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16 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. 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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5. Insertion Sequences as Highly Resolutive Genomic Markers for Sequence Type 1 Legionella pneumophila Paris

Author

Dominique Schneider, Max Maurin, Sophie Jarraud, Jean Thioulouse, Elisabeth Kay, Mike Vergnes, Christophe Ginevra, Philippe Normand, Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence des Légionella, Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM), Immunité infection vaccination (I2V), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-IFR128-Institut National de la Santé et de la Recherche Médicale (INSERM), 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-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 quantitative et évolutive des communautés, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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), Laboratoire de Bacteriologie, BRON, Hospices Civils de Lyon (HCL), CHU Grenoble, Université Joseph Fourier - Grenoble 1 (UJF)-CHU Grenoble, French Centre National de la Recherche Scientifique, Bonus Qualité Recherche grant, University Joseph Fourier, Agence Française de Sécurité Sanitaire de l’Environnement et du Travail (AFSSET, grant EST-2007-1), French Ministry of Education and Research, Delorme, Christine, Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR128-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, 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), CNRS UMR 5163, Université Joseph Fourier - Grenoble 1 (UJF), 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), Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] ( LAPM ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Centre National de la Recherche Scientifique ( CNRS ), Université Joseph Fourier - Grenoble 1 ( UJF ), Université de Lyon-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Immunité infection vaccination ( I2V ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-IFR128-Institut National de la Santé et de la Recherche Médicale ( INSERM ), 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 de Biométrie et Biologie Evolutive ( LBBE ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Hospices Civils de Lyon ( HCL ), Université Joseph Fourier - Grenoble 1 ( UJF ) -CHU Grenoble, and Schneider, Dominique

Subjects
Microbiology (medical), Genotype, Legionella, colonisation, infection humaine, marqueur génomique, Legionella pneumophila, Microbiology, 03 medical and health sciences, eau, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Environmental Microbiology, medicine, Humans, Typing, Serotyping, Insertion sequence, 030304 developmental biology, Genetics, Molecular Epidemiology, 0303 health sciences, biology, 030306 microbiology, Genetic Variation, Bacteriology, biology.organism_classification, medicine.disease, DNA Fingerprinting, Bacterial Typing Techniques, Electrophoresis, Gel, Pulsed-Field, DNA profiling, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], DNA Transposable Elements, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Legionnaires' disease, Legionnaires' Disease, Restriction fragment length polymorphism, france, Polymorphism, Restriction Fragment Length
Abstract

The causative agent of legionellosis, Legionella pneumophila , colonizes all natural and human-made water networks, thus constituting the source of contaminated aerosols responsible for airborne human infections. Efficient control of infections, especially during epidemics, necessitates the fastest and most resolutive identification possible of the bacterial source for subsequent disinfection of reservoirs. We thus compared recognized typing approaches for Legionella with a method based on characterization of insertion sequence (IS) content. A total of 86 clinical or environmental isolates of L. pneumophila , including 84 Paris isolates, sampled from 25 clinical investigations in France between 2001 and 2007, were obtained from the Legionella National Reference Center. All strains were typed by monoclonal antibody subgrouping, sequence-based typing, pulsed-field gel electrophoresis, and restriction fragment length polymorphism based on the presence or absence of IS elements. We identified six different types of IS elements in L. pneumophila Paris and used them as genomic markers in hybridization experiments. One IS type, IS Lpn11 , revealed a high discriminatory power. Simpson's index of discrimination, calculated from the distribution of IS elements, was higher than that obtained with the other typing methods used for L. pneumophila Paris. Moreover, specific IS Lpn11 copies were found only in strains isolated from particular cities. In more than half of the cases, each clinical isolate had an IS Lpn11 profile that was recovered in at least one environmental isolate from the same geographical location, suggesting that our method could identify the infection source. Phylogenetic analysis suggests a clonal expansion for the L. pneumophila Paris strain.

