Skip to content

📕 Research Data Spotlight — Edition 5

Ecem Yüksel

Spotlight on data by

Ecem Yüksel · Systems Biology

Interviewed on 2025-06-27

"One of the most effective habits is to document everything early and consistently, even small decisions like variable naming or code logic."

💬 The interview

Can you introduce yourself and tell us which research group you are part of?

My name is Ecem Yüksel, and I'm part of the A-LIFE research group at Vrije Universiteit Amsterdam, working under the supervision of Remco Kort. I have a background in Biomolecular Sciences, with a focus on cell biology and biological chemistry. Over the years, I've gained research experience in nutrition, particularly exploring the effects of dietary fibers on the human gut microbiome.

My interest in this field began during internships at Keep Food Simple and TNO, in collaboration with the VU. During those experiences, I encountered many passionate scientists whose dedication to nutrition and microbiome research who really inspired me. Nutrition has always excited me, especially when it comes to understanding what is actually healthy and how our dietary choices shape our health.

Throughout my academic journey, I've worked in both wet lab and dry lab environments, which gave me an introduction in data analysis alongside laboratory techniques. This combination has further deepened my interest in pursuing data-driven nutritional research.

What is your project about and what kind of data do you work with? How are you generally collecting or generating it?

I'm currently working on a randomized controlled trial (RCT) titled "Distinct modulatory effects of high-fiber and fermented-food diets on gut microbiota, immune function, transit time, and sleep quality in a citizen science randomized controlled trial." The study investigates how different dietary interventions, specifically high-fiber and fermented food diets, affect the gut microbiome, immune responses, transit time, and sleep quality. This project was a true collaborative effort, and I am thankful to have worked alongside esteemed colleagues Maartje van den Belt, Marieke van de Put, Nicole de Wit, and Remco Kort.

The trial includes three groups: a high dietary fiber group (HDF), a high fermented foods group (HFF), and a control group (CG). Data collection occurred over a 5-month period at three time points: baseline (week -1), after the ramp-up phase (week 2), and at the end of the intervention (week 8). Participants were split into two cohorts (n=34 and n=113). The data we collect is multi-dimensional, ranging from microbiome sequencing data, immune markers, and dietary intake records to sleep quality metrics. We primarily employed multivariate analysis to link the observed effects to microbiome composition, with the goal of identifying specific microbial taxa influenced by the dietary interventions.

Is your data available for others to access? If yes, where can we find it?

Yes, our dataset can be accessed via the VU Yoda environment and can be freely accessed. It is part of a collaborative research project titled: "Distinct modulatory effects of high-fiber and fermented-food diets on gut microbiota, immune function, transit time, and sleep quality in a citizen science randomized controlled trial", Maartje van den Belt, Marieke van de Put, Ecem Yüksel, Nicole de Wit, and Remco Kort, published 1 July 2025. Persistent Identifier (DOI): https://doi.org/10.48338/VU01-K0YFNS. We are proud to make the data openly available so it can support further research in nutrition, gut microbiome science, and personalized health.

What is something you wish you had known earlier when it comes to managing research data or collaborating with others?

One thing that became clear to me is how important it is to have a clear file structure and consistent naming formats from the start of a project. Since I joined the project in the later stages, I sometimes struggled to locate specific files or understand how data versions were organized.

Do you have any practical tips or good habits you would recommend to other A-LIFE researchers who want to manage their data and make it easier to collaborate?

Definitely. One of the most effective habits is to document everything early and consistently, even small decisions like variable naming or code logic. It helps when you or someone else revisits the project months later. Another useful practice is to keep all raw data separate from processed data, with clearly labeled versions so you always know what stage the data is in. And finally, explain where your data lives — having a README that explains where raw data, code, and analysis outputs can be found is incredibly helpful in collaborative environments.

⭐ Thank you, Ecem!

Thank you, Ecem, for taking the time to share your work with us. It was great to hear about your project, and your tips on managing data will be really helpful for other researchers.