Our gut is constantly under attack from bacteria, viruses, and the food we eat, so it has an alarm system that fires up when it detects danger.

Abarajitha Ramesh, our next pathbreaker, PhD student at Charité – Universitätsmedizin in Berlin, one of Europe’s leading medical research institutions, studies mucosal immunology essentially, the immune system of the gut.

Abarajitha talks to Shyam Krishnamurthy from The Interview Portal about her research which looks at how the gut stays healthy, and what goes wrong when it doesn’t. Specifically, she studies a signaling system in the gut lining that communicates with the immune system.

For students, your beginnings don’t decide your ending; a small or unsupported start is just a starting point, not a ceiling.

Abarajitha, Your background?

I’m Abarajitha Ramesh, from the Pudukkottai district in Tamil Nadu. My parents, Jaya and Ramesh, came from low-income families and worked hard to become government employees so my sister and I could have a better life. They taught me the value of money, education, and treating everyone with respect and kindness. Since my parents worked in different districts, my sister and I grew up mostly with our grandparents. I spent most of that time with my grandmother, still my favorite person in the world. I studied at a modest little school and, after fifth grade, moved back in with my parents. Money was tight, so my one clear goal became getting independent enough to take care of them someday. I stayed focused on academics through school, communicating mostly in Tamil despite English-medium classes. I was a curious kid, but also quietly low on confidence, so I stayed reserved and didn’t have many friends. In twelfth grade, I fell in love with biology thanks to my botany teacher, Dayana, and dreamed of becoming a cardiologist. When my cutoff fell short of a medical seat, my mother applied to SASTRA University for biotechnology on my behalf so I wouldn’t lose a year, a decision that quietly shaped everything that followed. I chose the field mostly out of instinct and curiosity, with no one in my family from a science background to guide me. My mother couldn’t explain the science, but she gave me something just as powerful: her belief in me. Looking back, I think that’s something worth telling younger students: you don’t need someone who’s already walked your exact path to guide you. Sometimes, having someone who simply believes you can walk it yourself is enough to take the first step.

What did you do for graduation?

I did my BTech in Biotechnology and MSc in Biology – Immunology and Microbiology from Uppsala University. I am currently doing my PhD in mucosal immunology at Charité – Universitätsmedizin.

I didn’t get a scholarship. For master’s I had to take a educational loan and my father also sponsored some part of it. For PhD, it was a salaried employment position.

College brought a whole new challenge. I was surrounded by classmates who were far more fluent in English and confident, and it made me feel like I didn’t belong. The first year was tough, though I made good friends. By the second year, I failed almost two subjects, which really shook me. I remember thinking, “What am I doing with my life?” But at the start of the third year, I realized the failure wasn’t about me; it was about the subjects. Those early years were packed with C, C++, physics, and mechanics, nothing to do with biology I actually loved. Once I reached immunology and the core biology subjects, everything changed, especially thanks to my professor, Dipita, whose teaching helped me score well and reminded me why I’d chosen this path. Lesson: sometimes what feels like failure just means you haven’t found the right subject yet.

What were some of the influences that led you to such an offbeat, unconventional and uncommon career in Immunology?

In my final semester, an opportunity came up to intern in Germany. My parents were understandably worried and initially said no, but I convinced them to let me try. Money was tight too, but my mother found a way to support me. From there, I was on my own, with no one to guide me through the visa and passport process, which I handled by myself, mistakes included, delaying things along the way. Meanwhile, I finished a final project at SASTRA that didn’t excite me much, but I pushed through because Germany was waiting on the other side.

Career path: How did you get here?

During my undergrad at SASTRA University, I got selected for a Semester Abroad Program basically a partnership that lets students spend a semester doing research at a university in another country. I went to Leibniz University in Germany, where I worked in a lab developing a special kind of medical implant. My specific job was to help purify and properly fold a protein called Smad8, which is part of a signaling pathway the body uses to control cell growth and repair. It wasn’t about the final application, yet  it was really about learning the hands-on skills of biotechnology and biochemistry: how to work carefully with proteins in the lab. That early hands-on training is actually what set me up to keep chasing more lab experience afterward, through my thesis and later research roles.

