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17 results on '"Delorme, Christine"'

1. An integrated catalog of reference genes in the human gut microbiome

Author

Li, Junhua, Jia, Huijue, Cai, Xianghang, Zhong, Huanzi, Feng, Qiang, Sunagawa, Shinichi, Arumugam, Manimozhiyan, Kultima, Jens Roat, Prifti, Edi, Nielsen, Trine, Juncker, Agnieszka Sierakowska, Manichanh, Chaysavanh, Chen, Bing, Zhang, Wenwei, Levenez, Florence, Wang, Juan, Xu, Xun, Xiao, Liang, Liang, Suisha, Zhang, Dongya, Zhang, Zhaoxi, Chen, Weineng, Zhao, Hailong, Al-Aama, Jumana Yousuf, Edris, Sherif, Yang, Huanming, Wang, Jian, Hansen, Torben, Nielsen, Henrik Bjørn, Brunak, Søren, Kristiansen, Karsten, Guarner, Francisco, Pedersen, Oluf, Dore, Joel, Ehrlich, Stanislav, Bork, Peer, Wang, Jun, Pons, Nicolas, Le Chatelier, Emmanuelle, Batto, Jean-Michel, Kennedy, Sean, Haimet, Florence, Winogradsky, Yohanan, Cultrone, Antonietta, Leclerc, Marion, Juste, Catherine, Guedon, Eric, Delorme, Christine, Layec, Séverine, Kaci, Ghalia, Van De Guchte, Maarten, Vandemeulebrouck, Gaetana, Jamet, Alexandre, Dervyn, Rozenn, Sanchez, Nicolas, Blottiere, Herve, Maguin, Emmanuelle, Renault, Pierre, Tap, Julien, BGI Shenzhen, School of Bioscience and Biotechnology, Southern University of Science and Technology [Shenzhen] (SUSTech), Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), European Molecular Biology Laboratory, Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Faculty of Health and Medical Sciences, US 1367 MetaGénoPolis, Institut National de la Recherche Agronomique (INRA)-Département Microbiologie et Chaîne Alimentaire (MICA), Institut National de la Recherche Agronomique (INRA)-MetaGénoPolis (MGP), Center for Biological Sequence Analysis, Technical University of Denmark [Lyngby] (DTU), Digestive System Research Unit, Vall d'Hebron University Hospital [Barcelona], Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, Department of Biological Sciences, Faculty of Science, Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), James D. Watson Institute of Genome Science, Zhejiang University, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Centre for Host-Microbiome Interactions, Dental Institute Central Office, King‘s College London, Max Delbrück Center for Molecular Medicine, Macau University of Science and Technology (MUST), Département Microbiologie et Chaîne Alimentaire (MICA), Institut National de la Recherche Agronomique (INRA), Beijing Genomics Institute [Shenzhen] (BGI), MetaGenoPolis, Max Delbrück Center for Molecular Medicine [Berlin] (MDC), and Helmholtz-Gemeinschaft = Helmholtz Association

Subjects
[SDV]Life Sciences [q-bio], reference genes, Applied Microbiology and Biotechnology, Genome, Human health, Microbiologie, Reference genes, population-size, health care economics and organizations, Genetics, 0303 health sciences, Microbiota, alignment, tool, twins, Intestines, impact, Molecular Medicine, Biotechnology, information science, Biomedical Engineering, Bioengineering, danish individual, Computational biology, Biology, Microbiology, metagenome, 03 medical and health sciences, Human gut, Catalogs as Topic, Humans, natural sciences, Host-Microbe Interactomics, Microbiome, Gene, VLAG, 030304 developmental biology, human gut microbiome, fecal microbiota, 030306 microbiology, eukaryotic diversity, metagenomic of the human intestinal tract, country specific gut microbial signature, Metagenomics, WIAS, sequences, genomes, chinese individual, Human Microbiome Project
Abstract

Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly sequenced samples of the Metagenomics of the Human Intestinal Tract (MetaHit) project with 1,018 previously sequenced samples to create a cohort from three continents that is at least threefold larger than cohorts used for previous gene catalogs. From this we established the integrated gene catalog (IGC) comprising 9,879,896 genes. The catalog includes close-to-complete sets of genes for most gut microbes, which are also of considerably higher quality than in previous catalogs. Analyses of a group of samples from Chinese and Danish individuals using the catalog revealed country-specific gut microbial signatures. This expanded catalog should facilitate quantitative characterization of metagenomic, metatranscriptomic and metaproteomic data from the gut microbiome to understand its variation across populations in human health and disease.

