Samuel Chaffron - PhD

Tara Oceans

I currently work as a bioinformatician in both international research projects Tara Oceans and Oceanomics.
http://taraexpeditions.org/
http://oceanomics.fr/

MiBioGate

I am involved in the MiBioGate project, which aims at studying host-microbiota interactions at biological barriers in chronic pathologies.

FLiN

I am also involved in the Flora Intestinal Nativa (FlIN) project, which aims at studying the influence of urbanization on the evolution of our microbiome.

SPRING database

I am developping the SPRING database, the first specialized resource on known and predicted microbial associations.

Microbial Eco-Systems Biology

Hello! I am a computational biologist and CNRS researcher at the Laboratoire des Sciences du Numérique de Nantes (LS2N), CNRS, EMN, Université de Nantes, in the team COMBI.
Previously, I was a FWO (Research Foundation Flanders) post-doctoral fellow in the group of Prof. Jeroen Raes at VIB, VUB and KU Leuven.
I hold a PhD degree from the University of Zurich obtained while working in the group of Prof. Christian von Mering.

My main research interest lies in understanding natural microbial communities and their structures at different levels of organization (from genes to species to ecosystems) in various habitats, including the human intestinal tract but also the world’s oceans. I use comparative and functional (meta-)genomics to reveal universal patterns conserved across the microbial tree of life as well as Systems Ecology approaches to understand natural community assembly rules at the functional level. I am also particularly interested in building computational models to gain a predictive understanding of community function and dynamics through metabolic modeling, and acquire a mechanistic understanding of microbial species interactions and ecosystem functioning.

Publications

Electronic versions of the publications listed below are available at Google scholar.

Tito R.Y., Chaffron S.*, Caenepeel C., Lima-Mendez G., Wang J., Vieira-Silva S., Falony G., et al. Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota. Gut, 2018. Europe PMC

Poling H.M., Wu D., Brown N., Baker M., Hausfeld T.A., Huynh N., Chaffron S. et al. Mechanically induced development and maturation of human intestinal organoids in vivo. Nature Biomedical Engineering, 2018. Europe PMC

Stec K.F., Caputi L., Buttigieg P.L., D'Alelio D., Ibarbalz F.M., Sullivan M.B., Chaffron S. et al. Modelling plankton ecosystems in the meta-omics era. Are we ready? Marine genomics, 2017. Europe PMC

Vieira-Silva S., Falony G., Darzi Y., Lima-Mendez G., Garcia Yunta R., Okuda S., Vandeputte D., Valles-Colomer M., Hildebrand F., Chaffron S. and Raes J.. Species–function relationships shape ecological properties of the human gut microbiome. Nature Microbiology, 2016. Europe PMC

Falony G.*, Joossens M.*, Vieira-Silva S.*, Wang J.* et al. Population-level analysis of gut microbiome variation. Science, 2016. Europe PMC

Guidi L.*, Chaffron S.*, Bittner L.*, Eveillard D.*, Larhlimi A., Roux S., Darzi Y. et al. Plankton networks driving carbon export in the oligotrophic ocean. Nature, 2016. Europe PMC

Takeuchi Y., Chaffron S.*, Salcher M.M., Shimizu-Inatsugi R., Kobayashi M.J., Diway B., von Mering C., Pernthaler J. and Shimizu K.K. Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes. Syst Appl Microbiol, 2015. Europe PMC

Sunagawa S.*, Coelho L.P.*, Chaffron S.*, Jens Roat Kultima, Karine Labadie, Guillem Salazar, Bardya Djahanschiri et al. Structure and Function of the Global Ocean Microbiome. Science, 2015. Europe PMC

Brum* J.R., Ignacio-Espinoza J.C.*, Roux S.*, Doulcier G., Acinas S., Alberti A., Chaffron S. et al. Patterns and ecological drivers of ocean viral communities. Science, 2015. Europe PMC

Lima-Mendez G.*, Faust K.*, Henry N.*, Decelle J., Colin S., Carcillo F., Chaffron S. et al. Determinants of community structure in the global plankton interactome. Science, 2015. Europe PMC

de Vargas C.*, Audic S.*, Henry N.*, Decelle J.*, Mahé F.*, Logares R., Lara E., Berney C., Le Bescot N., Probert I., Carmichael M., Poulain J., Romac S., Colin S., Aury J-M., Bittner L., Chaffron S. et al. Eukaryotic plankton diversity in the sunlit global ocean. Science, 2015. Europe PMC

Knief C., Delmotte N., Chaffron S., Stark M., Innerebner G., Wassmann R., von Mering C., and Vorholt J.A.. Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J, 2012. Europe PMC

Endt K.*, Stecher B.*, Chaffron S., Slack E., Tchitchek N., Benecke A., Van Maele L., Sirard J.C., Mueller A.J., Heikenwalder M. et al. The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea. PLoS Pathog 6: e1001097, 2010. Europe PMC

Chaffron S., Rehrauer H., Pernthaler J., and von Mering C. A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res 20: 947-59, 2010. Europe PMC

