ALBERT

Description: Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated network-generated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lima-Mendez, Gipsi -- Faust, Karoline -- Henry, Nicolas -- Decelle, Johan -- Colin, Sebastien -- Carcillo, Fabrizio -- Chaffron, Samuel -- Ignacio-Espinosa, J Cesar -- Roux, Simon -- Vincent, Flora -- Bittner, Lucie -- Darzi, Youssef -- Wang, Jun -- Audic, Stephane -- Berline, Leo -- Bontempi, Gianluca -- Cabello, Ana M -- Coppola, Laurent -- Cornejo-Castillo, Francisco M -- d'Ovidio, Francesco -- De Meester, Luc -- Ferrera, Isabel -- Garet-Delmas, Marie-Jose -- Guidi, Lionel -- Lara, Elena -- Pesant, Stephane -- Royo-Llonch, Marta -- Salazar, Guillem -- Sanchez, Pablo -- Sebastian, Marta -- Souffreau, Caroline -- Dimier, Celine -- Picheral, Marc -- Searson, Sarah -- Kandels-Lewis, Stefanie -- Tara Oceans coordinators -- Gorsky, Gabriel -- Not, Fabrice -- Ogata, Hiroyuki -- Speich, Sabrina -- Stemmann, Lars -- Weissenbach, Jean -- Wincker, Patrick -- Acinas, Silvia G -- Sunagawa, Shinichi -- Bork, Peer -- Sullivan, Matthew B -- Karsenti, Eric -- Bowler, Chris -- de Vargas, Colomban -- Raes, Jeroen -- New York, N.Y. -- Science. 2015 May 22;348(6237):1262073. doi: 10.1126/science.1262073.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. ; Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Universite Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. ; Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Universite Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France. ; Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. Interuniversity Institute of Bioinformatics in Brussels (IB), ULB Machine Learning Group, Computer Science Department, Universite Libre de Bruxelles (ULB), Brussels, Belgium. ; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA. ; VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France. ; Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Universite Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France. Institut de Biologie Paris-Seine, CNRS FR3631, F-75005, Paris, France. ; VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. ; Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. ; CNRS, UMR 7093, Laboratoire d'Oceanographie de Villefranche (LOV), Observatoire Oceanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universites, UPMC Paris 06, UMR 7093, Laboratoire d'Oceanographie de Villefranche (LOV), Observatoire Oceanologique, F-06230 Villefranche-sur-mer, France. ; Interuniversity Institute of Bioinformatics in Brussels (IB), ULB Machine Learning Group, Computer Science Department, Universite Libre de Bruxelles (ULB), Brussels, Belgium. ; Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Cientificas (CSIC), Pg. Maritim de la Barceloneta, 37-49, Barcelona E08003, Spain. ; Sorbonne Universites, UPMC, Universite Paris 06, CNRS-Institut pour la Recherche et le Developpement-Museum National d'Histoire Naturelle, Laboratoire d'Oceanographie et du Climat: Experimentations et Approches Numeriques (LOCEAN) Laboratory, 4 Place Jussieu, 75005, Paris, France. ; KU Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Charles Deberiotstraat 32, 3000 Leuven. ; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Hochschulring 18, 28359 Bremen, Germany. MARUM, Center for Marine Environmental Sciences, University of Bremen, Hochschulring 18, 28359 Bremen, Germany. ; Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Directors' Research, European Molecular Biology Laboratory, Heidelberg, Germany. ; Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011 Kyoto, Japan. ; Department of Geosciences, Laboratoire de Meteorologie Dynamique (LMD), Ecole Normale Superieure, 24 rue Lhomond, 75231 Paris Cedex 05, France. Laboratoire de Physique des Ocean, Universite de Bretagne Occidentale (UBO)-Institut Universaire Europeen de la Mer (IUEM), Palce Copernic, 29820 Polouzane, France. ; Commissariat a l'Energie Atomique (CEA), Genoscope, 2 rue Gaston Cremieux, 91000 Evry, France. CNRS, UMR 8030, 2 rue Gaston Cremieux, 91000 Evry, France. Universite d'Evry, UMR 8030, CP5706 Evry, France. ; Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. ; Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbruck-Centre for Molecular Medicine, 13092 Berlin, Germany. ; Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France. Directors' Research, European Molecular Biology Laboratory, Heidelberg, Germany. jeroen.raes@vib-kuleuven.be vargas@sb-roscoff.fr cbowler@biologie.ens.fr karsenti@embl.de. ; Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France. jeroen.raes@vib-kuleuven.be vargas@sb-roscoff.fr cbowler@biologie.ens.fr karsenti@embl.de. ; Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Universite Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. jeroen.raes@vib-kuleuven.be vargas@sb-roscoff.fr cbowler@biologie.ens.fr karsenti@embl.de. ; Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. jeroen.raes@vib-kuleuven.be vargas@sb-roscoff.fr cbowler@biologie.ens.fr karsenti@embl.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25999517" target="_blank"〉PubMed〈/a〉