Published
2014

2. Transcriptional interactions suggest niche segregation among microorganisms in the human gut

Author

Plichta, Damian Rafal, Juncker, Agnieszka Sierakowska, Bertalan, Marcelo, Rettedal, Elizabeth, Gautier, Laurent, Varela, Encarna, Manichanh, Chaysavanh, Fouqueray, Charlène, Levenez, Florence, Nielsen, Trine, Dore, Joel, Machado, Ana Manuel Dantas, de Evgrafov, Mari Cristina Rodriguez, Hansen, Torben, Jorgensen, Torben, Bork, Peer, Guarner, Francisco, Pedersen, Oluf, Consortium, MetaHit, Sommer, Morten O. A., Ehrlich, S. Dusko, Sicheritz-Ponten, Thomas, Brunak, Soren, Nielsen, H. Bjorn, Almeida, Mathieu, Batto, Jean-Michel, Blottiere, Herve, Cultrone, Antonietta, Delorme, Christine, derwyn, rozenn, Guédon, Eric, Haimet, Florence, Jamet, Alexandre, Juste, Catherine, Kennedy, Sean P., Kaci, Ghalia, Layec, Séverine, Leclerc, Marion, Léonard, Pierre, Maguin, Emmanuelle, Pons, Nicolas, Renault, Pierre, Sanchez, Nicolas, Van De Guchte, Maarten, Van Hylckama Vlieg, Johan, Vandemeulebrouck, Gaetana, Winogradsky, Yohanan, Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark [Lyngby] (DTU), A/S, Clinical-Microbiomics, Novo Nordisk Foundation Center for Biosustainability, Department of Systems Biology, DTU Multi-Assay Core, Digestive System Research Unit, Vall d'Hebron University Hospital, MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Faculty of Health Sciences, University of Southern Denmark (SDU), Faculty of Medicine, Aalborg University [Denmark] (AAU), Research Centre for Prevention and Health, Capital region, Glostrup University Hospital, University of Copenhagen = Københavns Universitet (KU), European Molecular Biology Laboratory [Hamburg] (EMBL), Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy’s Hospital, King‘s College London, Disease Systems Biology [Copenhagen], Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, Clinical Microbiomics, International Human Microbiome Standards [FP7-HEALTH-2010-261376], Metagenopolis [ANR-11-DPBS-0001], Novo Nordisk Foundation, Lundbeck Foundation, European Project: 201052, Vall d'Hebron University Hospital [Barcelona], Génie et Microbiologie des Procédés Alimentaires (GMPA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of Copenhagen = Københavns Universitet (UCPH), and University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences

Subjects
0301 basic medicine, Microbiology (medical), Feces/microbiology, Systems Analysis, ATP-Binding Cassette Transporters/genetics, Denmark, [SDV]Life Sciences [q-bio], Microbial Interactions/genetics, 030106 microbiology, Immunology, Gastrointestinal Microbiome/genetics, Biology, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, Feces, Microbial ecology, Journal Article, Genetics, Humans, Butyrates/metabolism, Microbiome, Regulation of gene expression, Ecology, Metabolic Networks and Pathways/genetics, Gene Expression Profiling, Niche segregation, Chemotaxis, Cell Biology, Carbon Dioxide, Gastrointestinal Microbiome, Gene expression profiling, Butyrates, 030104 developmental biology, Metagenomics, Spain, Bifidobacterium bifidum/genetics, Metagenome, Microbial Interactions, Carbon Dioxide/metabolism, ATP-Binding Cassette Transporters, Bifidobacterium bifidum, Adaptation, Metabolic Networks and Pathways
Abstract

The human gastrointestinal (GI) tract is the habitat for hundreds of microbial species, of which many cannot be cultivated readily, presumably because of the dependencies between species 1. Studies of microbial co-occurrence in the gut have indicated community substructures that may reflect functional and metabolic interactions between cohabiting species 2,3. To move beyond species co-occurrence networks, we systematically identified transcriptional interactions between pairs of coexisting gut microbes using metagenomics and microarray-based metatranscriptomics data from 233 stool samples from Europeans. In 102 significantly interacting species pairs, the transcriptional changes led to a reduced expression of orthologous functions between the coexisting species. Specific species-species transcriptional interactions were enriched for functions important for H 2 and CO 2 homeostasis, butyrate biosynthesis, ATP-binding cassette (ABC) transporters, flagella assembly and bacterial chemotaxis, as well as for the metabolism of carbohydrates, amino acids and cofactors. The analysis gives the first insight into the microbial community-wide transcriptional interactions, and suggests that the regulation of gene expression plays an important role in species adaptation to coexistence and that niche segregation takes place at the transcriptional level.

