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2. Transfer of the Integrative and Conjugative Element ICE St3 of Streptococcus thermophilus in Physiological Conditions Mimicking the Human Digestive Ecosystem

Author

Herviou, Pauline, primary, Balvay, Aurélie, additional, Bellet, Deborah, additional, Bobet, Sophie, additional, Maudet, Claire, additional, Staub, Johan, additional, Alric, Monique, additional, Leblond-Bourget, Nathalie, additional, Delorme, Christine, additional, Rabot, Sylvie, additional, Denis, Sylvain, additional, and Payot, Sophie, additional

Published
2023
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5. Evidence of gene transfer via Integrative and Conjugative Elements (ICEs) between bacteria in the human small intestine environment using the dynamic in vitro system TIM-1

Author

Denis, Sylvain, Herviou, Pauline, Staub, Johan, Mazal, Carine, Delorme, Christine, Rabot, Sylvie, Leblond-Bourget, Nathalie, Payot, Sophie, Microbiologie Environnement Digestif Santé (MEDIS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Dynamique des Génomes et Adaptation Microbienne (DynAMic), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology
Abstract

Session 3: New approaches to study the gut microbiome ; Communication P 100; International audience; Consumption of food brings large amounts of various bacteria able to interact and exchange genes with the host ones. Gene acquisition can confer novel properties to bacteria (antibiotic resistance, catabolic properties…) which may threat the equilibrium of digestive microbiota or lead to the emergence of new pathogens.Conjugation is the main mechanism of gene acquisition. Gene transfer can occur between strains belonging to the same species but also between very distantly related bacteria. Several classes of mobile genetic elements can be transferred by conjugation, in particular chromosomal elements called Integrative and Conjugative Elements (ICEs), a widespread but poorly known class of elements.To give a first insight on the incidence of gene transfers mediated by ICEs in the human digestive ecosystem, we evaluated their occurrence between dietary and intestinal commensal bacteria during digestion, using the TIM-1 model able to mimic gastric and small intestine environment. Different pairs of ICE donors (Streptococcus thermophilus, S. salivarius) and receptors (S. thermophilus, S. salivarius, Enterococcus faecalis) were immobilized on alginate/agar/chitosan beads and maintained in the jejunum and the ileum of the TIM-1 during milk digestion. Generation of transconjugants (receptors integrating ICE) was evaluated after an exposure of 5h to those conditions, and compared to exposure to undigested milk and M17 broth.Among the 11 pairs tested, 4 gave transconjugants during in vitro digestion whereas all generated conjugates in milk and/or M17. Remarkably, two pairs involved transfer between different genera (S. thermophilus x E. faecalis), whereas the other two involved the same species (S. thermophilus x S. thermophilus). Our study highlights that gene acquisition via transfer of ICEs should occur relatively frequently in the human digestive environment. Moreover, the use of dynamic in vitro models such as the TIM-1 gives a good alternative to in vivo study, to explore such phenomenon easily without ethical constraints.

Published
2021

7. Extent of horizontal gene transfer in evolution of streptococci of the salivarius group

Author

Delorme, Christine, Poyart, Claire, Ehrlich, S. Dusko, and Renault, Pierre

Subjects
Genetic research -- Analysis, Genetic transformation -- Research, Streptococcus -- Genetic aspects, Streptococcus -- Research, Biological sciences
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

8. Control of EpsE, the phosphoglycosyltransferase initiating exopolysaccharide synthesis in Streptococcus thermophilus, by EpsD tyrosine kinase

Author

Minic, Zoran, Marie, Corinne, Delorme, Christine, Faurie, Jean-Michel, Mercier, Gerald, Ehrlich, Dusko, and Renault, Pierre

Subjects
Protein tyrosine kinase -- Research, Phosphotransferases -- Research, Streptococcus -- Genetic aspects, Streptococcus -- Research, Biological sciences
Abstract

