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.
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/s00592-019-01312-x |
Diet-induced metabolic changes of the human gut microbiome: importance of short-chain fatty acids, methylamines and indoles |
Mohd Badrin Hanizam Abdul RahimJulien ChillouxLaura Martinez-GiliAna L. NevesAntonis MyridakisNigel GooderhamMarc-Emmanuel Dumas |
Acta Diabetologica | 22/03/2019 | Yes |
| https://doi.org/10.1186/s12864-019-5591-7 |
Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome |
Promi Das, Parizad Babaei and Jens Nielsen | BMC Genomics2019 20:208 | 12/03/2019 | Yes |
| https://doi.org/10.1038/s41598-019-40153-0 |
Systems Genetics of Hepatic Metabolome Reveals Octopamine as a Target for Non-Alcoholic Fatty Liver Disease Treatment |
Francois Brial, Aurélie Le Lay, Lyamine Hedjazi, Tsz Tsang, Jane F. Fearnside, Georg W. Otto, Fawaz Alzaid, Steven P. Wilder, Nicolas Venteclef, Jean-Baptiste Cazier, Jeremy K. Nicholson, Chris Day, Alastair D. Burt, Ivo G. Gut, Mark Lathrop, Marc-Emmanuel Dumas & Dominique Gauguier |
Scientific Reports volume 9, Article number: 3656 (2019) | 06/06/2019 | Yes |
| https://doi.org/10.1038/s41598-018-37019-2 | Identification of the novel role of butyrate as AhR ligand in human intestinal epithelial cells |
Ludovica Marinelli, Camille Martin-Gallausiaux, Jean-Marie Bourhis, Fabienne Béguet-Crespel, Hervé M. Blottière & Nicolas Lapaque |
Scientific Reports volume 9, Article number: 643 (2019) | 24/01/2019 | Yes |
| https://doi.org/10.3389/fmicb.2018.03289 |
Comparative Evaluation of Microbiota Engraftment Following Fecal Microbiota Transfer in Mice Models: Age, Kinetic and Microbial Status Matter |
Tiphaine Le Roy, Jean Debédat, Florian Marquet, Carla Da-Cunha, Farid Ichou, Michèle Guerre-Millo, Nathalie Kapel, Judith Aron-Wisnewsky and Karine Clément | Frontiers in Microbiology | 14/01/2019 | Yes |
| https://doi.org/10.1096/fj.201801897R |
Phosphatidylglycerols are induced by gut dysbiosis and inflammation, and favorably modulate adipose tissue remodeling in obesity |
Brandon D. Kayser, Marie Lhomme, Edi Prifti, Carla Da Cunha, Florian Marquet, Florian Chain, Isabelle Naas, Véronique Pelloux, Maria-Carlota Dao, Anatol Kontush, Salwa W. Rizkalla, Judith Aron-Wisnewsky, Luis G. Bermúdez-Humarán, Fiona Oakley, Philippe Langella, Karine Clément, and Isabelle Dugail | The FASEB Journal | 04/01/2019 | |
| https://doi.org/10.1016/j.inffus.2018.11.016 |
Revealing Causality between Heterogeneous Data Sources with Deep Restricted Boltzmann Machines |
Nataliya Sokolovska, Karine Clément, Jean-Daniel Zucker |
Information Fusion | 29/11/2018 | |
| https://doi.org/10.1017/S1368980018002951 |
Dietary assessment toolkits: an overview |
Maria Carlota Dao, Amy F Subar, Marisol Warthon-Medina, Janet E Ca | Cambridge Core University Press | 15/11/2018 | |
| https://doi.org/10.1093/nar/gky1085 |
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses |
Jaime Huerta-Cepas Damian Szklarczyk Davide Heller Ana Hernández-Plaza Sofia K Forslund Helen Cook Daniel R Mende Ivica Letunic Thomas Rattei Lars J Jensen | Nucleic Acids Research, gky1085, | 12/11/2018 | |
| https://doi.org/10.1016/j.cell.2018.09.055 |
Microbially Produced Imidazole Propionate Impairs Insulin Signaling through mTORC1 |
AraKoh, Antonio Molinar, et al | Cell
Volume 175, Issue 4, 1 November 2018, Pages 947-961.e17
|
01/11/2018 | |
| https://doi.org/10.1038/s41596-018-0064-z |
A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links |
Helle Krogh Pedersen, Sofia K. Forslund, Valborg Gudmundsdottir, Anders Østergaard Petersen, Falk Hildebrand, Tuulia Hyötyläinen, Trine Nielsen, Torben Hansen, Peer Bork, S. Dusko Ehrlich, Søren Brunak, Matej Oresic, Oluf Pedersen & Henrik Bjørn Nielsen | Nature Protocols (2018) | 31/10/2018 | |
| https://doi.org/10.1038/s41564-018-0257-9 |
