Contradictions drive research
“We need more sustainable practices,” says Mike Loomans, a PhD student in the Microbiome pillar. “Piglets are being perturbed from their natural life cycle, and antibiotics have become a standard response. That’s something we really need to rethink.”
Weaning is a critical moment in a piglet’s life. Within days, its diet changes, contact with the sow ends, and the carefully balanced microbial community in its gut is disrupted. The result is often diarrhea—and a familiar response from farmers: antibiotics. As pork production continues to grow worldwide, researchers are asking whether this cycle can be broken.
Mike’s research sits squarely at that intersection. He is part of the international PIG PARADIGM project, which brings together researchers across Europe to better understand pig health by studying the microbiome.
Mike didn’t start out in pig research—or bioinformatics. Trained in biomedical sciences, he later
specialized in biotechnology and systems biology. In between, he worked in the Dutch healthcare system during the COVID 19 pandemic.
“I used to be a wet lab guy,” he says. “But I slowly converted into a bioinformatician. Now I’m only working behind the computer—and I like it that way.”
That shift defines his PhD. Mike is responsible for building the Pig Gut Genome Catalog is a large reference database of microbial genomes found in pig gut fecal samples. It draws on thousands of fecal samples from different countries, farms, and life stages.
“We are planning on using digesta samples as well but the microbes in the intestines are different from those encountered in the feces samples we take - and the first iteration, we will just look at feces, PIG-PARADIGM fecal samples from Denmark actually."
“It’s an immense amount of information,” he says. “If you unzip all the sequencing data, you’re talking about six to eight terabytes. Your average laptop doesn’t stand a chance.”
Defining a “healthy” pig gut
Before the full dataset was available, Mike began by combining microbiome studies from around the world. His aim was deceptively simple: to understand what a healthy pig gut microbiome actually looks like.
“I'm looking into what groups of microbes can be stimulated or disturbed so that it can compete with the growth of microbes we have deemed to be pathogenic. A healthy gut microbiome is the end goal for sure, but it is a bit too optimistic.”
Through meta analyses, he explored why high protein diets sometimes promote harmful bacteria like E. coli and Clostridium, and which microbes support gut development at different stages of a pig’s life. Instead of focusing on single species, he studies microbial networks.
“I really like networks. I really like graphs,” he says. “You can see how microbes interact—and that tells you much more than looking at them in isolation.”
Across studies, a consistent pattern emerges. “After about three weeks post weaning, the gut reaches a kind of dynamic equilibrium,” Mike explains. “You start to see stable microbial groups that are characteristic for that stage of life.”
Unexpected results—and antibiotic resistance
Some results raise more questions than answers. In a collaboration with PhD student from Aarhus University, Maria Høgh Kroier, Mike analyzed data from pigs on different protein diets.
“We studied how protein levels and extra essential amino acids (EAAs) supplementation influence gut micro-biota composition and function, focusing on their potential to mitigate the adverse effects of a high-protein diet”.
Surprisingly, some well supplemented high protein diets were linked to less diarrhea.
“You would expect more protein to cause more disturbance,” Mike says. “But instead, you see the opposite effect. That’s a very strange thing.”
These contradictions now drive further research, including work on metabolites and the limits of current analysis methods. Today, much of Mike’s focus has shifted to antimicrobial resistance. Working with collaborators at the University of Copenhagen, he studies how antibiotic treatments shape resistance genes in the pig gut.
“If you give a pig tetracycline, you expect resistance to tetracycline to go up,” he says. “But what happens to everything else? That’s the real question.”
To tackle this, Mike has developed computational tools designed for massive datasets. These will be integrated into the Pig Gut Genome Catalog, which is expected to become publicly accessible.
“We hope people can easily explore what’s in there,” he says. “Maybe we’ll even find new resistance mechanisms or CRISPR Cas systems along the way.”
With about a year and a half left on his PhD, Mike is already thinking ahead. “You don’t realize at the start how much data there will be,” he reflects. “It really changes the direction of your PhD.”
Still, he sees that as part of the process. “Your proposal is never what you end up doing,” he says. “You learn to follow the data—wherever it takes you.”