List of scientific publications by year

D.O.I. Title Author(s) Title of the periodical or the series Date of publication Open access
https://doi.org/10.1007/s11892-017-0900-5 

T Cell Populations and Functions are Altered in Human Obesity and Type 2 Diabetes

Sothera Touch, Karine Clément, Sébastian André Current Diabetes Reports 04/08/2017 No
h10.1016/j.celrep.2017.06.039

Microbial-Host Co-metabolites Are Prodromal Markers Predicting Phenotypic Heterogeneity in Behavior, Obesity, and Impaired Glucose Tolerance

 Marc Dumas, Alice R Rothwell,Lesley Hoyles, Thomas Aranias, Julien Chilloux, Sophie Calderari, Elisa M.Noll, Noemie Pean, Claire L Boulangé, Christina Blancher, Richard H. Barton, Quan Gu, Jane F. Fearnside,Dominique Gaugier et al. Cell Reports Volume 20, Issue 1, 5 July 2017, Pages 136-148   05/07/2017 Yes 
 10.1109/IJCNN.2017.7965977

Efficient global network learning from local reconstructions

 

Severine Affeldt, Nataliya Sokolovska, Edi Prifti, Jean-Daniel Zucker

2017 International Joint Conference on Neural Networks 

 
14-19/05/2017  No 

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D.O.I. Title Author(s) Title of the periodical or the series Date of publication Open access
10.1016/j.jand.2016.10.030 Dietary Assessment in the MetaCardis Study: Development and Relative Validity of an Online Food Frequency Questionnaire Eric O. Verger,  Patrice Armstrong, PhD, Trine Nielsen, PhD, Rima Chakaroun, MD, Judith Aron-Wisnewsky, MD, PhD, Rikke Juul Gøbel, PhD, Tatjana Schütz, PhD, Fabien Delaere, PhD, Nicolas Gausseres, PhD, Karine Clément, MD, PhD, Bridget A. Holmes, PhD on behalf of the show MetaCardis Consortium  Journal of Academics of Nutrition and Dietetics 23/12/2016 Yes
10.1093/nar/gkw989 proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes Daniel R. Mende , Ivica Letunic , Jaime Huerta-Cepas , Simone S. Li , Kristoffer Forslund , Shinichi Sunagawa , Peer Bork Nucleic Acids Research 04/01/2017 Yes
10.1038/nm.4236 A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice Hubert Plovier , Amandine Everard , Céline Druart , Clara Depommier , Matthias Van Hul , Lucie Geurts , Julien Chilloux , Noora Ottman , Thibaut Duparc , Laeticia Lichtenstein , Antonis Myridakis , Nathalie M Delzenne , Judith Klievink , Arnab Bhattacharjee , Kees C H van der Ark , Steven Aalvink , Laurent O Martinez , Marc-Emmanuel Dumas , Dominique Maiter , Audrey Loumaye , Michel P Hermans , Jean-Paul Thissen , Clara Belzer , Willem M de Vos , Patrice D Cani Nature Medicine 28/11/2016 No
10.1186/s12859-016-1308
-y
Spectral consensus strategy for accurate reconstruction of large biological networks Séverine Affeldt , Nataliya Sokolovska , Edi Prifti , Jean-Daniel Zucker BMC Bioinformatics 01/12/2016 Yes
10.1093/bioinformatics/btw