Published
2011

6. 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

7. 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

8. The effect of hydroxylamine on the activity and aggregate structure of autotrophic nitrifying bioreactor cultures

Author

Willie F. Harper, Mustafa Mazher, Xavier Le Roux, Franck Poly, Ken Kristensen, Akihiko Terada, Barth F. Smets, Civil and Environmental Engineering Department [Pittsburgh] (PITT), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), Department of Bioengineering, Department of Environmental Engineering, Technical University of Denmark [Lyngby] (DTU), 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-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), Department of Biological Sciences [Auburn], Auburn University (AU), Department of Civil and Environmental Engineering [Pittsburgh], 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), University of Pittsburgh, Technical University of Denmark [Lyngby] ( DTU ), 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 ), Auburn University, and Delorme, Christine

Subjects
Nitrite Reductases, Cell Culture Techniques, Biomass, Bioengineering, ammonia oxidizers, Hydroxylamine, 010501 environmental sciences, 01 natural sciences, Applied Microbiology and Biotechnology, Polymerase Chain Reaction, Microbiology, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, microcolony, 03 medical and health sciences, chemistry.chemical_compound, Bioreactors, Microbial ecology, Ammonia, aggregate size, Bioreactor, Food science, Autotroph, Nitrosomonas, In Situ Hybridization, Fluorescence, 0105 earth and related environmental sciences, Trophic level, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Autotrophic Processes, biology, Bacteria, 030306 microbiology, Gene Expression Regulation, Bacterial, nitrite oxidizers, biology.organism_classification, nitrification, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, chemistry, Nitrifying bacteria, Nitrification, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Oxidoreductases, Biotechnology
Abstract

Addition of hydroxylamine (NH2OH) to auto- trophic biomass in nitrifying bioreactors affected the activ- ity, physical structure, and microbial ecology of nitrifying aggregates. When NH2OH is added to nitrifying cultures in 6-h batch experiments, the initial NH3-N uptake rates were physiologically accelerated by a factor of 1.4-13. NH2OH addition caused a 20-40% decrease in the median aggregate size, broadened the shape of the aggregate size distribution by up to 230%, and caused some of the microcolonies to appear slightly more dispersed. Longer term NH2OH addi- tion in fed batch bioreactors decreased the median aggregate size, broadened the aggregate size distribution, and decreased NH3-N removal from >90% to values ranging between 75% and 17%. This altered performance is explained by quantitative fluorescence in situ hybridization (FISH) results that show inhibition of nitrifying popula- tions, and by qPCR results showing that the copy numbers of amoA and nxrA genes gradually decreased by up to an order- of-magnitude. Longer term NH2OH addition damaged the active biomass. This research clarifies the effect of NH2OH on nitrification and demonstrates the need to incorporate NH2OH-related dynamics of the nitrifying biomass into mathematical models, accounting for both ecophysiological and structural responses. Biotechnol. Bioeng. 2009;102: 714-724.

Published
2008

9. How do grassland management history and bacterial micro-localisation affect the response of bacterial community structure to changes in aboveground grazing regime?

Author

Valérie Degrange, Jean-François Soussana, Agnès Richaume, Eléonore Attard, X. Le Roux, Katja Klumpp, 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), UR 0874 Unité de recherche sur l'Ecosystème Prairial, Institut National de la Recherche Agronomique (INRA)-Unité de recherche sur l'Ecosystème Prairial (UREP)-Ecologie des Forêts, Prairies et milieux Aquatiques (EFPA), Institut National de la Recherche Agronomique (INRA), 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), Domaine expérimental de Crouël (CL CROUELLE UE), 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), Unité de recherche d'Agronomie (UA), 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 ), Unité de recherche d'Agronomie ( UA ), Institut National de la Recherche Agronomique ( INRA ), and Delorme, Christine

Subjects
Ribosomal intergenic spacer analysis, Ribosomal Intergenic Spacer analysis, animal diseases, Soil Science, Context (language use), [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Microbiology, Grassland, Prairie, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, 03 medical and health sciences, Grazing, parasitic diseases, Microbial community, FRACTIONNEMENT DES SOLS, Herbivory, skin and connective tissue diseases, 2. Zero hunger, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, geography, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, geography.geographical_feature_category, Macropore, 030306 microbiology, Ecology, Soil fractionation, Community structure, DIVERISTE BACTERIENNE, 04 agricultural and veterinary sciences, Soil carbon, 15. Life on land, 6. Clean water, Plant species composition, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, Agronomy, Bacterial diversity, Soil water, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, sense organs, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BID] Life Sciences [q-bio]/Biodiversity
Abstract

