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Luxembourg National Research Fund

ATTRACT SPOTLIGHT: Exploring microbial ecosystems in humans


When he began his career as a scientist, Paul Wilmes never imagined that his home country would one day become the base for successful research. It was the beginning of the millennium and Luxembourg was still an unknown spot on the global scientific map.

Today, as Associate Professor, Wilmes heads the Eco-Systems Biology research group at the Luxembourg Centre for Systems Biomedicine (LCSB) of the University of Luxembourg after a productive period as an FNR ATTRACT Fellow. With their systems biological methods, his team is studying microbial communities in unprecedented detail.

In 2008, when asked whether he could imagine returning to Luxembourg, Wilmes happened to be in Antarctica. He was on a research expedition at the time while working at the University of California, Berkeley. “Up until then, I hadn’t given a single thought to returning to Luxembourg; there simply weren’t any serious prospects,” Wilmes recollects. “But the interest was there. The idea of helping to build something here did appeal to me.”

From the sewage plant to the patient

In 2010, with the support of the ATTRACT programme of the FNR, Wilmes moved from the USA first to the Public Research Centre Gabriel Lippmann, and then one year later relocated to the LCSB. In the ATTRACT-funded project, Wilmes developed among other things an analytical method for simultaneously identifying and characterising the DNA, transcripts, proteins and metabolites of individual microbes in bacterial communities and other samples. “That kept us busy these last three years, with success,” Wilmes states. “We are the first and only ones in the world to have achieved this to date.”

The researchers developed the now patented method on fat-accumulating bacteria from sewage plants. “At about 500 different species, the complexity of these bacterial communities is lower than in many other ecosystems, making them very suitable for developing methods,” Wilmes says.

Most recently, the researchers have been applying their methodology in the context of human biology. They are studying, for example, the composition and activity of microorganisms in the gut flora – known in the jargon as the microbiota – in diabetes and cancer patients. “Our aim is to understand this ecosystem well enough in the future to be able to stop adverse developments in disease cases, and to restore a healthy state, say, by modifying the diet,” Wilmes explains.

How do human and microbial cells interact?

For their study, the researchers have also developed a co-culture system for human and bacterial cells – called HuMiX. With HuMiX, the scientists are looking to answer questions such as how human cells are influenced by metabolites from bacteria, or how diet affects the gut microbiota and subsequently human cells. This project was funded through the CORE programme of the FNR. The INTER MOBILITY funding programme has further allowed them to collaborate with researchers of the University of Arizona and of the University of Michigan in the USA. Together, the scientists have shown that a low-fibre diet allows strains of bacteria that break down the mucosa to proliferate in the gut and thus predispose to inflammatory responses.

Paul Wilmes has now been successfully evaluated by international peers and promoted to the position of Associate Professor with tenure at the University of Luxembourg – and sees no reason to leave the country again. “When I look back now at the last five years, I can definitely be happy with what we have achieved here. And I am happy with my decision to have returned to my roots.”

This case study was originally featured in the FNR 2014 Annual Report