I still remember sitting on that flight to Germany, the first time I’d ever flown alone, headed to a country where I barely knew a soul, armed with just A1-level German. After landing, fear took over; every stranger felt suspicious, and there was a constant, quiet fear of being completely alone in an unfamiliar place. But then I met two people who changed everything: Dr. Ursula Rinas at Leibniz Universität Hannover and Bastian Quaas, a PhD student supervising me at the time.

Through them, I dove into molecular biology concepts and lab skills that genuinely excited me.

Everything around me was different: food, lifestyle, and language, and I felt a strange mix of excitement and fear doing almost anything. My scholarship even let me travel to Switzerland and Paris, places I never imagined I’d get to see.

Eventually I moved back to India and spent two months at home. Being with family made me happy, but part of me was restless; I wanted to keep learning science. So I took a year-long, unpaid internship at the Centre for Cellular and Molecular Biology (CCMB) in Hyderabad. My parents weren’t thrilled, but something in me just wanted to chase the learning.

At CCMB, my research was in microbiology, particularly bacterial genetics. in which I worked on one Particular Gene called “yfiH”. yfiH (also called pgeF) is a gene in E. coli that helps keep the bacterial cell wall’s building blocks correct. When we deleted it, the bacteria started making faulty cell walls  wrongly substituting one amino acid for another in over 20% of cases  which made the cells more sensitive to penicillin-type antibiotics and changed their shape. It’s a good teaching example because it shows students how a single gene mutation can disrupt a cell’s structure and drug resistance and how scientists figure out gene function through deletion experiments  even for genes, like this one, that started out completely mysterious.

CCMB was intense and competitive, and I learned a lot about cloning, bacterial cultures, and presenting my own research  but also carried a lot of self-doubt about whether I truly belonged there. Near the end, my supervisor told me plainly I wasn’t good enough for a PhD and should just get a job. It stung, and honestly, microbiology never excited me the way immunology had. But I set her words aside and decided to pursue my master’s anyway.

Tell us about your career path after your B.Tech.

My first target was Germany, mainly for the free tuition, but rejection after rejection followed, and my self-doubt came rushing back. So I turned to Sweden, applying to Uppsala, Karolinska, and Umeå under one application. While waiting for results, I spent a lot of time with my grandmother and parents, quietly believing something bigger was waiting for me. I got into Umeå  deep in Sweden’s cold north  and later learned, almost in disbelief, that a Nobel laureate had studied the same course. Swedish tuition is expensive; my father sponsored part of it, and I took an educational loan for the rest. Then, standing at the bank literally paying my Umeå fees, an email arrived: I’d been selected for Uppsala University, in immunology and microbiology, my actual first choice. I was on cloud nine and moved to Sweden in 2019.

It wasn’t smooth from there.  I was far from my family, adjusting to a new country and harsh climate, and then my father fell seriously ill right as COVID hit. I couldn’t go home for two years, and it shook me to my core. Yet in the middle of all that, I got the opportunity to pursue my master’s thesis at Karolinska Institutet, one of the biggest medical institutions in the world.

My master’s thesis was in the field of skin immunology. It’s the kind of translational/basic research that generates the mechanistic groundwork clinical studies later build on. Skin isn’t just a wall that keeps germs out; it can actually fight back. My master’s project asked, when skin gets irritated or inflamed, do skin cells start making their own germ-fighting molecules? I took real human skin cells, grew them in the lab, exposed them to inflammation-like signals, and measured whether they made more of these defense molecules. This is immunology because I wasn’t just looking at what inflamed skin looks like; I was asking how a “regular” body cell can behave like part of the immune system. That’s the same question I’m now exploring in the gut for my PhD, just in a different part of the body.

There, I have to give special thanks to my mentor, Dr. Avinash. We had a wonderful rapport, and despite my many mistakes, he believed in me anyway. From him I learned what it truly means to be a good scientist, down to the tiniest details, and it was Avinash who really pushed me toward a PhD.

