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 'People fall into three categories of gut microbiota, metagenomics study shows'
Publications
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, Weissenbach J, Ehrlich S, Bork PNATURE, 473, 174-80, 2011 Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specificationsYilmaz P, Kottmann R, Field D, Knight R, Cole J, Amaral-Zettler L, Gilbert J, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren B, Blaser M, Bonazzi V, Booth T, Bork P, Bushman F, Buttigieg P, Chain P, Charlson E, Costello E, Huot-Creasy H, Dawyndt P, Desantis T, Fierer N, Fuhrman J, Gallery R, Gevers D, Gibbs R, Gil I, Gonzalez A, Gordon J, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau A, Kelley S, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen r, Lauber C, Legg T, Ley R, Lozupone C, Ludwig W, Lyons D, Maguire E, Methe B, Meyer f, Muegge B, Nakielny S, Nelson K, Nemergut D, Neufeld J, Newbold L, Oliver a, Pace n, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman D, Assunta-Sansone S, Schloss P, Schriml L, Sinha R, Smith M, Sodergren E, Spor A, Stombaugh J, Tiedje J, Ward D, Weinstock G, Wendel D, White O, Whiteley A, Wilke A, Wortman J, Yatsunenko T, Glockner FNATURE BIOTECHNOLOGY, 29, 415-420, 2011 A human gut microbial gene catalogue established by metagenomic sequencingQin J, Li R, Raes J, Arumugam M, Burgdorf K, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende D, Li J, Xu J, Li E, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto J, Hansen T, Le Paslier D, Linneberg A, Nielsen H, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu h, Yu c, Li S, Jian M, Zhou Y, Li y, Zhang X, Qin N, Yang h, Wang J, Brunak S, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Antolin M, Artiguenave F, Blottiere H, Borruel N, Bruls T, Casellas F, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Forte M, Friss C, Van De Guchte M, Guedon E, Haimet F, Jamet A, Juste C, Kaci G, Kleerebezem M, Knol J, Kristensen M, Layec S, Le Roux K, Leclerc M, Maguin E, Melo Minardi R, Oozeer R, Rescigno M, Sanchez N, Tims S, Torrejon T, Varela E, De Vos W, Winogradsky Y, Zoetendal E, Bork P, Ehrlich SNATURE, 464, 59-65, 2010
News
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 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. 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. 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 RaesResearch area(s)BioPh.D.: Ghent University, Ghent, Belgium, 2003 Post-doc.: Dept of Plant Systems Biology, VIB, Ghent, Belgium, 2003-05 Post-doc.: EMBL, Heidelberg, Germany, 2005-07 Scientist at EMBL, Heidelberg, Germany, 2007-09 VIB Group leader since September 2009 Contact Info
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