697
MetaboSignal: a network-based approach for topological analysis of metabotype regulation viametabolic and signaling pathways Andrea Rodriguez-Martine1, Rafael Ayala, Joram M. Posma, Ana L. Neves, Dominique Gauguier, Jeremy K. Nicholson and Marc-Emmanuel Dumas Bioinformatics 22/12/2016 Yes
10.1016/j.abb.2015.09.016 Application of quantitative metabolomics in systems genetics in rodent models of complex phenotypes Dominique Gauguier Archives of Biochemistry and Biophysics 01/01/2016 Yes
10.1097/MCO.00000000000
00284
The microbial-mammalian metabolic axis Julien Chilloux , Ana Luisa Neves , Claire L. Boulangé , Marc-Emmanuel Dumas Current Opinion in Clinical Nutrition and Metabolic Care 01/01/2016 Yes
10.1016/j.abb.2015.10.013 Guest Editorial: Special issue on metabolomics Marc-Emmanuel Dumas , Jerzy Adamski , Karsten Suhre Archives of Biochemistry and Biophysics 01/01/2016 No
10.1093/nar/gkv1248 eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences Jaime Huerta-Cepas , Damian Szklarczyk , Kristoffer Forslund , Helen Cook , Davide Heller , Mathias C. Walter , Thomas Rattei , Daniel R. Mende , Shinichi Sunagawa , Michael Kuhn , Lars Juhl Jensen , Christian von Mering , Peer Bork Nucleic Acids Research 04/01/2016 Yes
10.1136/gutjnl-2014-308778 Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology Maria Carlota Dao , Amandine Everard , Judith Aron-Wisnewsky , Nataliya Sokolovska , Edi Prifti , Eric O Verger , Brandon D Kayser , Florence Levenez , Julien Chilloux , Lesley Hoyles , Marc-Emmanuel Dumas , Salwa W Rizkalla , Joel Doré , Patrice D Cani , Karine Clément Gut 01/03/2016 Yes
10.1016/j.ijar.2016.03.008 Deep kernel dimensionality reduction for scalable data integration Nataliya Sokolovska , Karine Clément , Jean-Daniel Zucker International Journal of Approximate Reasoning 01/04/2016 No
10.1093/bioinformatics/btw
183
MOCAT2: a metagenomic assembly, annotation and profiling framework Jens Roat Kultima , Luis Pedro Coelho , Kristoffer Forslund , Jaime Huerta-Cepas , Simone S. Li , Marja Driessen , Anita Yvonne Voigt , Georg Zeller , Shinichi Sunagawa , Peer Bork Bioinformatics 01/04/2016 Yes
10.1371/journal.pone.0153
294
Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults Carolin A. Kolmeder , Jarkko Salojärvi , Jarmo Ritari , Mark de Been , Jeroen Raes , Gwen Falony , Sara Vieira-Silva , Riina A. Kekkonen , Garry L. Corthals , Airi Palva , Anne Salonen , Willem M. de Vos PLoS One 12/04/2016 Yes
10.1126/science.aad3503 Population-level analysis of gut microbiome variation G. Falony , M. Joossens , S. Vieira-Silva , J. Wang , Y. Darzi , K. Faust , A. Kurilshikov , M. J. Bonder , M. Valles-Colomer , D. Vandeputte , R. Y. Tito , S. Chaffron , L. Rymenans , C. Verspecht , L. De Sutter , G. Lima-Mendez , K. Dhoe , K. Jonckheere , D. Homola , R. Garcia , E. F. Tigchelaar , L. Eeckhaudt , J. Fu , L. Henckaerts , A. Zhernakova , C. Wijmenga , J. Raes Science 29/04/2016 Yes