Recovery of gut microbiota of healthy adults following antibiotic exposure |
Albert Palleja, Kristian H. Mikkelsen, Sofia K. Forslund, Alireza Kashani, Kristine H. Allin, Trine Nielsen, Tue H. Hansen, Suisha Liang, Qiang Feng, Chenchen Zhang, Paul Theodor Pyl, Luis Pedro Coelho, Huanming Yang, Jian Wang, Athanasios Typas, Morten F. Nielsen, Henrik Bjorn Nielsen, Peer Bork, Jun Wang, Tina Vilsbøll, Torben Hansen, Filip K. Knop, Manimozhiyan Arumugam & Oluf Pedersen | Nature Microbiology volume 3, pages1255–1265 (2018) | 22/10/2018 | |
| doi: 10.1136/gutjnl-2018-316106 |
Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota |
Tito RY, Chaffron S, Caenepeel C, et al |
Gut | 31/08/2018 | |
| https://doi.org/10.1007/s00018-018-2901-1 |
Implication of gut microbiota metabolites in cardiovascular and metabolic diseases |
Francois Brial, Aurélie Le Lay, Marc-Emmanuel Dumas, Dominique Gauguier |
Cellular and Molecular Life Sciences , Volume 75, Issue 21, pp 3977–3990 | 12/08/2018 | Yes |
| https://doi.org/10.1002/path.5134 | Increased jejunal permeability in human obesity is revealed by a lipid challenge and is linked to inflammation and type 2 diabetes |
Laurent Genser, Doriane Aguanno , Hédi A. Soula, Liping Dong, Laurence Trystram, Karen Assmann, Joe‐Elie Salem, Jean‐Christophe Vaillant, Jean‐Michel Oppert, Fabienne Laugerette |
The Journal of Pathology | 09/07/2018 | |
| https://doi.org/10.1038/s41598-018-28048-y |
Butyrate produced by gut commensal bacteria activates TGF-beta1 expression through the transcription factor SP1 in human intestinal epithelial cells |
Camille Martin-Gallausiaux, Fabienne Béguet-Crespel, Ludovica Marinelli, Alexandre Jamet, Florence Ledue, Hervé M. Blottière & Nicolas Lapaque |
Scientific Reports Volume 8 | 27/06/2018 | Yes |
| https://doi.org/10.1016/j.scitotenv.2018.01.288 |
The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems |
Lucette Flandroya, Theofilos Poutahidis, Gabriele Berg, Gerard Clarke, Maria-Carlota Dao,Ellen Decaestecker, Eeva Furman, Tari Haahtela, Sébastien Massart, Hubert Plovier, Yolanda Sanz... |
Science of The Total Environment Volume 627, 15 June 2018, Pages 1018–1038 |
15/06/2018 | Yes |
| http://dx.doi.org/10.1136/gutjnl-2018-316103
|
Major microbiota dysbiosis in severe obesity: fate after bariatric surgery |
Judith Aron-Wisnewsky,Edi Prifti,Eugeni Belda,Farid Ichou, Brandon D Kayser, Maria Carlota Dao, Eric O Verger, Lyamine Hedjazil, Jean-Luc Bouillot, Jean-Marc Chevallier, Nicolas Pons, Emmanuelle Le Chatelier, Florence Levenez, Stanislav Dusko Ehrlich, Joel Dore, Jean-Daniel Zucker, Karine Clément |
GUT Journal |
13/06/2018 | |
| https://doi.org/10.1093/nar/gky299 |
iPath3.0: interactive pathways explorer v3 |
Youssef Darzi, Ivica Letunic, Peer Bork, Takuji Yamada |
Nucleic Acids Research |
30/04/2018 | Yes |
| https://doi.org/10.1096/fj.201800052RR
|
Mucosal-associated invariant T (MAIT) cells are depleted and prone to apoptosis in cardiometabolic disorders |
Sothea Touch, Karen E. Assmann, Judith Aron-Wisnewsky, Florian Marquet, Christine Rouault, Magali Fradet, Héléna Mosbah, MetaCardis Consortium, Richard Isnard, Gérard Helft, Agnès Lehuen, Christine Poitou, Karine Clément and Sébastien André, Jean-Michel Oppert, Jean Khémis... |
The FASEB Journal |
27/04/2018 | |
| https://doi.org/10.1002/cpbi.41 |
Exploring the Genetic Landscape of Metabolic Phenotypes with MetaboSignal |
Andrea Rodriguez‐Martinez, Rafael Ayala, Joram M. Posma, Marc‐Emmanuel Dumas |
Current Protocols in Bioinformatics Volume 61, Issue1 |
09/04/2018 | |
| https://doi.org/10.1101/277434 |
Microbiome inhibition of IRAK-4 by trimethylamine mediates metabolic and immune benefits in high-fat-diet-induced insulin resistance |