Published
2016

3. Richness of human gut microbiome correlates with metabolic markers

Author

Le Chatelier, Emmanuelle, Nielsen, Trine, Qin, Junjie, Prifti, Edi, Hildebrand, Falk, Falony, Gwen, Almeida, Mathieu, Arumugam, Manimozhiyan, Batto, Jean-Michel, Kennedy, Sean, Leonard, Pierre, Li, Junhua, Burgdorf, Kristoffer, Grarup, Niels, Jørgensen, Torben, Brandslund, Ivan, Nielsen, Henrik Bjørn, Juncker, Agnieszka S., Bertalan, Marcelo, Levenez, Florence, Pons, Nicolas, Rasmussen, Simon, Sunagawa, Shinichi, Tap, Julien, Tims, Sebastian, Zoetendal, Erwin G., Brunak, Søren, Clément, Karine, Doré, Joël, Kleerebezem, Michiel, Kristiansen, Karsten, Renault, Pierre, Sicheritz-Ponten, Thomas, de Vos, Willem M., Zucker, Jean-Daniel, Raes, Jeroen, Hansen, Torben, Guedon, Eric, Delorme, Christine, Layec, Séverine, Khaci, Ghalia, van de Guchte, Maarten, Vandemeulebrouck, Gaetana, Jamet, Alexandre, Dervyn, Rozenn, Sanchez, Nicolas, Maguin, Emmanuelle, Haimet, Florence, Winogradski, Yohanan, Cultrone, Antonella, Leclerc, Marion, Juste, Catherine, Blottière, Hervé, Pelletier, Eric, LePaslier, Denis, Artiguenave, François, Bruls, Thomas, Weissenbach, Jean, Turner, Keith, Parkhill, Julian, Antolin, Maria, Manichanh, Chaysavanh, Casellas, Francesc, Boruel, Natalia, Varela, Encarna, Torrejon, Antonio, Guarner, Francisco, Denariaz, Gérard, Derrien, Muriel, van Hylckama Vlieg, Johan E. T., Veiga, Patrick, Oozeer, Raish, Knol, Jan, Rescigno, Maria, Brechot, Christian, M’Rini, Christine, Mérieux, Alexandre, Yamada, Takuji, Bork, Peer, Wang, Jun, Ehrlich, S. Dusko, Pedersen, Oluf, MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Beijing Genomics Institute [Shenzhen] (BGI), Department of Structural Biology, Flanders Institute for Biotechnology, Department of Bioscience Engineering, Vrije Universiteit Brussel (VUB), European Molecular Biology Laboratory, School of Bioscience and Biotechnology, Southern University of Science and Technology [Shenzhen] (SUSTech), Research Centre for Prevention and Health (RCPH), Department of Public Health [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Capital Region of Denmark, University of Copenhagen = Københavns Universitet (KU), Faculty of Medicine, Institute of Public Health, Aalborg University [Denmark] (AAU), Department of Clinical Biochemistry, Vejle Hospital, Institute of Regional Health Research, University of Southern Denmark (SDU), Center for Biological Sequence Analysis & Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark [Lyngby] (DTU), Laboratory of Microbiology, Wageningen University and Research [Wageningen] (WUR), U872 Centre de Recherche des Cordeliers, Nutriomique, Équipe 7, Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Paris Descartes - Paris 5 (UPD5)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC), Centre de Recherche en Nutrition Humaine d'Ile-de-France (CRNH Ile-de-France), Institute of Cardiometabolism and Nutrition, Assistance Publique - Hôpitaux de Paris, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Biology [Copenhagen], Faculty of Science [Copenhagen], Department of Bacteriology and Immunology [Helsinki], Haartman Institute [Helsinki], Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki-Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Faculty of Health Sciences, King Abdulaziz University, Center for Sequencing, Aarhus University [Aarhus], Hagedorn Research Institute, Faculty of Health, Département Microbiologie et Chaîne Alimentaire (MICA), European Community (HEALTH-F4-2007-201052) - Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care (LuCamp) - ANR MicroObes, the Metagenopolis grant (ANR-11-DPBS-0001 ) - Region Ile de France (CODDIM) - Fondacoeur - Novo Nordisk Foundation, US 1367 MetaGénoPolis, Institut National de la Recherche Agronomique ( INRA ) -MetaGénoPolis ( MGP ) -Microbiologie et Chaîne Alimentaire ( MICA ), Faculty of Health and Medical Sciences, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen ( KU ), Beijing Genomics Institute, Vrije Universiteit [Brussel] ( VUB ), South University of Science and Technology of China, Research Centre for Prevention and Health, Glostrup University Hospital, Aalborg University [Denmark] ( AAU ), UNIVERSITY OF SOUTHERN DENMARK, Technical University of Denmark [Lyngby] ( DTU ), Wageningen University and Research Centre [Wageningen] ( WUR ), Centre de Recherche des Cordeliers ( CRC (UMR_S 872) ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Université Pierre et Marie Curie - Paris 6 ( UPMC ), MICrobiologie de l'ALImentation au Service de la Santé humaine ( MICALIS ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Department of Biology, Department of Bacteriology and Immunology, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] ( UMMISCO ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop ( UCAD ) -Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 [Cameroun]-University Cadi Ayyad ( UCA ), Department of Biology / Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, The Novo Nordisk Foundation Center for Basic Metabolic Research / Institute of Biomedical Science, Département Microbiologie et Chaîne Alimentaire ( MICA ), Institut National de la Recherche Agronomique ( INRA ), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut National de la Recherche Agronomique (INRA)-Département Microbiologie et Chaîne Alimentaire (MICA), Institut National de la Recherche Agronomique (INRA)-MetaGénoPolis (MGP), Vrije Universiteit [Brussels] (VUB), Wageningen University and Research Centre [Wageningen] (WUR), Université Cadi Ayyad [Marrakech] (UCA)-Universtié Yaoundé 1 [Cameroun]-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Southern University of Science and Technology (SUSTech), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Capital Region of Denmark, University of Copenhagen = Københavns Universitet (UCPH), Vejle Hospital [Danemark], Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Faculty of Medecine [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)

Subjects
Male, [SDV]Life Sciences [q-bio], body-mass index, Overweight, Weight Gain, Body Mass Index, 0302 clinical medicine, Microbiologie, insulin resistance, Phylogeny, 2. Zero hunger, 0303 health sciences, education.field_of_study, adiposity, Multidisciplinary, reared apart, Ecology, twins, 3. Good health, Europe, 030220 oncology & carcinogenesis, Enterotype, Biological Markers, Female, medicine.symptom, weight-loss, Adult, diet-induced obesity, Population, European Continental Ancestry Group, Zoology, body mass index, wide association, Biology, Microbiology, White People, insulin-resistance, 03 medical and health sciences, Thinness, diet induced obesity, Weight Loss, medicine, Humans, Microbiome, Host-Microbe Interactomics, Obesity, education, 030304 developmental biology, VLAG, Dyslipidemias, disease, Bacteria, [ SDV ] Life Sciences [q-bio], medicine.disease, Diet, Gastrointestinal Tract, Metagenomics, Genes, Bacterial, inflammation, Case-Control Studies, WIAS, Metagenome, Species richness, Insulin Resistance, weight loss, Energy Metabolism, Weight gain, Biomarkers
Abstract