International audience; In a context of frequent intensification or de-intensification of management in grasslands, a better understanding of how quickly soil microbiota responds to changes in management is required. The kinetics of changes in the structure of the bacterial community (using ribosomal intergenic spacer analysis) was studied in grassland mesocosms after changes of aboveground grazing regime, taking into account bacteria micro-localisation by separating the bacteria located inside stable aggregates (inner soil fraction) and the bacteria easily washed out, i.e. mainly located in macropores (outer soil fraction). Four treatments were used: (i) control grazed mesocosms, (ii) control ungrazed mesocosms, (iii) application of grazing on previously ungrazed mesocosms, (iv) cessation of grazing on previously grazed mesocosms. Each grazing event was simulated by application of synthetic sheep urine and plant clipping. Application of grazing led to a change in the structure of the whole soil bacterial community within 5 months, whereas changes were observed only 12 months after cessation of grazing. Changes in plant species composition and soil organic carbon content observed after cessation of grazing were found to be possible drivers of the changes in the bacterial community structure. However, after application of grazing, changes of the bacterial community structure occurred prior to changes in plant species composition and soil organic carbon content, suggesting that supply of urine and/or impact of labile carbon were likely the main drivers of changes. After 12 months, the application of grazing significantly affected the bacterial community structure in both inner and outer soil fractions. Conversely, 12 months after cessation of grazing, community structure was affected only for bacteria located in the outer fraction. This study shows that the bacterial community structure responded faster and more deeply after application than after cessation of grazing, and may be driven by different environmental factors between both scenarios. This study also shows that, 2 years after the changes in grazing regime, the bacterial community structure was determined by both the past and new grazing regimes.

Published
2008

10. 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

11. Phase Variation and Genomic Architecture Changes in Azospirillum

Author

René Bally, Patrick Mavingui, Yvan Moënne-Loccoz, Jacqueline Haurat, Florence Wisniewski-Dyé, Céline Lavire, Ludovic Vial, Didier Blaha, 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), 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
DNA, Bacterial, phenotypic switch, Molecular Sequence Data, PFGE, plasmid pattern, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Microbiology, genome plasticity, Plant Roots, 03 medical and health sciences, Plant Microbiology, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, Genetic variation, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Molecular Biology, Soil Microbiology, 030304 developmental biology, 2. Zero hunger, Genetics, Phase variation, Gene Rearrangement, 0303 health sciences, Rhizosphere, Ralstonia solanacearum, biology, Base Sequence, 030306 microbiology, Genetic Variation, Oryza, Gene rearrangement, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Electrophoresis, Gel, Pulsed-Field, Rec A Recombinases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Azospirillum lipoferum, Replicon, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Azospirillum, Soil microbiology, Bacteria, Genome, Bacterial, Plasmids
Abstract

