Baris Ozdinc: On a mission to decode the microbial map of the piglet gut
By Shaila Ann Sigsgaard
Baris Ozdinc is a PhD student halfway through his doctoral journey at Wageningen University in the Netherlands. He’s juggling hundreds of piglet samples, multiple layers of microbial complexity, and has a burning curiosity about how tiny organisms shape animal health. His project? Nothing short of mapping the microbial biogeography of the piglet gut—across time, space, and species.
Originally from Turkey, Baris’ academic path took him through University College London, where he trained as an evolutionary geneticist. But it was microbial ecology that truly captured his imagination. “I like microbial ecology,” he says, “and I like to apply my knowledge in genetics, sequencing, genomics, meta genomics, and microbial settings.” That passion led him into the microbiome industry, where he became a skilled bioinformatician, analyzing complex datasets and developing pipelines to study microbial communities.
Then came the PhD opportunity at Wageningen—a project investigating the developing piglet gut microbiome. “It was a match at first glance,” Baris recalls. “I always wanted to work with a non-human model, and piglets are especially interesting because their digestive tract is so similar to humans.” Plus, the project offered a chance to learn wet lab techniques alongside his computational expertise. “It was a good bargain,” he laughs.
But starting out wasn’t easy. “I was a bit lost,” he admits. “I knew I liked microbiomes. I knew my project was about understanding piglet gut biogeography over time. But the scope wasn’t definitively shaped.” Through discussions with his team, the project began to take form: studying microbial communities across different gut sections (from the duodenum to the distal colon), across different tissues (digesta and mucosa), and across developmental stages (from newborns to 67-day-old piglets) in healthy piglets.
Why does this matter? Because piglets are at the center of a major antimicrobial use issue in livestock. The abrupt weaning process—where piglets are separated from their mothers and switched from milk to plant-based feed—often leads to stress, digestive issues, and diarrhea. That, in turn, drives the use of antimicrobials. “Understanding what makes a piglet healthy helps us understand what makes a piglet sick after weaning ,” Baris explains.
His research unfolds in three stages:
Stage 1: Who’s there?
Baris is currently extracting DNA from over 600 piglet samples to identify which bacteria and archaea are present. He uses amplicon sequencing (specifically 16S rRNA gene sequencing), a robust method especially suited for mucosal samples where pig DNA can interfere with other techniques.
Stage 2: What can they do?
Once he knows which microbes are present, Baris uses nanopore shotgun sequencing to explore their genomes. This helps him understand their functional capacities—what they can digest, resist, or secrete. For example, some bacteria produce bacteriocins, enzymes that kill other microbes. “Knowing who’s there doesn’t tell you what they can do,” he says. “Genomes reveal their capabilities.”
Stage 3: Who’s hunting whom?
The final stage dives into phages—viruses that prey on bacteria. Baris wants to know if certain phages consistently appear in healthy piglets and whether they help maintain gut health by keeping harmful bacteria in check. But studying phages is tricky. Their DNA is a tiny fraction of the total sample, often drowned out by pig and bacterial DNA. So Baris is developing methods to selectively enrich phage DNA, making sequencing more efficient and cost-effective.
“It’s a multi-layered process,” he says. “I’m progressing in every layer. The soonest results will come from the first stage, but I’m also piloting nanopore sequencing and optimizing phage enrichment methods.”
Baris’ work is ambitious, complex, and deeply relevant. By mapping the microbial landscape of the piglet gut, he’s not just advancing science—he’s contributing to solutions for antimicrobial resistance, animal welfare, and perhaps even human health.
And he’s doing it with a mix of curiosity, creativity, and a touch of humor. “It’s very extensive,” he says, “but very interesting.”
Phages: A bacteriophage is a virus that specifically targets bacteria. The name comes from Greek: phagein meaning “to eat,” so it literally means “bacteria eater.”