We are facing a global metabolic health crisis provoked by an obesity epidemic. Here we report the human gut microbial composition in a population sample of 123 non-obese and 169 obese Danish individuals. We find two groups of individuals that differ by the number of gut microbial genes and thus gut bacterial richness. They contain known and previously unknown bacterial species at different proportions; individuals with a low bacterial richness (23% of the population) are characterized by more marked overall adiposity, insulin resistance and dyslipidaemia and a more pronounced inflammatory phenotype when compared with high bacterial richness individuals. The obese individuals among the lower bacterial richness group also gain more weight over time. Only a few bacterial species are sufficient to distinguish between individuals with high and low bacterial richness, and even between lean and obese participants. Our classifications based on variation in the gut microbiome identify subsets of individuals in the general white adult population who may be at increased risk of progressing to adiposity-associated co-morbidities.

Published
2013

4. Etude de l'adaptation de Lactococcus lactis a l'environnement digestif : approche génétique

Author

Corthier, Gerard, Gilbert, Sophie, Muller, M.C., Delorme, Christine, Drouault, S., Guedon, E., RAPINE, P., Renault, P., Unité de recherche d'Écologie et Physiologie du Système Digestif (UEPSD), Institut National de la Recherche Agronomique (INRA), Unité de recherche Génétique Microbienne (UGM), and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], PHYSIOLOGIE, [SDV]Life Sciences [q-bio], LACTOCOCCUS LACTIS, ComputingMilieux_MISCELLANEOUS, TUBE DIGESTIF
Abstract

National audience

Published
1999

5. Physiologie des bactéries lactiques dans le tractus digestif

Author

Corthier, Gerard, Delorme, Christine, Renault, P., ProdInra, Migration, Unité de recherche d'Écologie et Physiologie du Système Digestif (UEPSD), Institut National de la Recherche Agronomique (INRA), and Unité de recherche Génétique Microbienne (UGM)

Subjects
[SDV] Life Sciences [q-bio], PHYSIOLOGIE, [SDV]Life Sciences [q-bio], LACTOCOCCUS LACTIS, ComputingMilieux_MISCELLANEOUS, TUBE DIGESTIF
Abstract

National audience

Published
1997

6. Assessment of bacterial physiology in the digestive tract by use of luciferase as promoter probe

Author

Corthier, Gerard, Delorme, Christine, Ehrlich, S.D., Renault, P., ProdInra, Migration, Unité de recherche d'Écologie et Physiologie du Système Digestif (UEPSD), Institut National de la Recherche Agronomique (INRA), and Unité de recherche Génétique Microbienne (UGM)

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], LACTOCOCCUS LACTIS, ComputingMilieux_MISCELLANEOUS, TUBE DIGESTIF
Abstract

National audience

Published
1997

7. Human gut microbes impact host serum metabolome and insulin sensitivity

Author

Pedersen, Helle Krogh, Gudmundsdottir, Valborg, Nielsen, Henrik Bjørn, Hyotylainen, Tuulia, Nielsen, Trine, Jensen, Benjamin A H, Forslund, Kristoffer, Hildebrand, Falk, Prifti, Edi, Falony, Gwen, Le Chatelier, Emmanuelle, Levenez, Florence, Dore, Joel, Mattila, Ismo, Plichta, Damian R, Pöhö, Päivi, Hellgren, Lars I, Arumugam, Manimozhiyan, Sunagawa, Shinichi, Vieira-Silva, Sara, Jørgensen, Torben, Holm, Jacob Bak, Trošt, Kajetan, Kristiansen, Karsten, Brix, Susanne, Raes, Jeroen, Wang, Jun, Hansen, Torben, Bork, Peer, Brunak, Søren, Oresic, Matej, Ehrlich, S. Dusko, Pedersen, Oluf, MetaHIT Consortium, ., Almeida, Mathieu, Batto, Jean-Michel, Blottiere, Hervé, Cultrone, Antonietta, Delorme, Christine, Dervyn, Rozenn, Guedon, Eric, Haimet, Florence, Jamet, Alexandre, Juste, Catherine, Kennedy, Sean, Kaci, Ghalia, Kleerebezem, Michiel, Layec, Séverine, Leclerc, Marion, Léonard, Pierre, Maguin, Emmanuelle, Manichanh, Chaysavanh, Pons, Nicolas, Renault, Pierre, Sanchez, Nicolas, Van De Guchte, Maarten, Van Hylckama Vlieg, Johan, Vandemeulebrouck, Gaetana, Winogradsky, Yohanan, Center for Biological Sequence Analysis - Department of Systems Biology, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of Denmark, Turku Centre for Biotechnology, University of Turku-Åbo Academy University, Åbo Akademi University [Turku], Örebro University, VTT Technical Research Centre of Finland (VTT), Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Laboratory of Genomics and Molecular Biomedicine - Department of Biology, University of Copenhagen = Københavns Universitet (UCPH), European Molecular Biology Laboratory, Department of Bioscience Engineering, University of Antwerp (UA), Center for the Biology of Disease, VIB, MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Centter for the Biology of Disease, Department of Microbiology and Immunology, Rega Institute for Medical Research, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Steno Diabetes Center, Faculty of Pharmacy, University of Valencia, Institute of Microbiology, Université de Lausanne = University of Lausanne (UNIL), Centre for the Biology of Disease, Research Centre for Prevention and Health - Centre for Health, Glostrup Hospital, Beijing Genomics Institute [Shenzhen] (BGI), Vrije Universiteit Brussel [Bruxelles] (VUB), Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Macau University of Science and Technology (MUST), Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Faculty of Health Sciences, Aarhus University [Aarhus], Molecular Medicine Partnership Unit, Heidelberg University, Max Delbrück Center for Molecular Medicine [Berlin] (MDC), Helmholtz-Gemeinschaft = Helmholtz Association, Department of Bioinformatics, Erasmus University Medical Center [Rotterdam] (Erasmus MC), Disease Systems Biology [Copenhagen], Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, Centre for Biotechnology, Silesian University of Technology, Université Paris-Saclay, Centre for Host–Microbiome Interactions - Dental Institute Central Office, King‘s College London, Guys Hospital, Génie et Microbiologie des Procédés Alimentaires (GMPA), Département Microbiologie et Chaîne Alimentaire (MICA), Danone Research, Groupe Danone, International Human Microbiome Standards [FP7-HEALTH-2010-261376], Metagenopolis [ANR-11-DPBS-0001], Novo Nordisk Foundation, Lundbeck Foundation, European Project: 222720,EC | FP7 | SP1 | KBBE ,FP7-KBBE-2007-2A,TORNADO(2009), Technical University of Denmark [Lyngby] (DTU), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), University of Copenhagen = Københavns Universitet (KU), Jouy-en-Josas, Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [APHP], Université de Lausanne (UNIL), BGI Shenzhen, Vrije University, University of Heidelberg, Max Delbrück Center for Molecular Medicine, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, US 1367 MGP MetaGénoPolis, Laboratory of Microbiology, CHU Rouen, Normandie Université (NU)-Normandie Université (NU), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Digestive System Research Unit, Vall d'Hebron University Hospital [Barcelona], European Project: 201052, Faculty of Sciences and Bioengineering Sciences, Microbial Interactions, Department of Bio-engineering Sciences, and Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)