Azospirillum is a plant growth-promoting rhizobacterium associated with roots of monocots, including important crops, such as wheat, corn, and rice. Both in greenhouse and in field trials, Azospirillum was shown to exert beneficial effects on plant growth and crop yields, under various soil and climatic conditions (15). The actual benefit from biological nitrogen fixation has been questioned, and plant growth promotion by Azospirillum seems to be due mainly to production of phytohormones (9, 15). The most abundant phytohormone produced is indole-3-acetic acid, allowing an increase in the number of lateral roots and root hairs; this results in a higher absorption of water and minerals from the soil (9). Bacterial populations, especially in soil or in the rhizosphere, have to endure fluctuating environmental conditions. Bacteria have evolved different strategies to adapt to these environments. Phase variation is one adaptive process by which bacteria undergo frequent, usually reversible phenotypic changes resulting from genetic or epigenetic alterations at specific genetic loci (29). This process is used by several bacterial species to generate intrapopulation diversity that increases bacterial fitness and is important in niche adaptation or to escape host defenses (reviewed in references 46 and 55). In contrast to spontaneous mutations, which occur at a frequency of approximately 10−8 to 10−6 mutations per growing cell per generation, phase variation occurs at frequencies higher than 10−5 switches per cell per generation (29). Various mechanisms control phase variation. These include DNA inversion or duplication, deletion, transposition, homologous recombination, slipped-strand mispairing, and differential methylation (reviewed in reference 55). Phase variation in pathogenic bacteria—for example, switching of type IV pili in Neisseria gonorrhoeae (27), differential expression of surface layer proteins in Campylobacter fetus (16), and loss of virulence in the phytopathogen Ralstonia solanacearum (43)—has been extensively studied. However, phase variation is not restricted to pathogenic bacteria. Indeed, it also occurs during rhizosphere colonization of various plants by several strains of beneficial plant-associated Pseudomonas (1, 48). For instance, the regulation of biocontrol traits (production of antifungal metabolites, chitinases, and biosurfactants) by phase variation was reported for Pseudomonas spp. strains (54). Azospirillum lipoferum 4B, a strain isolated from a rice rhizosphere, generates in vitro at high frequencies (10−4 to 10−3 per cell per generation) a stable phase variant named 4VI (3, 30). Variant colonies are readily distinguishable from wild-type colonies by the differential absorption of dyes incorporated into the growth medium. The 4VI variant exhibits pleiotropic modifications; it gained assimilation of certain sugars but lost the ability to assimilate other sugars (3), to reduce triphenyl tetrazolium chloride, to bind some dyes, to swim (4), and to reduce nitrous oxide (our unpublished results). A. lipoferum 4T, a nonswimming strain displaying all of the features of the 4VI variant, and strain A. lipoferum 4B have been isolated simultaneously from rice rhizosphere at the same frequency (8). A. lipoferum 4T retains the ability to efficiently colonize rice roots (2). Like 4VI, A. lipoferum 4T was found to be genetically very close to A. lipoferum 4B (3, 8, 28), suggesting that A. lipoferum 4T could in fact be a 4VI variant of strain 4B generated within the soil ecosystem. We recently showed that inactivating recA in strain 4B resulted in a higher frequency of generation of variants (57), contrasting with many studies of other bacteria showing either no effect or the abolition of phase variation process in recA mutants. This finding suggests the possibility that phase variation is accompanied by genetic rearrangements. As of now, the molecular mechanism underlying these nonreversible changes in A. lipoferum 4B remains to be determined. In this study, the objective was to determine whether genomic rearrangements take place during phase variation of strain 4B and related Azospirillum strains. The current work shows that genomic rearrangements are concomitant with phase variation in three species of Azospirillum.

Published
2006

12. Distribution and genetic diversity of bacterial thiopurine methyltransferases in soils emitting dimethyl selenide

Author

Sylvie Nazaret, Benoit Cournoyer, Lionel Ranjard, L. Champier, Sabine Adelaide Eugenie Favre-Bonte, 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-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), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Microbiologie, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), 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, 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
Molecular Sequence Data, thiopurine methyltransferase, Biology, tpm gene, Biochemistry, Polymerase Chain Reaction, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, soil, 03 medical and health sciences, chemistry.chemical_compound, Pseudomonas fragi, Organoselenium Compounds, Gene family, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, bacteria, selenium, Gene, Phylogeny, Soil Microbiology, 030304 developmental biology, 2. Zero hunger, Genetics, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Genetic diversity, Selenocysteine, Phylogenetic tree, Base Sequence, Pseudomonas, Genetic Variation, 04 agricultural and veterinary sciences, General Medicine, Methylation, Methyltransferases, 15. Life on land, biology.organism_classification, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, chemistry, 13. Climate action, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, France, methylation, GENETIQUE DES POPULATIONS
Abstract