10.1016/j.abb.2016.03.029 A multiplexed targeted assay for high-throughput quantitative analysis of serum methylamines by ultra performance liquid chromatography coupled to high resolution mass spectrometry Hanane Kadar , Justine Dubus , Jérémie Dutot , Lyamine Hedjazi , Suman Srinivasa , Kathleen V. Fitch , Steven K. Grinspoon , Jeremy K. Nicholson , Marc-Emmanuel Dumas , Dominique Gauguier Archives of Biochemistry and Biophysics 01/05/2016 No
10.1016/j.abb.2016.03.029 A multiplexed targeted assay for high-throughput quantitative analysis of serum methylamines by ultra performance liquid chromatography coupled to high resolution mass spectrometry Hanane Kadar , Justine Dubus , Jérémie Dutot , Lyamine Hedjazi , Suman Srinivasa , Kathleen V. Fitch , Steven K. Grinspoon , Jeremy K. Nicholson , Marc-Emmanuel Dumas , Dominique Gauguier Archives of Biochemistry and Biophysics 01/05/2016 Yes
10.1016/j.abb.2016.03.029 A multiplexed targeted assay for high-throughput quantitative analysis of serum methylamines by ultra performance liquid chromatography coupled to high resolution mass spectrometry Hanane Kadar , Justine Dubus , Jérémie Dutot , Lyamine Hedjazi , Suman Srinivasa , Kathleen V. Fitch , Steven K. Grinspoon , Jeremy K. Nicholson , Marc-Emmanuel Dumas , Dominique Gauguier Archives of Biochemistry and Biophysics 01/05/2016 No
10.1038/nmicrobiol.2016.88 Species–function relationships shape ecological properties of the human gut microbiome Sara Vieira-Silva , Gwen Falony , Youssef Darzi , Gipsi Lima-Mendez , Roberto Garcia Yunta , Shujiro Okuda , Doris Vandeputte , Mireia Valles-Colomer , Falk Hildebrand , Samuel Chaffron , Jeroen Raes Nature Microbiology 13/06/2016 No
10.1038/nature18646 Human gut microbes impact host serum metabolome and insulin sensitivity Helle Krogh Pedersen , Valborg Gudmundsdottir , Henrik Bjørn Nielsen , Tuulia Hyotylainen , Trine Nielsen , Benjamin A. H. Jensen , Kristoffer Forslund , Falk Hildebrand , Edi Prifti , Gwen Falony , Emmanuelle Le Chatelier , Florence Levenez , Joel Doré Shinichi Sunagawa , Sara Vieira-Silva , MetaHIT Consortium ,, Susanne Brix , Jeroen Raes , Jun Wang , Torben Hansen , Peer Bork , Søren Brunak , Matej Oresic , S. Dusko Ehrlich , Oluf Pedersen Nature 13/07/2016 Yes
10.1186/s13073-016-026
6-3
Is the way we’re dieting wrong? Marc-Emmanuel Dumas Genome Medicine 01/12/2016 Yes
10.1186/s13073-016-030
3-2
Impact of the gut microbiota on inflammation, obesity, and metabolic disease Claire L. Boulangé , Ana Luisa Neves , Julien Chilloux , Jeremy K. Nicholson , Marc-Emmanuel Dumas Genome Medicine 01/12/2016 Yes