Subjects
0301 basic medicine, Male, [SDV]Life Sciences [q-bio], Prevotella, Gastrointestinal Microbiome/physiology, Bacteroides/physiology, Type 2 diabetes, Fasting/blood, SERUM, Mice, 0302 clinical medicine, insulin resistance, Bacteroides, Netherlands, Multidisciplinary, biology, Research Support, Non-U.S. Gov't, Gastrointestinal Microbiome, Prevotella/physiology, Fasting, 3. Good health, Cardiovascular diseases, Cardiovascular Diseases/metabolism, Metabolome, Amino Acids, Branched-Chain/biosynthesis, medicine.medical_specialty, Glyco-Forum Section, Serum/metabolism, mice, 030209 endocrinology & metabolism, metagenome, 03 medical and health sciences, Insulin resistance, Internal medicine, Glucose Intolerance, medicine, Animals, Humans, Microbiome, Glucose Intolerance/blood, ta1182, biology.organism_classification, medicine.disease, Obesity, Mice, Inbred C57BL, 030104 developmental biology, Endocrinology, Metagenome, Insulin Resistance, Amino Acids, Branched-Chain
Abstract

MetaHIT Consortium: Almeida M, Antolin M, Artiguenave F, Batto JM, Bertalan M, Blottiere H, Boruel N, Brechot C, Bruls T, Burgdorf K, Casellas F, Cultrone A, de Vos WM, Delorme C, Denariaraz G., Derrien M, Dervyn R, Feng Q, Grarup N, Guarner F, Guedon E, Haimet F, Jamet A, Juncker A, Juste C, Kennedy S, Khaci G, Kleerebezem M, Knoll J, Layec S, Leclerc M, Leonard P, LePaslier D, m'Rini C, Maguin E, Manichanh C, Mende D, Merieux A, Oozer R, Parkhill J, Pelletier E, POns N, QinJ, rasmussen S, Renault P, Rescigno M, Sanchez N, Sicheritz-Ponten T, Tap J, Tims S, Torrejon A, Turner K, van de Guchet M, van hylckama Vlieg JE, Vandemeulebrouck G, Varela E, Veiga P, Weissenbach J, Winogradski Y, Yamada T, Zoetendal EG; Insulin resistance is a forerunner state of ischaemic cardiovascular disease and type 2 diabetes. Here we show how the human gut microbiome impacts the serum metabolome and associates with insulin resistance in 277 non-diabetic Danish individuals. The serum metabolome of insulin-resistant individuals is characterized by increased levels of branched-chain amino acids (BCAAs), which correlate with a gut microbiome that has an enriched biosynthetic potential for BCAAs and is deprived of genes encoding bacterial inward transporters for these amino acids. Prevotella copri and Bacteroides vulgatus are identified as the main species driving the association between biosynthesis of BCAAs and insulin resistance, and in mice we demonstrate that P. copri can induce insulin resistance, aggravate glucose intolerance and augment circulating levels of BCAAs. Our findings suggest that microbial targets may have the potential to diminish insulin resistance and reduce the incidence of common metabolic and cardiovascular disorders.

