Jeroen Raes Lab*

Research focus

> Lees de Nederlandstalige beschrijving van het onderzoek van Jeroen Raes (in Dutch)

The functioning of the human body constitutes a complex interplay of human processes and “services” rendered to us by the 1,000 trillion microbial cells we carry. Disruption of this natural microbial flora is linked to infection, autoimmune diseases and cancer, but detailed knowledge about our microbial component remains scarce. Recent technological advances such as metagenomics and next-generation sequencing make it possible, for the first time, to study the various microbiota of the human body at a previously unseen scale. These advances have allowed the initiation of the International Human Microbiome Project, aiming at genomically characterizing the totality of human-associated micro-organisms (the “microbiome”).
However, the complexity of metagenomic datasets makes their analysis a major bottleneck. This allowed the birth of a new, exciting subfield in computational biology which will eventually allow classical, cellular-level systems biology to progress towards modeling entire communities (“ecosystems biology”) and untangling interspecies networks of competition, collaboration and communication at the molecular level.
The Raes lab combines large-scale, next-generation sequencing with novel computational approaches to investigate the functioning and variability of the healthy human microbiome at the systems level and study its alteration in disease. In this context, we recently discovered the existence of discrete gut flora types (enterotypes), that are independent of host properties such as nationality, sex or race and are studying the predictive power of microbial markers for various intestinal diseases. In addition, we focus on the development of computational methods for the analysis of (next-generation) sequence data and the investigation of community properties from metagenomics,  metatranscriptomics and meta-metabolomics data, which are applied in a wide range of environments (ocean, soil, etc.).

The links below cover Jeroen Raes' latest press release 'World’s first population-level microbiome study reveals links between lifestyle and gut flora'

The links below cover Jeroen Raes' press release 'People fall into three categories of gut microbiota, metagenomics study shows' 

Read also the survey in the recent Nature Biotechnology issue:
'Jeroen Raes is one of the leading scientists that have garnered momentum in microbiome research'

*Affiliation and postal address:
Bioinformatics and (eco-)systems biology lab
Department of Microbioloby and Immunology, Rega Institute
O&N 1, Herestraat 49 - bus 1028
3000 Leuven


Plankton networks driving carbon export in the oligotrophic oceanGuidi L* Chaffron S* Bittner L* Eveillard D* Larhlimi A Roux S El Darzi Y Audic S Berline L Brum J Coelho L Espinoza J Malviya S Sunagawa S Dimier C Kandels-Lewis S Picheral M Poulain J Searson S Stemmann L Not F Hingamp P Speich S Follows M Karp-Boss L Boss E Ogata H Pesant S Weissenbach J Wincker P Acinas S Bork P De Vargas C Iudicone D Sullivan M Raes J Karsenti E Bowler C Coordinators T Gorsky GNATURE, 532, 465-70, 2016* These authors contributed equally
Population-level analysis of gut microbiome variationFalony G* Joossens M* Araujo Vieira Da Silva S* Wang J* El Darzi Y Faust K Kurilshikov A Bonder M Vallès Colomer M Vandeputte D Tito-Tadeo R Chaffron S Rymenans L Verspecht C De Sutter L Lima Mendez G D'hoe K Jonckheere K Homola D Garcia Yunta R Tigchelaar E Eeckhaudt L Fu J Henckaerts L Zhernakova A Wijmenga C Raes JSCIENCE, 352, 560-4, 2016* These authors contributed equally
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiotaForslund K* Hildebrand F* Nielsen T* Falony G* Le Chatelier E* Sunagawa S Prifti E Araujo Vieira Da Silva S Gudmundsdottir V Krogh Pedersen H Arumugam M Kristiansen K Yvonne Voigt A Vestergaard H Hercog R Igor Costea P Roat Kultima J Li J Jorgensen T Levenez F Dore J Bjorn Nielsen H Brunak S Raes J Hansen T Wang J Dusko Ehrlich S Bork P Consortium M Pedersen ONATURE, 528, 262-6, 2015* These authors contributed equally
Ocean plankton. Determinants of community structure in the global plankton interactomeLima-Mendez G* Faust K* Henry N* Decelle J Colin S Carcillo F Chaffron S Ignacio-Espinosa J Roux S Vincent F Bittner L Darzi Y Wang J Audic S Berline L Bontempi G Cabello A Coppola L Cornejo-Castillo F D'ovidio F De Meester L Ferrera I Garet-Delmas M Guidi L Lara E Pesant S Royo-Llonch M Salazar G Sanchez P Sebastian M Souffreau C Dimier C Picheral M Searson S Kandels-Lewis S Gorsky G Not F Ogata H Speich S Stemmann L Weissenbach J Wincker P Acinas S Sunagawa S Bork P Sullivan M Karsenti E Bowler C De Vargas C Coordinators T Raes JSCIENCE, 348, 1262073, 2015* These authors contributed equally
Enterotypes of the human gut microbiomeArumugam M* Raes J* Pelletier E Le Paslier D Yamada T Mende D Fernandes G Tap J Bruls T Batto J Bertalan M Borruel N Casellas F Fernandez L Gautier L Hansen T Hattori M Hayashi T Kleerebezem M Kurokawa K Leclerc M Levenez F Manichanh C Nielsen H Nielsen T Pons N Poulain J Qin J Sicheritz-Ponten T Tims S Torrents D Ugarte E Zoetendal E Wang J Guarner F Pedersen O De Vos W Brunak S Doré J Antolin M Artiguenave F Blottiere H Almeida M Brechot C Cara C Chervaux C Cultrone A Delorme C Denariaz G Dervyn R Foerstner K Friss C Van De Guchte M Guedon E Haimet F Huber W Van Hylckama-Vlieg J Jamet A Juste C Kaci G Knol J Lakhdari O Layec S Le Roux K Maguin E Merieux A Melo Minardi R M'rini C Muller J Oozeer R Parkhill J Renault P Rescigno M Sanchez N Sunagawa S Torrejon A Turner K Vandemeulebrouck G Varela E Winogradsky Y Zeller G Weissenbach J Ehrlich S Consortium M Bork PNATURE, 473, 174-80, 2011* These authors contributed equally