Julien Chilloux, Francois Brial, Amandine Everard, David Smyth, Liyong Zhang, Hubert Plovier, Antonis Myridakis, Lesley Hoyles, Julian E Fuchs, Christine Blancher, Selin Gencer, Laura Martinez-Gili, Jane F Fearnside, Richard H Barton, Ana L Neves, Alice Rothwell, Christelle Gerard, Sophie Calderari, Claire L Boulange, Saroor Patel, James Scott, Robert C Glen, Nigel J Gooderham, Jeremy K Nicholson, Dominique Gauguier, Peter P Liu, Patrice D Cani, Marc-Emmanuel E Dumas |
BioRxiv |
07/03/2018 | Yes |
| https://doi.org/10.1016/j.ejim.2017.10.005
|
Gut microbiota and obesity: Concepts relevant to clinical care | Maria Carlota Dao, Karine Clément
|
European Journal of Internal Medicine Volume 48, February 2018, Pages 18-24 |
February 2018 | |
| doi:10.1038/s41598-017-18259-0 |
SCFAs strongly stimulate PYY production in human enteroendocrine cells |
P. Larraufie, C. Martin-Gallausiaux, N. Lapaque, J. Dore, F. M. Gribble, F. Reimann & H. M. Blottiere |
Scientific Reports volume 8, Article number: 74 (2018) |
08/01/2018 | Yes |
| D.O.I. | Title | Author(s) | Title of the periodical or the series | Date of publication | Open access |
| doi:10.1038/s41564-017-0072-8 |
Enterotypes in the landscape of gut microbial community composition |
Paul I. Costea, Falk Hildebrand, […]Peer Bork |
Nature Microbiology volume 3, pages8–16 (2018) |
18/12/2017 | No |
| doi 10.15252/msb.20177589 |
Subspecies in the global human gut microbiome |
Paul I Costea, Luis Pedro Coelho, Shinichi Sunagawa, Robin Munch, Jaime Huerta‐Cepas, Kristoffer Forslund, Falk Hildebrand, Almagul Kushugulova, Georg Zeller, Peer Bork | Molecular Systems Biology (2017) 13, 960 | 14/12/2017 | Yes |
|
Quantitative microbiome profiling links gut community variation to microbial load |
Doris Vandeputte, Gunter Kathagen, Kevin D’hoe, Sara Vieira-Silva, Mireia Valles-Colomer, João Sabino, Jun Wang, Raul Y. Tito, Lindsey De Commer, Youssef Darzi, Séverine Vermeire, Gwen Falony & Jeroen Raes | Nature 551, pages507–511 (23 November 2017) | 15/11/2017 | No | |
| 10.1016/j.jand.2016.10.030 |
Dietary Assessment in the MetaCardis Study: Development and Relative Validity of an Online Food Frequency Questionnaire |
Verger EO, Armstrong P, Nielsen T, Chakaroun R, Aron-Wisnewsky J, Gøbel RJ, Schütz T, Delaere F, Gausseres N, Clément K, Holmes BA; MetaCardis Consortium. | Journal of the Academy of Nutrition and Dietics,Volume 117, Issue 6 | 01/07/2017 | Yes |
| 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 |
| 10.21037/amj.2017.07.10 |
Dietary choline derived TMAO: new role in thrombosis |
Judith Aron-wisnewsky, Karine Clement | AME Medical Journal | 18/08/2017 | Yes |
| doi: 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 |
| doi: 10.1016/j.ejim.2017.10.005 |
Gut microbiota and obesity: Concepts relevant to clinical care. (first version) |
Dao MC, Clément K. | European journal of internal medicine 2017 Oct 27 | 01/10/2017 | No |
| doi: 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 |
| 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 |
| 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 | |
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| 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 |
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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 | |
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| 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 |
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| 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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| 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 |
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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
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).
Read more ...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.
Read more ...© MetaCardis 2012 - 2015
This project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement HEALTH-F4-2012-305312.