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8. Critical interaction between E1 and E2 glycoproteins determines binding and fusion properties of hepatitis C virus during cell entry

Author

Judith Fresquet, Thomas Baumert, Dimitri Mompelat, Mirjam B. Zeisel, Florian Douam, Guillemette Maurin, François-Loïc Cosset, Dimitri Lavillette, Viet Loan Dao Thi, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Virologie humaine, École normale supérieure - Lyon (ENS Lyon)-IFR128-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), ANR - Agence Nationale de la Recherche sur le Sida et les hepatites virales (ANRS) et FINOVI foundation et the European Research Council (ERC-2008-AdG-233130-HEPCENT) and the LabEx HEPSYS (ANR-10-LAB-28), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), École normale supérieure - Lyon ( ENS Lyon ) -IFR128-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Medicine II, University of Freiburg [Freiburg], Plate-forme de R&D - Puces à Cellules Transfectées (PCT), Cancéropôle du Grand-Est (CGE)-Centre Européen de Biologie et de Génomique Structurale (CEBGS)-Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-IFR128-Institut National de la Santé et de la Recherche Médicale (INSERM), and Delorme, Christine

Subjects
INVOLVEMENT, [SDV.BA] Life Sciences [q-bio]/Animal biology, [SDV]Life Sciences [q-bio], [ SDV.TOX ] Life Sciences [q-bio]/Toxicology, Plasma protein binding, Hepacivirus, [ SDV.BA ] Life Sciences [q-bio]/Animal biology, Membrane Fusion, 0302 clinical medicine, Protein structure, Viral Envelope Proteins, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Claudin-1, INFECTION, TRANSMEMBRANE DOMAINS, Receptor, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, chemistry.chemical_classification, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [ SDV.MHEP.ME ] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.BA]Life Sciences [q-bio]/Animal biology, Liver Neoplasms, LOCALIZATION, Scavenger Receptors, Class B, Hepatitis C, 3. Good health, Cell biology, [SDV.TOX] Life Sciences [q-bio]/Toxicology, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, Crosstalk (biology), [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.TOX]Life Sciences [q-bio]/Toxicology, CORECEPTOR, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, 030211 gastroenterology & hepatology, COMPLEXES, Dimerization, BROADLY NEUTRALIZING ANTIBODIES, Protein Binding, Carcinoma, Hepatocellular, PROTEINS, Molecular Sequence Data, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, Tetraspanin 28, 03 medical and health sciences, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, MUTAGENESIS, Hepatology, RECEPTOR, HEK 293 cells, Lipid bilayer fusion, Virology, Protein Structure, Tertiary, Rats, HEK293 Cells, chemistry, Glycoprotein, [SDV.BID] Life Sciences [q-bio]/Biodiversity, CD81
Abstract

Affiliation ECOFECT; International audience; Hepatitis C virus (HCV) envelope glycoproteins E1 and E2 are important mediators for productive cell entry. However, knowledge about their structure, intra- or intermolecular dialogs, and conformational changes is scarce, limiting the design of therapeutic strategies targeting E1E2. Here we sought to investigate how certain domains of E1 and E2 have coevolved to optimize their interactions to promote efficient HCV entry. For this purpose we generated chimeric E1E2 heterodimers derived from two HCV 1a strains to identify and characterize crosstalk between their domains. We found an E1E2 combination that drastically impaired the infectivity of cell culture-derived HCV particles, whereas the reciprocal E1E2 combination led to increased infectivity. Using HCV pseudoparticle assays, we confirmed the opposing entry phenotypes of these heterodimers. By mutagenesis analysis, we identified a particular crosstalk between three amino acids of E1 and the domain III of E2. Its modulation leads to either a full restoration of the functionality of the suboptimal heterodimer or a destabilization of the functional heterodimer. Interestingly, we found that this crosstalk modulates E1E2 binding to HCV entry receptors SR-BI and CD81. In addition, we found for the first time that E1E2 complexes can interact with the first extracellular loop of Claudin-1, whereas soluble E2 did not. These results highlight the critical role of E1 in the modulation of HCV binding to receptors. Finally, we demonstrated that this crosstalk is involved in membrane fusion. Conclusions: These results reveal a multifunctional and crucial interaction between E1 and E2 for HCV entry into cells. Our study highlights the role of E1 as a modulator of HCV binding to receptors and membrane fusion, underlining its potential as an antiviral target. (Hepatology 2014;59:776-788).

Published
2014

9. Emergence of a cell wall protease in the [i]Streptococcus thermophilus[/i] population

Author

Christine Delorme, Pierre Renault, Claire Bartholini, Alexander Bolotine, S. Dusko Ehrlich, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Delorme, Christine

Subjects
Streptococcus thermophilus, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Population, Streptococcus suis, Biology, Applied Microbiology and Biotechnology, émergence, 03 medical and health sciences, Bacterial Proteins, Cell Wall, Evolutionary and Genomic Microbiology, Insertion sequence, education, Gene, Phylogeny, 030304 developmental biology, Synteny, 2. Zero hunger, Genetics, 0303 health sciences, education.field_of_study, streptococcus thermophilus, Base Sequence, Ecology, 030306 microbiology, Serine Endopeptidases, Genetic Variation, biology.organism_classification, Horizontal gene transfer, Multilocus sequence typing, Food Science, Biotechnology
Abstract

Streptococcus thermophilus is perceived as a recently emerged food bacterium that evolved from a commensal ancestor by loss and gain of functions. Here, we provide data allowing a better understanding of this evolutionary scheme. A multilocus sequence typing approach that we developed showed that S. thermophilus diverges significantly from its potential ancestors of the salivarius group and displays a low level of allelic variability, confirming its likely recent emergence. An analysis of the origin and dissemination of the prtS gene was carried out within this evolutionary scheme. This gene encodes a protease that allows better growth in milk by facilitating casein breakdown to supply amino acids. The S. thermophilus protease exhibits 95% identity to the animal Streptococcus suis protein PrtS. Genomic analysis showed that prtS is part of an island flanked by two tandem insertion sequence elements and containing three other genes which present the best identities and synteny with the S. suis genome. These data indicate a potential origin for this “ecological” island in a species closely related to S. suis . The analysis of the distribution of the prtS gene in S. thermophilus showed that the gene is infrequent in historical collections but frequent in recent industrial ones. Moreover, this “ecological” island conferring an important metabolic trait for milk adaptation appears to have disseminated by lateral transfer in the S. thermophilus population. Taken together, these data support an evolutionary scheme of S. thermophilus where gene acquisition and selection by food producers are determining factors. The source and impact of genes acquired by horizontal gene transfer on the physiology and safety of strains should be addressed.