International audience; Dimethyl selenide (DMSe) and dimethyl diselenide (DMDSe) emissions by soil samples spiked with selenite or (methyl)selenocysteine, with or without a supplement of nutrient broth and glucose were measured. DMSe was the main form of volatile Se produced, and was observed for both Se-substrates. DMDSe was only emitted from soils spiked with (methyl)selenocysteine. Two bacterial thiopurine methyltransferases (TPMTs), TPMT-I and TPMT-E, have been reported to be involved in DMSe and DMDSe emissions [J. Bacteriol. 184 (2002) 3146; Appl. Environ. Microbiol. 69 (2003) 3784]. To establish if these TPMTs or other members of their gene family could have contributed to the DMSe emissions observed, the diversity of bTPMT gene (tpm) sequences among the soils of this study was investigated. Total DNAs from these soils were extracted and screened using the tpm PTCF2–PTCR2 consensus primers defined to PCR amplify this gene family. The PCR products obtained from two soils were cloned, analysed by PCR-RFLP, and sequenced. Their analysis showed an important diversity of tpm lineages (around 12) in soils. Phylogenetic analysis of the deduced TPMT sequences of these soils revealed lineages not previously recorded in the databases, sequences closely related or identical to freshwater TPMTs, or sequences encoding TPMTs closely related to those of Pseudomonas fragi TPMT-K, Pseudomonas Hsa.28 TPMT-I, or Colwellia psychrerythraea TPMT-Z. Nested PCRs, allowing detection of about 13 distinct tpm soil and freshwater lineages by PTCF2–PTCR2 PCR screenings, were performed on the soil total DNAs. These PCRs confirmed the sequencing data, and allowed to recover lineages not detected by the cloning strategy. These results indicate that soils, like the freshwater samples, harbour TPMT-I gene sequences but may also have distinct tpm lineages. This study further supports our hypothesis that TPMTs contribute to DMSe soil emissions.

Published
2006

13. Improved yield of micropropagated sugarcane following inoculation by endophytic Burkholderia vietnamiensis

Author

Munusamy Govindarajan, Jacques Balandreau, C. Lakshminarasimhan, G. Revathi, Ramachandran Muthukumarasamy, Delorme, Christine, Main Biocontrol Research Laboratory, Main Biocontrol Research laboratory, 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), PR Group of Institutions, 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), 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
Herbaspirillum, Soil Science, Plant Science, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Herbaspirillum seropedicae, Endophyte, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Saccharum officinarum, Botany, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, [SDV.EE.ECO] Life Sciences [q-bio]/Ecology, environment/Ecosystems, 2. Zero hunger, 0303 health sciences, biology, 030306 microbiology, Inoculation, 04 agricultural and veterinary sciences, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [ SDV.EE.ECO ] Life Sciences [q-bio]/Ecology, environment/Ecosystems, Horticulture, Burkholderia, Burkholderia vietnamiensis, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Gluconacetobacter, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

During a survey of nitrogen-fixing Burkholderia associated with sugarcane in Tamil Nadu, some endophytes were isolated on PCAT medium. Isolation was based on the use of the selective PCAT medium. Four isolates were studied, all belonging to the genus Burkholderia. One of them, MG43 was consistently more active in reducing acetylene and was identified as Burkholderia vietnamiensis. This isolate was used to inoculate micro-propagated sugarcane plantlets in a comparison with two other diazoptrophs, viz. Gluconacetobacter diazotrophicusT and Herbaspirillum seropedicaeT. Inoculated plants and uninoculated controls were used in a pot experiment followed by two field experiments under different rates of nitrogen fertilisers. MG43 and G. diazotrophicus performed best in sugarcane, their natural host. Biomass increase due to MG43 inoculation reached 20% in the field. Inoculated plants were heavily colonised by the inoculated bacterium (up to 115,000 CFU g−1 root fresh weight). Inoculation by a combinaison of the three strains performed less well than inoculation by a single MG43 suspension. Ecological implications are discussed, as well as the potential of these bacteria to provide a feasible alternative to higher N fertilisers rates in a low input and long term sustainable rural economy.