After my thesis, a PhD didn’t come immediately, so I worked in a COVID testing lab, babysat, and taught biology to Swedish students to stay afloat. By the end of 2021, I became a research assistant at Karolinska in the Department of Immunology and Allergy. I didn’t want to rush into a PhD. I wanted more experience first, to understand my real niche. My PI gave me a lot of freedom, and there I met Danijela, my favorite mentor and friend rolled into one; we learned so much together over the two years I was there.

My scientific path has followed one thread, how the body’s barrier tissues, like skin and gut, interact with the immune system, just viewed from different angles at each stage. As a research assistant at Karolinska, I shifted from skin to gut and from inflammation-from-within to inflammation-triggered-from-outside. As part of a European research consortium called IMPTOX, I studied how microplastics, tiny plastic particles now found throughout our environment and even inside our bodies, might disrupt immune responses and intestinal function .That experience pointed me toward the gut as my real focus, and directly shaped my PhD.

During this time, my grandmother was diagnosed with cancer, and I went back and forth to India multiple times to be with her. Losing her shattered me completely, and for a while I couldn’t bring myself to apply for anything. I felt deeply lonely in Sweden, carrying that grief so far from home. Still, I kept looking for a PhD in Germany, and after a full year of rejections, I received two offers. I chose Berlin, at Charité – Universitätsmedizin, to pursue my PhD in mucosal immunology, studying the gut, often called the “second brain,” and how keeping it healthy shapes overall well-being. Looking back at everything: the self-doubt, the rejections, the losses, the small wins. I can honestly say that today, I feel confident in my abilities for the first time in a long while.

How did you get your first break?

My first break was that internship in Germany during my final year at SASTRA. It wasn’t easy to deal with hesitant parents, tight money, and an entire visa process I navigated alone, mistakes included. But I pushed through because I wanted it badly. That trip changed everything. Working with Dr. Ursula Rinas and Bastian Quaas at Leibniz Universität Hannover gave me my first real taste of hands-on science, and for the first time, I saw myself as someone who could do research, not just study it. I think a “first break” is rarely one dramatic thing; it’s simply the moment you say yes to something scary, even when you’re full of doubt.

What were the challenges, and how did you address them?

There were challenges at almost every stage. The language barrier: barely speaking English through school, then learning German just to get by abroad. Money: Every big move, from Sweden to Germany, meant loans and my parents stretching themselves for me. And self-doubt, the longest-running one, from feeling out of place in college to a supervisor telling me flatly I wasn’t good enough for a PhD. Then there was grief: losing my grandmother while I was far away in Sweden shattered me completely. She once told me, “I am the best granddaughter one could ever have,” and I promised her I’d make her, my grandfather, and my parents proud, a promise I still carry with me.

I didn’t have some clever strategy for getting through it all; I mostly just kept going. I let myself feel the doubt and fear without letting them make the final decision. When someone said I wasn’t good enough, I chose not to believe it. When money was tight, I took on odd jobs instead of giving up. When grief hit, I leaned on my family and gave myself time, instead of pretending I was fine. If there’s a pattern, it’s this: I never stopped moving forward, even in small, imperfect steps, even when I didn’t feel ready.

Where do you work now?

I’m currently a PhD student at Charité – Universitätsmedizin in Berlin, one of Europe’s leading medical research institutions, working in a lab that studies mucosal immunology essentially, the immune system of the gut.

What problems do you solve?

My research looks at how the gut stays healthy, and what goes wrong when it doesn’t. Specifically, I study a signaling system in the gut lining that communicates with the immune system, and how this connection plays into conditions like inflammatory bowel disease and colon cancer. I’m essentially trying to figure out one small piece of the puzzle of why some guts stay healthy while others develop chronic inflammation or disease  with the hope that this could one day lead to better treatments.

What skills are needed, and how did you acquire them?

A mix of technical and thinking skills. Technically, I work with mouse models, grow “mini-guts” called organoids, and use techniques like microscopy, cell sorting, and molecular biology methods. Just as important are problem-solving, patience (experiments fail a lot), critical thinking, and the ability to communicate findings clearly. I didn’t get these skills from one place;  they built up slowly through my bachelor’s, internships in Germany and India, my master’s in Sweden, and now my PhD, with every failed experiment and every mentor teaching me something I still use today.

What’s a typical day like?

