Life isn’t linear: failures, mentors, friends, and microbes in my scientific journey.
By David Anthony Alvarado
Beginning with imagination, ending with academic probation…
Did I always know I’d end up in science or research? Not at all. Like many kids, I imagined myself in a white coat, ready to help fix people. Medicine was the only path I knew. Yet even then, I sensed the doctors were standing on the shoulders of unseen scientists. I just didn’t have the proof, or the language, to fully comprehend how the world worked.
Sci-fi was my second classroom. Many movies and series like Star Wars, X-Men, Resident Evil, Pokémon, and Doctor Who each stretched my imagination further. A virus that could amplify human physiology? Fascinating. Sure, the story ended with zombies, but I could do better! So, I applied to several pre-med programs in Chicago, and I got into my first pick.
My first year was a bust. Life hit harder than I was ready for; the problem wasn’t my ability to learn, it was motivation. Failure drained the spark from my imagination. I slipped into a dark place. School had always been my safe place, but this time no professor asked why I stopped showing up. The only email I received was the one that placed me on academic probation.
When perfection wasn’t so perfect …
This was my first real academic failure; the spark was gone, and my perfectionism no longer held together. My mom urged me to start over at community college. But the same apathy crept in. I was skipping classes again. Then came the email from my chemistry professor, an Obi-Wan moment I hadn’t expected. She noticed me and taught me what mentoring looked like. I hadn’t expected this level of care at a community college, where my four-year school offered none. She pushed me to lead the American Chemical Society chapter and tutor chemistry. I thrived.
Through tutoring, I met my best friend, someone who became an anchor in the support system I’d been missing, a reminder that people could appreciate me for my imagination in science. We both planned to (re)apply to the university that had put me on probation. My friend got in; I didn’t. Another failure? Maybe not. Life had other plans, I had just adopted a 3-month-old puppy, my Krypto to Clark Kent (Figure 1). That joy and sense of purpose kept me grounded through the pivot. Did I really want to return to a place that had shown me no support? At the last minute, I applied elsewhere, a place that let me stay close to my dog, and I got accepted.
Figure 1. Toby (dog) at 3 months old, just adopted, on a car ride home.
Figure 2. Me doing undergraduate research in the biosafety cabinet.
Discovering research, re-discovering myself …
I was remembering my love for learning science, fiction and real, but I still didn’t feel fully part of the scientific community. Halfway through my bachelor’s program, I realized I still had big-picture questions. Chemistry explained matter and reactions, but how did forces and motion drive them? Why did these interactions matter for living systems? So, I doubled down: a double major in Chemistry and Biology, plus a minor in Physics.
Still, classroom learning didn’t feel real, no matter how many courses I took. In one of my microbiology classes, I noticed people preparing bacterial cultures and media. At first, I thought they were external technicians. But to my surprise, they were undergraduates like me, some part of the McNair Scholars program. I applied, was accepted, and suddenly I had the chance to do real research. I worked with the professor of pathogenic microbiology, under her mentorship, I practiced the scientific method and immersed myself in lab life: late nights running experiments, collecting data, making agar art, building posters and presentations, sharing my work at conferences, and even winning awards. Each piece fueled the spark I thought would never fully return. As graduation neared, I looked at my mentor, she had a PhD. I wanted one too. I wanted to keep doing science (Figure 2).
From microbes to the microbiome …
My undergraduate research focused on pathogens, antibiotic-resistant variants with health consequences. As important as the work was, I saw the limitations: much of it might never work or reach patients. I wanted to see research with more immediate impact. While reading the work of potential graduate mentors, I stumbled into a field blending microbiology, food science, and bioinformatics. I knew nothing about food science (I was a picky eater) or about bioinformatics beyond computers plus biology. But the gut microbiome hooked me. Nutrition shaping the brain through the gut-brain axis? My imagination was booming. I lost sleep reading about it, excited. I hadn’t lost my childhood dream of helping people, and now I saw a new path.
I applied to what my budget allowed: ten programs in Microbiology, four in Biochemistry, and (on a gut feeling) one in Food Science and Human Nutrition (FSHN). I ended up trusting my gut and accepting the program in FSHN, joining the Nutrition and Human Microbiome team. Working with gut microbes to change health outcomes? I was in.