Published
2006

14. Geodermatophilaceae fam. nov., a formal description

Author

Philippe Normand, 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), Delorme, Christine, 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), 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
Zoology, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Microbiology, DNA, Ribosomal, Genus Modestobacter, 03 medical and health sciences, Species Specificity, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, RNA, Ribosomal, 16S, Actinomycetales, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Ecology, Evolution, Behavior and Systematics, Geodermatophilaceae, Formal description, Phylogeny, 030304 developmental biology, 0303 health sciences, Blastococcus, biology, 030306 microbiology, Dermatophilaceae, Type genus, Genes, rRNA, General Medicine, Sequence Analysis, DNA, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Genealogy, Bacterial Typing Techniques, Geodermatophilus, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Taxonomy (biology), [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

The family name ‘Geodermatophilaceae’ was first published by Normand et al. (1996) to contain the genera Geodermatophilus and Blastococcus, but a formal description and the designation of the type genus were not included, thus making the name invalid. Since then, the genus Modestobacter has been described as a member of the family ‘Geodermatophilaceae’ by Mevs et al. (2000) . We hereby formally describe the family ‘Geodermatophilaceae’ which includes the recently described genus Modestobacter. The type genus of the family is Geodermatophilus.

Published
2006

15. Effect of Azospirillum brasilense inoculation on rhizobacterial communities analyzed by denaturing gradient gel electrophoresis and automated ribosomal intergenic spacer analysis

Author

Sylvie Nazaret, Edouard Jurkevitch, Yoav Herschkovitz, Yaacov Okon, Anat Lerner, Yvan Moënne-Loccoz, Ezékiel Baudoin, Department of Plant Pathology and Microbiology ant the Otto Warburg Minerva Center of Agricultural Biotechnology, The Hebrew University of Jerusalem (HUJ)-Faculty of Agricultural Food and Environmental Quality Sciences, 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), Delorme, Christine, 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), The Hebrew University of Jerusalem ( HUJ ) -Faculty of Agricultural Food and Environmental Quality Sciences, 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
Ribosomal Intergenic Spacer analysis, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Soil Science, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Rhizobacteria, Microbiology, 03 medical and health sciences, Intergenic region, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [ SDV.SA.AGRO ] Life Sciences [q-bio]/Agricultural sciences/Agronomy, Botany, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, [SDV.EE.ECO] Life Sciences [q-bio]/Ecology, environment/Ecosystems, 030304 developmental biology, 2. Zero hunger, [SDV.SA.AGRO] Life Sciences [q-bio]/Agricultural sciences/Agronomy, 0303 health sciences, Rhizosphere, biology, 030306 microbiology, fungi, food and beverages, Spacer DNA, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, 15. Life on land, Azospirillum brasilense, biology.organism_classification, 16S ribosomal RNA, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [ SDV.EE.ECO ] Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Temperature gradient gel electrophoresis, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Nucleic acid-based techniques allow the exploration of microbial communities in the environments such as the rhizosphere. Azospirillum brasilense, a plant growth promoting rhizobacterium (PGPR), causes morphological changes in the plant root system. These changes in root physiology may indirectly affect the microbial diversity of the rhizosphere. In this study, the changes in the rhizobacterial structure following A. brasilense inoculation of maize (Zea mays) plants was examined by PCR-denaturating gradient gel electrophoresis (DGGE) and automated ribosomal intergenic spacer analysis (ARISA), using two universal primers sets for the 16S rRNA gene, and an intergenic 16S–23S rDNA primer set, respectively. Similar results were obtained when using either ARISA or DGGE performed with these different primer sets, and analyzed by different statistical methods: no prominent effect of A. brasilense inoculation was observed on the bacterial communities of plant roots grown in two different soils and in different growth systems. In contrast, plant age caused significant shifts in the bacterial populations. q 2005 Elsevier Ltd. All rights reserved.

Published
2006

16. Horizontal gene transfer by natural transformation in soil environment

Author

Elisabeth Kay, Anne Mercier, Pascal Simonet, 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 ), P. Nannipieri, K. Smalla, 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-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), and Delorme, Christine

Subjects
0303 health sciences, Ralstonia solanacearum, biology, 030306 microbiology, biology.organism_classification, Natural (archaeology), 03 medical and health sciences, Transformation (genetics), [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Horizontal gene transfer, Botany, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Acinetobacter calcoaceticus, 030304 developmental biology

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