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D.O.I. Title Author(s) Title of the periodical or the series Date of publication Open access
10.1097/QAD.00000000000
00565
Plaque burden in HIV-infected patients is associated with serum intestinal microbiota-generated trimethylamine Suman Srinivasa , Kathleen V. Fitch , Janet Lo , Hanane Kadar , Rachel Knight , Kimberly Wong , Suhny Abbara , Dominique Gauguier , Jacqueline Capeau , Franck Boccara , Steven K. Grinspoon AIDS 01/01/2015 No
10.1242/dmm.017400 How informative is the mouse for human gut microbiota research? T. L. A. Nguyen , S. Vieira-Silva , A. Liston , J. Raes DMM Disease Models and Mechanisms 01/01/2015 Yes
10.1017/S00296651140015
66
Functional metagenomics to decipher food–microbe–host crosstalk Pierre Larraufie , Tomas de Wouters , Gabrielle Potocki-Veronese , Hervé M. Blottière , Joël Doré Proceedings of the Nutrition Society 01/02/2015 No
  Akkermansia Muciniphila and Gut Microbiota Richness are Associated with Improved Metabolic Status after Calorie Restriction Maria Dao, Amandine Everard, Judith Aron-Wisnewsky, Nataliya Sokolovska, Eric Verger, Salwa Rizkalla, Joel Doré, Patrice Cani and Karine Clément FASEB Journal 01/04/2015 No
10.1371/journal.pone.0125
718
Bariatric Surgery Induces Disruption in Inflammatory Signaling Pathways Mediated by Immune Cells in Adipose Tissue: A RNA-Seq Study Christine Poitou , Claire Perret , François Mathieu , Vinh Truong , Yuna Blum , Hervé Durand , Rohia Alili , Nadjim Chelghoum , Véronique Pelloux , Judith Aron-Wisnewsky , Adriana Torcivia , Jean-Luc Bouillot , Brian W. Parks , Ewa Ninio , Karine Clément , Laurence Tiret PLoS One 04/05/2015 No
10.1136/gutjnl-2014-3087
78
Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology M. C. Dao , A. Everard , J. Aron-Wisnewsky , N. Sokolovska , E. Prifti , E. O. Verger , B. D. Kayser , F. Levenez , J. Chilloux , L. Hoyles , M.-E. Dumas , S. W. Rizkalla , J. Dore , P. D. Cani , K. Clement , S. Le Mouhaer , A. Cotillard , S. P. Kennedy , N. Pons , E. Le Chatelier , M. Almeida , B. Quinquis , N. Galleron , J.-M. Batto , P. Renault , J.-D. Zucker , S. D. Ehrlich , H. Blottiere , M. Leclerc , C. Juste , T. de Wouters , P. Lepage Gut 01/06/2015 No
10.1016/j.mib.2015.04.004 Metagenomics meets time series analysis: unraveling microbial community dynamics Karoline Faust , Leo Lahti , Didier Gonze , Willem M de Vos , Jeroen Raes Current Opinion in Microbiology 01/06/2015 Yes
10.1136/gutjnl-2015-3096
18
Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates D. Vandeputte , G. Falony , S. Vieira-Silva , R. Y. Tito , M. Joossens , J. Raes Gut 11/06/2015 Yes
10.3389/fgene.2015.00219 From next-generation sequencing to systematic modeling of the gut microbiome Boyang Ji , Jens Nielsen Frontiers in Genetics 23/06/2015 Yes
10.1016/j.cmet.2015.05.02
0
Jejunal T Cell Inflammation in Human Obesity Correlates with Decreased Enterocyte Insulin Signaling Milena Monteiro-Sepulveda , Sothea Touch , Carla Mendes-Sá , Sébastien André , Christine Poitou , Omran Allatif , Aurélie Cotillard , Hélène Fohrer-Ting , Edwige-Ludiwyne Hubert , Romain Remark , Laurent Genser , Joan Tordjman , Kevin Garbin , Céline Osinski , Catherine Sautès-Fridman , Armelle Leturque , Karine Clément , Edith Brot-Laroche Cell Metabolism 01/07/2015 No
10.1016/j.copbio.2014.12.0
13
New paradigms for metabolic modeling of human cells Adil Mardinoglu , Jens Nielsen Current Opinion in Biotechnology 01/08/2015 No
10.1016/j.cmet.2015.07.001 Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome Saeed Shoaie , Pouyan Ghaffari , Petia Kovatcheva-Datchary , Adil Mardinoglu , Partho Sen , Estelle Pujos-Guillot , Tomas de Wouters , Catherine Juste , Salwa Rizkalla , Julien Chilloux , Lesley Hoyles , Jeremy K. Nicholson , Joel Dore , Marc E. Dumas , Karine Clement , Fredrik Bäckhed , Jens Nielsen Cell Metabolism 01/08/2015 No