Published
2010

10. Evolution and Diversity of Frankia

Author

Normand, Philippe, Fernandez, M., Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), and Delorme, Christine

Subjects
[SDE.BE.BIOD] Environmental Sciences/Biodiversity and Ecology/domain_sde.be.biod, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV]Life Sciences [q-bio], [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [ SDE.BE.BIOD ] Environmental Sciences/Biodiversity and Ecology/domain_sde.be.biod, [SDE.BE.BIOD]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.biod, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]
Abstract

International audience; Frankia is an actinobacterium that induces symbiotic nodules on the root of 25 genera of woody dicotyledonous plants (Benson and Silvester 1993). It took a century of unsuccessful efforts before it could be isolated in pure culture and its taxonomic status thus remained disputed for a long time. Pure cultures can be grouped according to host infectivity into (1) strains infective on Alnus, (2) strains infective on Casuarina, (3) strains infective on Elaeagnaceae, (4) unisolated strains and (5) uninfective isolates. These strains have been grouped into genospecies and there are between 3–7 Alnusinfective, 1 Casuarina-infective and 8–12 Elaeagnus-infective species. The phylogeny of these species has been reconstructed using rrs sequences and Frankia is now ascribed to the Frankiaceae, one of the six families of the suborder Frankinae. Genus Frankia is subdivided into phylogenetic clusters: #1-Frankia alni and related (contains Casuarinainfective and most Alnus-infective strains), #2-Unisolated strains present on Rosaceous, Datisca, Coriaria and Ceanothus, #3-Elaeagnaceae-infective strains and #4-a large group of “atypical” strains.

Published
2009

11. Extent of horizontal gene transfer in evolution of Streptococci of the salivarius group

Author

Pierre Renault, Claire Poyart, Christine Delorme, Stanislav Dusko Ehrlich, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut Cochin (IC UM3 (UMR 8104 / U1016)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), ProdInra, Archive Ouverte, Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), US 1367 MetaGénoPolis, Institut National de la Recherche Agronomique (INRA)-Département Microbiologie et Chaîne Alimentaire (MICA), Institut National de la Recherche Agronomique (INRA)-MetaGénoPolis (MGP), Delorme, Christine, MICrobiologie de l'ALImentation au Service de la Santé humaine (MICALIS), Institut National de la Recherche Agronomique (INRA) - AgroParisTech, Institut Cochin (UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5) - Institut National de la Santé et de la Recherche Médicale (INSERM) - Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA) - MetaGénoPolis (MGP) - Microbiologie et Chaîne Alimentaire (MICA)

Subjects
Gene Transfer, Horizontal, Sequence analysis, [SDV]Life Sciences [q-bio], Molecular Sequence Data, medicine.disease_cause, Microbiology, commensalisme, Evolution, Molecular, 03 medical and health sciences, medicine, analyse par cluster, Allele, Molecular Biology, 030304 developmental biology, Genetics, 0303 health sciences, Base Sequence, biology, 030306 microbiology, Streptococcus, infection bactérienne, Genetic transfer, Meeting Presentations, streptococcus, Genomics, biology.organism_classification, 3. Good health, [SDV] Life Sciences [q-bio], stomatognathic diseases, Streptococcus salivarius, Streptococcus vestibularis, Horizontal gene transfer, Multilocus sequence typing, cavité buccale, streptococcus salivarius, transfert horizontal de gènes
Abstract

The phylogenetically closely related species Streptococcus salivarius and Streptococcus vestibularis are oral bacteria that are considered commensals, although they can also be found in human infections. The relationship between these two species and the relationship between strains isolated from carriers and strains responsible for invasive infections were investigated by multilocus sequence typing and additional sequence analysis. The clustering of several S. vestibularis alleles and the extent of genomic divergence at certain loci support the conclusion that S. salivarius and S. vestibularis are separate species. The level of sequence diversity in S. salivarius alleles is generally high, whereas that in S. vestibularis alleles is low at certain loci, indicating that the latter species might have evolved recently. Cluster analysis indicated that there has been genetic exchange between S. salivarius and S. vestibularis at three of the nine loci investigated. Horizontal gene transfer between streptococci belonging to the S. salivarius group and other oral streptococci was also detected at several loci. A high level of recombination in S. salivarius was revealed by allele index association and split decomposition sequence analyses. Commensal and infection-associated S. salivarius strains could not be distinguished by cluster analysis, suggesting that the pathogen isolates are opportunistic. Taken together, our results indicate that there is a high level of gene exchange that contributes to the evolution of two streptococcal species from the human oral cavity.

