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From Petri Dishes to Next-Generation Sequencing

Joël Doré is an INRA research director. He is also a co-director of the very large Joint Research Unit for Food and Gut Microbiology for Human Health and the scientific director of MetaGenoPolis. With the help of his research team, he is exploring the roles played by intestinal microorganisms, which may have a major influence on human health and nutrition.

Joël Doré © Inra, Christophe Maître
By Emmanuelle Manck and Cécile Poulain, translated by Jessica Pearce
Updated on 11/20/2017
Published on 11/25/2013

Extraordinary applications in the field of human health

Up until a few years ago, science had an incomplete understanding of the microorganisms that inhabit our intestines. Thanks to the development of high-throughput genomic tools, Joël Doré and his team have taken part in a complete re-evaluation of this renowned set of microbiota. “Before, we had to rely on our ability to culture bacteria in the lab. Since most of these species are anaerobic and thus difficult to grow in lab cultures, less than half of the bacterial ecosystem that exists in our intestines had been characterized,” explains Doré. He continues, “Now, we have access to all of the genetic information (DNA or RNA) contained in intestinal bacteria, which means that we can describe the microbiota more fully and at a very fine scale.” Because of these new tools, the team has contributed to some surprising discoveries. For instance, even if we share certain species, each of us has our own unique flora. Doré says, “Even though, from an enzymatic perspective, the intestine has pretty much the same function in everyone, the diversity of species it contains is entirely different from one person to the next. What’s more, this community is resilient and relatively stable over time. Even when we take antibiotics, it seems to return to its initial state afterwards.”

From fundamental research to its applications for human health

The progressive characterization of these bacteria and the roles that they play has led Doré to produce numerous publications that have set the stage for remarkable applications in the realms of human health and nutrition. He comments, “In addition to genetic predisposition, the intestinal flora is an important factor that we know plays a role in the development of major chronic diseases in modern societies. We don’t yet know which bacteria are behind these diseases, but we are trying to determine if it is possible to avoid the use of surgery by replacing it with less invasive treatments, such as a tailored diet that would lengthen remission periods between flare-ups or delay the onset of more severe symptoms.

Looking to Europe to establish projects of broader scope

Doré first arrived at INRA in 1983, when he did an internship in applied animal physiology for his master of advanced studies. He fell in love, with “research and the intellectual exercise that it represents, the relatively large amount of intellectual freedom permitted at INRA, and, of course, the work that [he] was doing at the time.” He specifies,“I was comparing strains of pathogenic bacteria found in humans versus other animals.” He then applied for a job at INRA, in order to work on the ecology of intestinal microbes. The young researcher subsequently got an offer to do a PhD at a US university. He spent four years completing his doctorate. He says, “After my return to France, I was able to pursue my research projects with a great deal of autonomy, taking advantage of both French and European institutions and the skills I had acquired in the United States. I also had the freedom to travel and solidify my network abroad.” Since 1992, which is when he submitted his first European research proposal, Doré has expanded his international network and has participated in different projects of broad scope. He comments, “From a career perspective, it is interesting work. We meet with our collaborators, we compare our results. As a consequence, we exchange a great deal of knowledge.” He is positioned in the vanguard of metagenomic research, and his work, which received considerable INRA support, is now headed to the next level thanks to first-rate French and European projects. He is also a major player in the international quest to sequence the metagenome, the “other” human genome.

From researcher to manager

Doré is a researcher and an expert, an author of scientific articles and a speaker at scientific conferences. He also welcomes French and foreign researchers into his team; he is training the next generation. Doré comments, amused, that he has never done the same job for very long: “I started at INRA as a researcher, conducting my own experiments. Now, I am more of a manager—I supervise people and direct the research being done.” He continues, “It isn’t an easy task to coordinate all the work being done by a research group. It certainly isn’t something that they teach in school. However, it is also the most fulfilling work that I have ever done.”

In 2010, he became one of the five co-directors of Micalis, a joint research unit that links INRA and AgroParisTech. Its goal is to develop innovative research in the field of food and gut microbiology with a view to improving human health. This unit is composed of more than 350 people, including 125 researchers, engineers, and university-affiliated researchers as well as over 120 PhD students, postdocs, and interns. It is also home to four technological platforms and an industrial biotechnology catalyst, whose aim is to turn research projects into commercially viable products.

Doré manages the research group called “Food and Gut Microbial Ecosystems: Food-Microbiota-Host Functional Interactions”. His ten research teams are studying what the microbial ecosystem does when it comes in contact with food and are trying to interpret the dialogue that takes place between human cells and microorganisms. In particular, their work is focused on the role of microbiota in severe chronic diseases. Since 2012, Doré has been serving as the scientific director of MetaGenoPolis, an industrial biotechnology catalyst financed by a French grant programme for cutting-edge research (Stimulus Initiative Programme). He says, “It is an amazing adventure that is pushing us to come up with all the possible applications that could emerge from our exploration of the metagenome. This brainstorming is taking place in close collaboration with our colleagues in the clinical sciences, as well as with people in the French private sector, who will allow us to translate our discoveries into products that are useful to society.

And to avoid the high stress levels that plague those in management, Doré forces himself to take breathers: “Because I am involved in a variety of activities and my days are almost entirely booked, unless I am on a work-related trip, I take the weekend off. I spend it with my family and go rocking climbing and jogging.”

CV in Brief
  • Born in August 1959
  • Married with three children
  • Research director
  • Master of Advanced Studies in Applied Animal Physiology, PhD from the Department of Animal Sciences at the University of Illinois at Urbana-Champaign in the United States