10.1016/j.cmet.2015.07.009 Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation Valentina Tremaroli , Fredrik Karlsson , Malin Werling , Marcus Ståhlman , Petia Kovatcheva-Datchary , Torsten Olbers , Lars Fändriks , Carel W. le Roux , Jens Nielsen , Fredrik Bäckhed Cell Metabolism 01/08/2015 Yes
10.1016/j.ebiom.2015.07.0
07
Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children Chenhong Zhang et al EBioMedicine 01/08/2015  
10.1016/j.abb.2015.09.016 Application of quantitative metabolomics in systems genetics in rodent models of complex phenotypes Dominique Gauguier Archives of Biochemistry and Biophysics 01/09/2015 No
10.1096/fj.15-276675 Adipose tissue adaptive response to trans-10,cis-12-conjugated linoleic acid engages alternatively activated M2 macrophages M. Pini , S. Touch , H. Poirier , E. Dalmas , I. Niot , C. Rouault , C. Druart , N. Delzenne , K. Clement , S. Andre , M. Guerre-Millo FASEB Journal 11/09/2015 No
10.15252/msb.20156487 The gut microbiota modulates host amino acid and glutathione metabolism in mice A. Mardinoglu , S. Shoaie , M. Bergentall , P. Ghaffari , C. Zhang , E. Larsson , F. Backhed , J. Nielsen Molecular Systems Biology 01/10/2015 Yes
10.15252/msb.20156487 The gut microbiota modulates host amino acid and glutathione metabolism in mice A. Mardinoglu , S. Shoaie , M. Bergentall , P. Ghaffari , C. Zhang , E. Larsson , F. Backhed , J. Nielsen Molecular Systems Biology 01/10/2015 Yes
10.1038/srep14841 Extensive weight loss reveals distinct gene expression changes in human subcutaneous and visceral adipose tissue Adil Mardinoglu , John T. Heiker , Daniel Gärtner , Elias Björnson , Michael R. Schön , Gesine Flehmig , Nora Klöting , Knut Krohn , Mathias Fasshauer , Michael Stumvoll , Jens Nielsen , Matthias Blüher Scientific Reports 05/10/2015 Yes
10.1371/journal.pone.0138
880
Lactobacillus rhamnosus CNCMI-4317 Modulates Fiaf/Angptl4 in Intestinal Epithelial Cells and Circulating Level in Mice Elsa Jacouton , Núria Mach , Julie Cadiou , Nicolas Lapaque , Karine Clément , Joël Doré , Johan E. T. van Hylckama Vlieg , Tamara Smokvina , Hervé M Blottière PLoS One 06/10/2015  
10.1146/annurev-micro-091014-104422 Microbiology Meets Big Data: The Case of Gut Microbiota–Derived Trimethylamine Gwen Falony , Sara Vieira-Silva , Jeroen Raes Annual Review of Microbiology 15/10/2015 No
10.1016/j.coph.2015.09.013 The microbiome and its pharmacological targets: therapeutic avenues in cardiometabolic diseases Ana Luisa Neves , Julien Chilloux , Magali H Sarafian , Mohd Badrin Abdul Rahim , Claire L Boulangé , Marc-Emmanuel Dumas Current Opinion in Pharmacology 01/12/2015 No
10.1186/s13059-015-0639-8 Temporal and technical variability of human gut metagenomes Anita Y Voigt , Paul I Costea , Jens Roat Kultima , Simone S Li , Georg Zeller , Shinichi Sunagawa , Peer Bork Genome Biology 01/12/2015 Yes
10.1186/s13059-015-0646-9 Inter-individual differences in the gene content of human gut bacterial species Ana Zhu , Shinichi Sunagawa , Daniel R Mende , Peer Bork Genome Biology 01/12/2015 Yes
10.1016/j.coph.2015.09.013 The microbiome and its pharmacological targets: therapeutic avenues in cardiometabolic diseases Ana Luisa Neves , Julien Chilloux , Magali H Sarafian , Mohd Badrin Abdul Rahim , Claire L Boulangé , Marc-Emmanuel Dumas Current Opinion in Pharmacology 01/12/2015 Yes
10.1038/nature15766 Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota Kristoffer Forslund , Falk Hildebrand , Trine Nielsen , Gwen Falony , Emmanuelle Le Chatelier , Shinichi Sunagawa , Edi Prifti , Sara Vieira-Silva , , , Karsten Kristiansen , Anita Yvonne Voigt , Henrik Vestergaard , Rajna Hercog , Paul Igor Costea , Jens Roat Kultima , Junhua Li , Torben Jørgensen , Florence Levenez , Joël Dore , H. Bjørn Nielsen , Søren Brunak , Jeroen Raes , Torben Hansen , Jun Wang , S. Dusko Ehrlich , Peer Bork , Oluf Pedersen Nature 02/12/2015  