The Flemish Gut Flora Project Is Flourishing

26/08/2016 - ​Did you know that one of the world’s largest gut microbiome research efforts is run by a VIB lab? Jeroen Raes and his team started a bottom-up initiative in 2012 that would soon turn out to be a huge research project

Unraveling the food web in your gut

13/06/2016 - Using a manually curated metabolic module framework for (meta-)genomic data analysis, Sara Vieira-Silva, Gwen Falony and colleagues from the Jeroen Raes lab (VIB/KU Leuven) studied species-function relationships in gut microbial genomes and microbiomes.

Gut Flora may lead to better diagnosis tool for liver disease and this opens new avenues for treatment

23/05/2016 - ​Primary sclerosing cholangitis, also known as PSC, is a liver disease with no effective medical treatment. Liver transplantation is the only proven long-term treatment of PSC, although only a fraction of individuals with PSC will ultimately require it.

World’s first population-level microbiome study reveals links between lifestyle and gut flora

28/04/2016 - The Flemish Gut Flora Project, one of the largest population-wide studies on gut flora variation among healthy volunteers, has presented its first major results. These results provide important information for future disease research and clinical studies.

Plankton network linked to ocean’s biological carbon pump revealed

10/02/2016 - first overview of the network of species linked to the oceanic biological pump has revealed some new players as well as the main bacterial functions participating in the process.

Focus on our oceans’ microbiome

06/07/2015 - An international team of scientists, including Jeroen Raes, Gipsi Mendez, Karoline Faust and Samuel Chaffron (VIB/KU Leuven), has vastly increased our understanding of microscopic life in the oceans.

Tara Oceans expedition sheds light on the world of plankton

21/05/2015 - Plankton is our most important source of oxygen.

Intestinal flora linked to health of obese people

27/08/2013 - In Nature is published that there is a link between richness of bacterial species in the intestines and the susceptibility for medical complications related to obesity.

Diabetes is characterized by specific intestinal flora

26/09/2012 - ​Whether you have an increased risk of developing type 2 diabetes, in the future may be derived from the composition of your intestinal flora.

Human Microbiome Project maps bacterial populations in and on the human body

13/06/2012 - For the first time an international consortium of researchers, amongst whom VIB-VUB scientists, has mapped the different bacterial populations in the entire human body.

VIB-BGI Genomics meeting (15 February 2012) - Registrations closed

05/01/2012 - VIB and BGI are organising a genomics meeting on 15 Feb 2012 in Leuven, Belgium. Executives and investigators from both institutions will share their expertise on large scale genomcs and computational analysis

Both Nature and Science select VIB-VUB research as 2011 highlights

04/01/2012 - Great news to start 2012. Top journals Nature and Science are featuring research from VIB researchers at Vrije Universiteit Brussel in their 2011 highlights.

People fall into three categories of gut microbiota, called enterotypes, metagenomics study shows

20/04/2011 - Every person’s intestinal system falls into one of three clearly distinguishable types of gut microbiota, called enterotypes, according to a metagenomics study co-authored by Jeroen Raes.

The largest meta-genomic study ever - We’re more microbe than human

03/03/2010 - Of all the DNA that we carry around with us, less than 1% is of human composition. The rest has originated primarily from the massive amount of bacteria that live in our intestines.

Jeroen Raes

Jeroen Raes

Research area(s)


​​PhD: Ghent University, Ghent, Belgium, 2003
Postdoc: Dept of Plant Systems Biology, VIB, Ghent, Belgium, 2003-05
Postdoc: EMBL, Heidelberg, Germany, 2005-07
Scientist at EMBL, Heidelberg, Germany, 2007-09
VIB Group leader since September 2009

Contact Info

VIB lab for Bioinformatics and (eco-)systems biologyKULeuvenO&N4Campus GasthuisbergHerestraat 49 3000 LEUVEN