It varies a lot. Some days are almost entirely in the lab running experiments, checking on mouse studies, growing organoid cultures, doing microscopy. Other days are spent at my desk analyzing data, reading papers, or writing. There are also meetings  discussing results with my supervisor, or brainstorming with labmates when something isn’t working as expected, which happens often in research. No two days look exactly alike.

What do you love about this job?

The curiosity of it , asking a question nobody has fully answered yet, and slowly working toward an answer. I love the small “aha” moments, when data finally makes sense after weeks of confusion. And I love that this work isn’t just abstract, it has a real chance to help people someday, especially those living with gut diseases. After years of doubting whether I belonged in science at all, this is where I finally feel like I’m exactly where I’m meant to be.

How does your work benefit society?

Your gut is constantly under attack from bacteria, viruses, and the food you eat, so it has an alarm system that fires up when it detects danger. But like a smoke alarm that won’t stop beeping, sometimes this alarm goes off too much or for too long, and when that happens, the gut becomes inflamed, cells multiply out of control, and diseases like Crohn’s, colitis, and bowel cancer can develop. My research uncovered something nobody knew before: the gut has its own natural off switch for this alarm, a tiny receptor on the gut lining cells, switched on by the very same alarm it calms, creating a self-regulating loop. Even more surprisingly, this off switch receives signals from neighboring cells that produce a molecule related to the body’s own natural painkillers. When we removed this off switch in mice, their guts became overactivated, cells multiplied excessively, and their immune systems went into overdrive, mirroring the early stages of bowel disease and cancer in humans. Understanding this natural braking system and why it sometimes fails could open new treatment paths for the millions worldwide living with inflammatory bowel disease and colorectal cancer.

A memorable piece of work close to you?

For about two months, my organoid cultures, tiny lab-grown “mini-guts” I use to study gut biology, kept failing inconsistently, which was almost more frustrating than an outright failure. Some batches grew fine, others didn’t, and I couldn’t pin down why. It was genuinely discouraging, since these organoids are central to my entire project. I spent a lot of time troubleshooting, reading protocols, and asking around.

Then one Sunday, I sat down and reworked the entire crypt isolation protocol, the very first step of extracting the tiny gut structures before growing them into organoids, combining ideas from published papers with tips from colleagues and testing a new fractionation-based approach. It worked: the crypt preparations came out noticeably cleaner, and the cultures became far more reliable afterward. What makes this memorable isn’t just that it solved a technical problem; it reminded me of something I’d learned over and over throughout my journey: when something isn’t working, the answer usually isn’t to give up; it’s to go back to the basics and rebuild it patiently, piece by piece, until it holds. That’s true in the lab, and it’s been true in life too.

Advice to students?

  • Your beginnings don’t decide your ending; a small or unsupported start is just a starting point, not a ceiling.
  • Dream big, even when your reality feels small; don’t shrink your dreams to fit your current circumstances.
  • Rejection is redirection. Every “no” I got eventually led me somewhere better, even when I couldn’t see it at the time.
  • Don’t let someone else’s opinion become your final truth; listen, but don’t let it become your ceiling.
  • Say yes to the scary thing; growth almost always lives on the other side of fear.

Future plans?

I have about three more years left in my PhD, and my immediate goal is to finish strong, publish meaningful research on the gut-immune connection I’ve been studying, and contribute something that genuinely adds to the field. Beyond that, I’d love to stay in research, possibly through a postdoc, continuing to explore gut health and immunity. Longer term, I’d love for my work to eventually connect back to real patients, whether through translational research or closer collaboration with clinicians.

Something close to my heart, though, goes beyond the lab: I want to return to my own town one day and motivate kids from underprivileged backgrounds to pursue science. I know firsthand what it feels like to have curiosity but no one to guide you, to doubt whether you even deserve a seat at the table. If I can be that guide for even one child who reminds me of myself, someone with no mentor, no roadmap, just curiosity and grit, that would mean as much to me as any publication. And on a personal note, after years of chasing opportunities across countries, I’d love to find a place I can call home for a while. But if there’s one thing my journey has taught me, it’s to hold plans loosely; some of the best turns in my story came from paths I never planned for.