Description: Fecal microbiome variation in the average, healthy population has remained under-investigated. Here, we analyzed two independent, extensively phenotyped cohorts: the Belgian Flemish Gut Flora Project (FGFP; discovery cohort; N = 1106) and the Dutch LifeLines-DEEP study (LLDeep; replication; N = 1135). Integration with global data sets (N combined = 3948) revealed a 14-genera core microbiota, but the 664 identified genera still underexplore total gut diversity. Sixty-nine clinical and questionnaire-based covariates were found associated to microbiota compositional variation with a 92% replication rate. Stool consistency showed the largest effect size, whereas medication explained largest total variance and interacted with other covariate-microbiota associations. Early-life events such as birth mode were not reflected in adult microbiota composition. Finally, we found that proposed disease marker genera associated to host covariates, urging inclusion of the latter in study design.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Falony, Gwen -- Joossens, Marie -- Vieira-Silva, Sara -- Wang, Jun -- Darzi, Youssef -- Faust, Karoline -- Kurilshikov, Alexander -- Bonder, Marc Jan -- Valles-Colomer, Mireia -- Vandeputte, Doris -- Tito, Raul Y -- Chaffron, Samuel -- Rymenans, Leen -- Verspecht, Chloe -- De Sutter, Lise -- Lima-Mendez, Gipsi -- D'hoe, Kevin -- Jonckheere, Karl -- Homola, Daniel -- Garcia, Roberto -- Tigchelaar, Ettje F -- Eeckhaudt, Linda -- Fu, Jingyuan -- Henckaerts, Liesbet -- Zhernakova, Alexandra -- Wijmenga, Cisca -- Raes, Jeroen -- New York, N.Y. -- Science. 2016 Apr 29;352(6285):560-4. doi: 10.1126/science.aad3503. Epub 2016 Apr 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. ; KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium. ; Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia. Novosibirsk State University, Novosibirsk, Russia. ; University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, Netherlands. ; VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium. ; University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, Netherlands. Top Institute Food and Nutrition, Wageningen, Netherlands. ; University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, Netherlands. University of Groningen, University Medical Center Groningen, Department of Pediatrics, 9700 RB Groningen, Netherlands. ; KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. KU Leuven-University Hospitals Leuven, Department of General Internal Medicine, Leuven, Belgium. ; KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium. jeroen.raes@kuleuven.be.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27126039" target="_blank"〉PubMed〈/a〉

Description: The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4851848/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4851848/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guidi, Lionel -- Chaffron, Samuel -- Bittner, Lucie -- Eveillard, Damien -- Larhlimi, Abdelhalim -- Roux, Simon -- Darzi, Youssef -- Audic, Stephane -- Berline, Leo -- Brum, Jennifer R -- Coelho, Luis Pedro -- Espinoza, Julio Cesar Ignacio -- Malviya, Shruti -- Sunagawa, Shinichi -- Dimier, Celine -- Kandels-Lewis, Stefanie -- Picheral, Marc -- Poulain, Julie -- Searson, Sarah -- Tara Oceans Consortium Coordinators -- Stemmann, Lars -- Not, Fabrice -- Hingamp, Pascal -- Speich, Sabrina -- Follows, Mick -- Karp-Boss, Lee -- Boss, Emmanuel -- Ogata, Hiroyuki -- Pesant, Stephane -- Weissenbach, Jean -- Wincker, Patrick -- Acinas, Silvia G -- Bork, Peer -- de Vargas, Colomban -- Iudicone, Daniele -- Sullivan, Matthew B -- Raes, Jeroen -- Karsenti, Eric -- Bowler, Chris -- Gorsky, Gabriel -- England -- Nature. 2016 Apr 28;532(7600):465-70. doi: 10.1038/nature16942. Epub 2016 Feb 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sorbonne Universites, UPMC Universite Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Oceanologique, 06230 Villefranche-sur-Mer, France. ; Department of Oceanography, University of Hawaii, Honolulu, Hawaii 96822, USA. ; Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. ; Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. ; Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. ; Sorbonne Universites, UPMC Univ Paris 06, CNRS, Institut de Biologie Paris-Seine (IBPS), Evolution Paris Seine, F-75005, Paris, France. ; Ecole Normale Superieure, PSL Research University, Institut de Biologie de l'Ecole Normale Superieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005 Paris, France. ; Sorbonne Universites, UPMC Universite Paris 06, CNRS, Laboratoire Adaptation et Diversite en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France. ; LINA UMR 6241, Universite de Nantes, EMN, CNRS, 44322 Nantes, France. ; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA. ; Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany. ; Directors' Research European Molecular Biology Laboratory Meyerhofstr. 1, 69117 Heidelberg, Germany. ; CEA - Institut de Genomique, GENOSCOPE, 2 rue Gaston Cremieux, 91057 Evry, France. ; Aix Marseille Universite, CNRS, IGS, UMR 7256, 13288 Marseille, France. ; Department of Geosciences, Laboratoire de Meteorologie Dynamique (LMD), Ecole Normale Superieure, 24 rue Lhomond, 75231 Paris CEDEX 05, France. ; Dept of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. ; School of Marine Sciences, University of Maine, Orono, Maine 04469, USA. ; Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan. ; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, 28359 Bremen, Germany. ; MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany. ; CNRS, UMR 8030, CP 5706 Evry, France. ; Universite d'Evry, UMR 8030, CP 5706 Evry, France. ; Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Maritim de la Barceloneta 37-49, Barcelona E0800, Spain. ; Max-Delbruck-Centre for Molecular Medicine, 13092 Berlin, Germany. ; Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26863193" target="_blank"〉PubMed〈/a〉