Thrown into the deep end …
My master’s in FSHN began with a Summer Predoctoral Fellowship. I learned the dynamics of the lab, the available resources, and the project’s aims. Unlike undergrad, where I focused on ways to neutralize harmful bacteria, here I was working on optimizing the good ones (probiotics). Our goal was to improve their survivability through simulated digestion using the food matrix.
By Fall, I hit the ground running, reviewing protocols, recruiting a team of undergrads, and juggling seven courses. We failed many pilot runs, and while I didn’t always know exactly what I was doing, each failure brought us closer to being ready for the trials. With the hard work of my undergrads, we managed to complete two trials. Then came the pandemic. Uncertainty loomed, and many plans and experiments put on pause. Still, I completed my master’s within two years, mentally and physically exhausted not just from the academic workload but from everything happening in the United States politically. I lost friends and family in the aftermath. I managed thanks to the support of my mentor, the friends I made along the way, and the grounding thought of my dog when everything else felt unstable (Figure 3). After depositing my thesis, I began the doctoral program, eager in theory but exhausted in practice.
Reigniting the fire post-pandemic …
Starting my PhD with the same mentor, I was presented with a few projects to choose from. It felt like I was picking my starter Pokémon; each looking at different aspects of the microbiome. However, the clinical trial on the gut-brain axis was calling me and instantly became my Charmander (Figure 4). During my first year, my previous work was accepted by ISAPP-SFA (2022) to be presented in Spain. It was my first solo international trip, and navigating Spain became its own adventure. I hopped on the wrong bus, ended up 30 minutes off course, and with no rideshare option, I walked. Sea breeze, Mediterranean sun, and striking architecture; what started as a mistake became a gift. I arrived sweaty but exhilarated, and the ISAPP-SFA officers welcomed me warmly.
Figure 3. Memory of Toby and I at a Christmas gathering.
Figure 4. Me doing PhD research, organizing samples for sequencing.
The first night, we stayed up late talking about everything from microbes in space to U.S. politics to favorite drinks. For the first time at a conference, I felt like I was meeting people like me. Instead of just two-minute pitches, I was truly connecting. I also realized my private battles (perfectionism, procrastination, burnout, impostor syndrome) were not mine alone in the scientific community. The pandemic had left me feeling gray, but this group of scientists re-sparked my fire for learning.
Coming full circle, starting again …
Fast-forward to May 2025: I attended my hooding ceremony and attended ISAPP in Banff to present my work as a student one last time (Figure 5). It was a full circle moment, reuniting with friends from my first ISAPP conference, seeing my former PI, lab mates, and colleagues. As before, each day added knowledge and helped me sharpen the kinds of scientific questions I want to learn to ask.
Now, as summer ends, I’m preparing to begin a postdoctoral position in the Department of Pathobiology. My academic journey has built in layers: first, I learned the basic principles of life and physical sciences; then, developed strategies to overcome resistance in pathogens; next, how to optimize probiotics to enhance survivability in food matrices; finally, how nutrition and the gut microbiome relate to the brain through cognitive measures. Now, my focus shifts to uncovering mechanistic and causal interactions between microbial ecology and host health; bringing me closer to that childhood dream.
Like much of the data I have analyzed, life isn’t linear, but the arc makes sense in hindsight. There will always be twists, setbacks, plateaus, and shifting of priorities, but each challenge became a pivot point, offering a crucial lesson if I was ready and willing to learn from it. Do I know exactly what comes after my postdoc? No. But I do know this, as I move into the next chapter, my aim is simple: turn curiosity into causality, and evidence into insights that expand our scientific understanding. Each detour taught me a method; each mentor, a habit; each study, a question; each friend, a spark. And my dog, a reminder that life is beautiful.
If there’s one thing my nonlinear path has taught me, it’s that the guilt of not trying burns longer than the sting of failure. So, chase the things that scare you; like Jean Grey becoming the Phoenix, your greatest spark may only rise after you’ve walked through the fire.
Figure 5. Me graduating from my PhD program.