Chaffron S.*, Stecher B.*, Kappeli R.*, Hapfelmeier S., Freedrich S., Weber T.C., Kirundi J., Suar M., McCoy K.D., von Mering C. et al. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog 6: e1000711, 2010. Europe PMC

Delmotte N.*, Knief C.*, Chaffron S., Innerebner G., Roschitzki B., Schlapbach R., von Mering C., and Vorholt J.A. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci U S A 106: 16428- 16433, 2009. Europe PMC

Jensen L.J., Kuhn M., Stark M., Chaffron S., Creevey C., Muller J., Doerks T., Julien P., Roth A., Simonovic M. et al. STRING 8–a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 37: D412-416, 2009. Europe PMC

Stecher B., Robbiani R., Walker A.W., Westendorf A.M., Barthel M., Kremer M., Chaffron S., Macpherson A.J., Buer J., Parkhill J. et al. Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol 5: 2177-2189, 2007. Europe PMC

Chaffron S. and von Mering C. Termites in the woodwork. Genome Biol 8: 229, 2007. Europe PMC

von Mering C., Jensen L., Kuhn M., Chaffron S., Doerks T., Kruger B., Snel B., and Bork P. STRING 7–recent developments in the integration and prediction of protein interactions. 10.1093/nar/gkh084 35: 358-362, 2007. Europe PMC

CV


Professional Experience

Since 2016: CNRS researcher (CRCN) at the Laboratoire des Sciences du Numérique de Nantes (LS2N), CNRS, EMN, Université de Nantes, in the team COMBI.

2012 - 2016: VIB and Univeristy of Brussels, Brussels, Belgium.
Post-doctoral research fellow (FWO Research Foundation Flanders 3-years grant).
Research: Human microbiome, small non-coding RNAs, gut and ocean metagenomics, functional genomics, and heterogeneous data integration.
Peer reviewer for several international journals (NAR, Microbiology Open).

2007 - 2011: University of Zurich and Swiss Institute of Bioinformatics, Zurich, Switzerland.
Ph.D. and post-doctoral research.
Research: Microbial diversity, environmental genomics and proteomics, comparative genomics, microbial coexistence and genome evolution. High-throughput sequencing data analysis (454 and Illumina).
Assisting in peer reviewing for several high-ranking journals (Nature, Science, PNAS, PLoS CB).

2006: European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
Development of the STRING database: http://string-db.org/. Programming languages: Perl, JavaScript (AJAX).

Languages

French: native speaker | English: proficient | Spanish: independent | German: basic

Education

2012 – 2016: Post-doctoral research scientist, VIB Department of Structural Biology and Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Belgium. http://systemsbiology.vub.ac.be/

2010 – 2011: Post-doctoral research scientist, Swiss Institute of Bioinformatics and Institute of Molecular Life Sciences, University of Zurich, Switzerland. http://www.imls.uzh.ch/research/vonmering.html

2007 – 2010: Ph.D. thesis, under the supervision of Prof. Christian von Mering at the Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland.
Title: Tracing Microbes and their Genes through the Environment: Diversity, Ecology and Evolution. http://www.zora.uzh.ch/45544/

2004 – 2006: Master in Bioinformatics, University of Bordeaux 1 and 2, France. Genome biology, structural biology, data-mining and programming.

Communications

- Bioinformatics Center, University of Kyoto, 2018 - Kyoto, Japan (invited speaker).
- VivaTechnology, Google booth, 2018 – Paris, France (invited speaker).
- Tara South America Meeting, Universidad de Concepción, 2017 - Concepción, Chile (invited speaker).
- 8th Interdisciplinary School on Complex Systems, 2016 – Rennes, France (invited speaker).
- ISME16, 16th International Symposium on Microbial Ecology 2016 – Montreal, Canada (selected talk).
- International Environmental Synthesis Conference 2014 (iEOS2014) - Liverpool, UK (invited speaker).
- 15th International Symposium on Microbial Ecology 2014 (ISME15) - Seoul, South Korea (selected talk).
- 5th Congress of European Microbiologists (FEMS 2013), Leipzig, Germany (invited speaker).
- Jacques Monod 2011 conference on integrative ecological genomics, Roscoff, France (invited speaker).
- Conference on Intelligent Systems for Molecular Biology 2010 (ISMB), Boston, USA (poster).
- Swiss Institute of Bioinformatics 2009 meeting, Montreux, Switzerland (poster).
- University Research Priority Program 2009 meeting, Ascona, Switzerland (selected talk).
- Metagenomics 2008 conference, San Diego, USA (poster).
- Swiss Institute of Bioinformatics 2007 meeting, Grindelwald, Switzerland (poster).
- Jacques Monod 2007 conference on environmental genomics, Roscoff, France (poster).

Contact

INFORMATION

  • LS2N - CNRS UMR 6004 - University of Nantes

    Team COMBI

    UFR Sciences et techniques, Université de Nantes

    2, rue de la Houssiniere

    44322 Nantes | France

  • +33 251 125 985

  • samuel.chaffron(at)univ-nantes.fr

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