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D.O.I. Title Author(s) Title of the periodical or the series Date of publication Open access
10.3389/fgene.2014.00086 Elucidating the interactions between the human gut microbiota and its host through metabolic modeling Saeed Shoaie , Jens Nielsen Frontiers in Genetics 22/04/2014 Yes
10.1038/nbt.2942 An integrated catalog of reference genes in the human gut microbiome Junhua Li et al. Nature Biotechnology 06/07/2014 No
10.1016/j.immuni.2014.06.014 Symbiotic Bacterial Metabolites Regulate Gastrointestinal Barrier Function via the Xenobiotic Sensor PXR and Toll-like Receptor 4 Madhukumar Venkatesh , Subhajit Mukherjee , Hongwei Wang , Hao Li , Katherine Sun , Alexandre P. Benechet , Zhijuan Qiu , Leigh Maher , Matthew R. Redinbo , Robert S. Phillips , James C. Fleet , Sandhya Kortagere , Paromita Mukherjee , Alessio Fasano , Jessica LeVen , Jeremy K. Nicholson , Marc E. Dumas , KamalM. Khanna , Sridhar Mani Immunity 01/08/2014 No
10.1371/journal.pone.0109434 Dietary Patterns Differently Associate with Inflammation and Gut Microbiota in Overweight and Obese Subjects Ling Chun Kong , Bridget A. Holmes , Aurelie Cotillard , Fatiha Habi-Rachedi , Remi Brazeilles , Sophie Gougis , Nicolas Gausseres , Patrice D. Cani , Soraya Fellahi , Jean-Philippe Bastard , Sean P. Kennedy , Joel Doré , Stanislav Dusko Ehrlich , Jean-Daniel Zucker , Salwa W. Rizkalla , Karine Clement PLoS One 20/10/2014 Yes
10.1371/journal.pone.0109434 Dietary Patterns Differently Associate with Inflammation and Gut Microbiota in Overweight and Obese Subjects Ling Chun Kong , Bridget A. Holmes , Aurelie Cotillard , Fatiha Habi-Rachedi , Rémi Brazeilles , Sophie Gougis , Nicolas Gausserès , Patrice D. Cani , Soraya Fellahi , Jean-Philippe Bastard , Sean P. Kennedy , Joel Doré , Stanislav Dusko Ehrlich , Jean-Daniel Zucker , Salwa W. Rizkalla , Karine Clément PLoS One 20/10/2014 Yes
10.15252/msb.20145645 Potential of fecal microbiota for early-stage detection of colorectal cancer G. Zeller , J. Tap , A. Y. Voigt , S. Sunagawa , J. R. Kultima , P. I. Costea , A. Amiot , J. Bohm , F. Brunetti , N. Habermann , R. Hercog , M. Koch , A. Luciani , D. R. Mende , M. A. Schneider , P. Schrotz-King , C. Tournigand , J. Tran Van Nhieu , T. Yamada , J. Zimmermann , V. Benes , M. Kloor , C. M. Ulrich , M. von Knebel Doeberitz , I. Sobhani , P. Bork Molecular Systems Biology 01/11/2014 Yes
10.1371/journal.pone.0111122 A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation Kalliopi Trachana , Kristoffer Forslund , Tomas Larsson , Sean Powell , Tobias Doerks , Christian von Mering , Peer Bork PLoS One 04/11/2014 No
10.1021/pr500586e Defining the Human Adipose Tissue Proteome To Reveal Metabolic Alterations in Obesity Adil Mardinoglu , Caroline Kampf , Anna Asplund , Linn Fagerberg , Bjorn M. Hallstrom , Karolina Edlund , Matthias Bluher , Fredrik Ponton , Mathias Uhlen , Jens Nielsen Journal of Proteome Research 07/11/2014 No

