to understand a little more about what mechanism may be happening and ask more pointed questions for further exploration. 

Cody: So would you say that your research is more wet-lab or dry-lab research?

Aaron: The work I do is a mix of dry lab and wet lab so a mix of wet lab and computational experiments. But in my thesis, I focused mostly on my computational stuff so when I joined my lab in the sophomore year, I was completely set on a wet lab project. 100%. But obviously March 2020 hit and COVID made me change everything about my project. At that point, I didn’t know how to code, analyze data, or any statistics. But I picked all of those skills because of my amazing mentors. So my thesis focused on analyzing these data sets which allowed me to have those findings I wrote in the project.

Cody: So what were the main challenges in the project and what kept you motivated throughout the process?

Aaron: Honestly, I think what kept me most motivated throughout my senior thesis project was thinking about the “why?”. And why I was doing this. For me, even though I loved the day-by-day science, my why was sort of a social impact of the project. I really cared because it was making an impact on global health and global health inequality. More specifically, trying to help the young women in South Africa who are at a higher risk of HIV. So I absolutely loved the science and computational stuff but what kept me grounded was knowing that this science could have an impact on people’s lives and achieving equity and greater global health equity in general. And the biggest takeaway from the project is that I always found that science to be super interesting but siloed and thought to be in a vacuum but my project was more translational and more trying to understand how we can use science to make an impact on people’s lives and addressing health problems that are often neglected. I think coming in as a first year, I didn’t think that connection was possible. So I feel really lucky that I found a lab that has values that align with my values and that care more about people and communities. 

Cody: So I guess an additional question I have is what are your plans after senior year? Any big goals? 

Aaron: So, this summer I will be resting at home with my family which I am very excited about. And starting in October, I will be in the UK getting a masters in medicine, health, and society so continuing to explore the questions that I have about the role of science in society and how science can be used as a tool for social justice which I am really interested in. After that, sometime after that, probably medical school.

Cody: So the last two questions I have are (1) how do you see your work related to your work as a HF intern and (2) any advice for future thesis writers?

Aaron: I think I'm here at the foundation because I care about supporting marginalized communities and students with marginalized identities. And that has always been central during my time at Harvard and I have tried to incorporate that into everything that I do. So access to social justice, racial justice. I think my project has been shaped around that interest and motivation. In addition to young women in South Africa being more vulnerable to HIV because of their microbiome composition. It is also known that Black women in the United States and around the world tend to have more of these diverse microbiomes which is associated with poor health outcomes. So no one knows why that is but there has been a big discussion over and over in the lab about how the implications of our research isn’t really isolated to a certain community or country but is really a larger question about how we perform social issues-informed science. And I think racial equity is a big thing that is informed when I’m in the lab I’m in. And I think that also mirrors why I’m here at the Foundation as well.

In regards to the thesis, I would like to say to make your thesis process be a reflective process. Like just resist the urge to work, work, work and try to understand why you’re doing it. That would make the process much more enjoyable and also true to build a community of your friends either if they’re thesising or not thesising. Try to have a common shared goal and try to work together for that. Like my roommate was thesising, for example, so it was easier for us to work together. But my other roommate who wasn’t thesising took on this really big art project so it was really nice for all of us to have this huge capstone senior project. I think it really helped us stay motivated and support each other in the process. 

Cody: And finally, what is the last thing you’re looking forward to accomplishing before your last few weeks here?

Aaron: Definitely jumping off the bridge into the Charles River.