Published
2007

12. Perspectives: From the Lamto Experience to Critical Issues for Savanna Ecology Research

Author

Gignoux, Jacques, Le Roux, Xavier, Abbadie, Luc, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Biogéochimie et écologie des milieux continentaux (Bioemco), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Luc Abbadie (Editeur), Jacques Gignoux (Editeur), Xavier Le Roux (Editeur), Michel Lepage (Editeur), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), and Delorme, Christine

Subjects
[SDV.EE]Life Sciences [q-bio]/Ecology, environment, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BID]Life Sciences [q-bio]/Biodiversity, ComputingMilieux_MISCELLANEOUS, ECOLOGIE, [SDV.BID] Life Sciences [q-bio]/Biodiversity, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment
Abstract

International audience

Published
2006

13. Environmental constraints on living organisms

Author

Xavier Le Roux, Jacques Gignoux, Luc Abbadie, Michel Lepage, Université Pierre et Marie Curie - Paris 6 (UPMC), Institut de Recherche pour le Développement (IRD [Réunion]), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Luc Abbadie (Editeur), Jacques Gignoux (Editeur), Xavier Le Roux (Editeur), Michel Lepage (Editeur), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Delorme, Christine, ProdInra, Migration, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), and Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[ SDV.BID ] Life Sciences [q-bio]/Biodiversity, 0106 biological sciences, Limiting factor, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Herbivore, 010504 meteorology & atmospheric sciences, Soil nutrients, Ecology, [SDV]Life Sciences [q-bio], Fuel load, FEU, [SDV.BID]Life Sciences [q-bio]/Biodiversity, 15. Life on land, 010603 evolutionary biology, 01 natural sciences, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, Tropical savanna climate, [SDV] Life Sciences [q-bio], [SDV.EE] Life Sciences [q-bio]/Ecology, environment, Nutrient, parasitic diseases, Environmental science, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, [SDV.BID] Life Sciences [q-bio]/Biodiversity
Abstract

The high rainfall occurring in Lamto savannas directly reduces the role of water as a limiting factor. It also promotes fire as the key driving factor, especially for tree dynamics. As a result of both of these factors, nutrient losses are potentially high and thus the apparent soil nutrient poverty is reinforced. It is therefore not surprising that nutrients become a major limiting factor, both for grass production and for herbivore diversity. Lamto savannas could thus be qualified as oligotrophic savannas.

Published
2006

14. Modeling the Relationships between Vegetation Structure and Functioning, and Modeling Savanna Functioning from Plot to Region

Author

Le Roux , Xavier, Gignoux , Jacques, Simioni , Guillaume, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Biogéochimie et écologie des milieux continentaux (Bioemco), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Cooperative Research Centre, Luc Abbadie (Editeur), Jacques Gignoux (Editeur), Xavier Le Roux (Editeur), Michel Lepage (Editeur), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Delorme, Christine, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS )

Subjects
[ SDV.BID ] Life Sciences [q-bio]/Biodiversity, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, TECHNIQUE DE PREVISION, RELATION STRUCTURE-FONCTION, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BID]Life Sciences [q-bio]/Biodiversity, ComputingMilieux_MISCELLANEOUS, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, [SDV.BID] Life Sciences [q-bio]/Biodiversity
Abstract

International audience

Published
2006

15. Tree/Grass Interactions

Author

Le Roux, Xavier, Mordelet, Patrick, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Luc Abbadie (Editeur), Jacques Gignoux (Editeur), Xavier Le Roux (Editeur), Michel Lepage (Editeur), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), and Delorme, Christine

Subjects
[ SDV.BID ] Life Sciences [q-bio]/Biodiversity, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, DISPONIBILITE D'ELEMENT NUTRITIF, [SDV]Life Sciences [q-bio], RELATION SOL-PLANTE-EAU, [SDV.BID]Life Sciences [q-bio]/Biodiversity, [SDV.BID] Life Sciences [q-bio]/Biodiversity, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, RESSOURCE EN SOL
Abstract

E-mail Address : patrick.mordelet@cesbio.cnes.fr; International audience

Published
2006

16. A synthetic overview of Lamto Savanna ecology: Importance of structure-functioning-dynamics relationships

Author

Le Roux, Xavier, Abbadie, Luc, Gignoux, Jacques, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Biogéochimie et écologie des milieux continentaux (Bioemco), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Luc Abbadie (Editeur), Jacques Gignoux (Editeur), Xavier Le Roux (Editeur), Michel Lepage (Editeur), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Delorme, Christine, École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.EE]Life Sciences [q-bio]/Ecology, environment, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, RELATION STRUCTURE-FONCTION, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BID]Life Sciences [q-bio]/Biodiversity, ComputingMilieux_MISCELLANEOUS, ECOLOGIE, [SDV.BID] Life Sciences [q-bio]/Biodiversity, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment
Abstract

International audience

Published
2006

17. Soil-plant-atmosphere exchanges

Author

Le Roux, Xavier, Monteny, Bruno, ProdInra, Migration, Luc Abbadie (Editeur), Jacques Gignoux (Editeur), Xavier Le Roux (Editeur), Michel Lepage (Editeur), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Institut de Recherche pour le Développement (IRD), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), and Delorme, Christine

Subjects
[ SDV.BID ] Life Sciences [q-bio]/Biodiversity, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [SDV] Life Sciences [q-bio], [SDV.EE] Life Sciences [q-bio]/Ecology, environment, [SDV]Life Sciences [q-bio], [SDV.BID]Life Sciences [q-bio]/Biodiversity, RELATION SOL-PLANTE-ATMOSPHERE, [SDV.BID] Life Sciences [q-bio]/Biodiversity, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment
Published
2006

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