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D.O.I. Title Author(s) Title of the periodical or the series Date of publication Open access
10.3945/ajcn.113.058743 Gut microbiota after gastric bypass in human obesity: increased richness and associations of bacterial genera with adipose tissue genes L. Kong American Journal of Clinical Nutrition 29/05/2013 Yes
10.1016/j.mib.2013.07.002 Colonic bacterial metabolites and human health W Russell L Hoyles Current Opinion in Microbiology 01/06/2013 No
10.1038/nature12480 Dietary intervention impact on gut microbial gene richness A. Cotillard Nature 29/08/2013 No
10.1038/nmeth.2575 Accurate and universal delineation of prokaryotic species. Mende,Sunagawa, Zeller, Bork Nature Methods 02/09/2013 No
10.3945/ajcn.113.058099 Insulin resistance and inflammation predict kinetic body weight changes in response to dietary weight loss and maintenance in overweight and obese subjects L. Kong American Journal of Clinical Nutrition 30/10/2013 Yes
10.1053/j.gastro.2013.11.001 Metabolic Phenotyping and Systems Biology Approaches to Understanding Metabolic Syndrome and Fatty Liver Disease Dumas ME Gastroenterology 07/11/2013 No

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Scientific Publications

Metabolic Phenotyping and Systems Biology Approaches to Understanding Metabolic Syndrome and Fatty Liver Disease

Abstract

Metabolic Phenotyping and Systems Biology Approaches to Understanding Metabolic Syndrome and Fatty Liver Disease - Gastroenterology

Metabolic syndrome, a cluster of risk factors for type 2 diabetes mellitus and cardiovascular disease, is becoming an increasing global health concern. Insulin resistance is often associated with metabolic syndrome and also typical hepatic manifestations such as nonalcoholic fatty liver disease. Profiling of metabolic products (metabolic phenotyping or metabotyping) has provided new insights into metabolic syndrome and nonalcoholic fatty liver disease. Data from nuclear magnetic resonance spectroscopy and mass spectrometry combined with statistical modeling and top-down systems biology have allowed us to analyze and interpret metabolic signatures in terms of metabolic pathways and protein interaction networks and to identify the genomic and metagenomic determinants of metabolism. For example, metabolic phenotyping has shown that relationships between host cells and the microbiome affect development of the metabolic syndrome and fatty liver disease. We review recent developments in metabolic phenotyping and systems biology technologies and how these methodologies have provided insights into the mechanisms of metabolic syndrome and nonalcoholic fatty liver disease. We discuss emerging areas of research in this field and outline our vision for how metabolic phenotyping could be used to study metabolic syndrome and fatty liver disease.

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Gut microbiota after gastric bypass in human obesity: increased richness and associations of bacterial genera with adipose tissue genes

Background: Roux-en-Y gastric bypass (RYGB) surgery is one of the most efficient procedures for treating morbid obesity and results in weight-loss and improvements in metabolism and inflammation.

Objective: We examined the impact of RYGB on modifications of gut microbiota and its potential associations with changes in gene expression in white adipose tissue (WAT).

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Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults

Abstract

Recent metagenomic studies have demonstrated that the overall functional potential of the intestinal microbiome is rather conserved between healthy individuals. Here we assessed the biological processes undertaken in-vivo by microbes and the host in the intestinal tract by conducting a metaproteome analysis from a total of 48 faecal samples of 16 healthy adults participating in a placebo-controlled probiotic intervention trial. Half of the subjects received placebo and the other half consumed

Lactobacillus rhamnosus

GG for three weeks (10

10

cfu per day). Faecal samples were collected just before and at the end of the consumption phase as well as after a three-week follow-up period, and were processed for microbial composition and metaproteome analysis. A common core of shared microbial protein functions could be identified in all subjects. Furthermore, we observed marked differences in expressed proteins between subjects that resulted in the definition of a stable and personalized microbiome both at the mass-spectrometry-based proteome level and the functional level based on the KEGG pathway analysis. No significant changes in the metaproteome were attributable to the probiotic intervention. A detailed taxonomic assignment of peptides and comparison to phylogenetic microarray data made it possible to evaluate the activity of the main phyla as well as key species, including

Faecalibacterium prausnitzii

. Several correlations were identified between human and bacterial proteins. Proteins of the human host accounted for approximately 14% of the identified metaproteome and displayed variations both between and within individuals. The individually different human intestinal proteomes point to personalized host-microbiota interactions. Our findings indicate that analysis of the intestinal metaproteome can complement gene-based analysis and contributes to a thorough understanding of the activities of the microbiome and the relevant pathways in health and disease.

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