We studied the roles of Streptococcus thermophilus phosphogalaetosyltransferase (EpsE) (the priming enzyme), tyrosine kinase (EpsD), phosphatase (EpsB), and a membrane-associated protein with no known biochemical function (EpsC) in exopolysaccharide (EPS) synthesis. These proteins are well-conserved among bacteria and are usually encoded by clustered genes. Exopolysaccharide synthesis took place in the wild-type strain and a mutant lacking EpsB but not in mutants lacking EpsC, EpsD, or EpsE. The three mutants unable to synthesize EPS lacked the EpsE phosphogalactosyltransferase activity, while the two EPS-synthesizing strains possessed this activity, showing that EpsC and EpsD are required for EpsE function. An EpsD phosphorylated form was found in all strains except the epsC mutant, indicating that EpsC is necessary for EpsD phosphorylation. Moreover, the phosphorylated form of EpsD, a supposedly cytoplasmic protein, was found to be associated with the plasma membrane, possibly due to interaction with EpsC. Finally, the EpsD and EpsE elution profiles in a gel filtration chromatography assay were similar, suggesting that these two proteins colocalize in the membrane. Mutation of Tyr200, predicted to be a phosphorylation site and present in a conserved motif in bacterial phosphoglycosyltransferases, led to EpsE inactivation. In contrast, mutation of Tyr162 or Tyr199 had no effect. Taken together, these data show that EpsD controls EpsE activity. Possible mechanisms for this control are discussed.

Published
2007

9. 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, Bork, Peer, Wang, Jun, Ehrlich, Dusko S., Pedersen, Oluf, 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, and Yamada, Takuji

Published
2013
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10. Transcriptional pattern of genes coding for the proteolytic system of Lactococcus lactis and evidence for coordinated regulation of key enzymes by peptide supply

Author

Guedon, Eric, Renault, Pierre, Ehrlich, S. Dusko, and Delorme, Christine

Subjects
Lactococcus -- Genetic aspects, Genetic transcription -- Regulation, Proteases -- Genetic aspects, Enzymes -- Synthesis, Biological sciences
Abstract

Results show that the proteolytic system of Lactococcus lactis consists of 16 genes whose transcription is regulated by the peptide availability. Data further reveal that of the 15 promoters involved, transcription of eight promoters is dependent on the peptide content in the medium and that of pepP by carbon source.

Published
2001

11. Enterotypes of the human gut microbiome

Author

Arumugam, Manimozhiyan, Raes, Jeroen, Pelletier, Eric, Le Paslier, Denis, Yamada, Takuji, Mende, Daniel R., Fernandes, Gabriel R., Tap, Julien, Bruls, Thomas, Batto, Jean-Michel, Bertalan, Marcelo, Borruel, Natalia, Casellas, Francesc, Fernandez, Leyden, Gautier, Laurent, Hansen, Torben, Hattori, Masahira, Hayashi, Tetsuya, Kleerebezem, Michiel, Kurokawa, Ken, Leclerc, Marion, Levenez, Florence, Manichanh, Chaysavanh, Nielsen, Bjørn H., Nielsen, Trine, Pons, Nicolas, Poulain, Julie, Qin, Junjie, Sicheritz-Ponten, Thomas, Tims, Sebastian, Torrents, David, Ugarte, Edgardo, Zoetendal, Erwin G., Wang, Jun, Guarner, Francisco, Pedersen, Oluf, de Vos, Willem M., Brunak, Søren, Doré, Joel, Antolín, María, Artiguenave, François, Blottiere, Hervé M., Almeida, Mathieu, Brechot, Christian, Cara, Carlos, Chervaux, Christian, Cultrone, Antonella, Delorme, Christine, Denariaz, Gérard, Dervyn, Rozenn, Foerstner, Konrad U., Friss, Carsten, van de Guchte, Maarten, Guedon, Eric, Haimet, Florence, Huber, Wolfgang, van Hylckama-Vlieg, Johan, Jamet, Alexandre, Juste, Catherine, Kaci, Ghalia, Knol, Jan, Lakhdari, Omar, Layec, Severine, Le Roux, Karine, Maguin, Emmanuelle, Mérieux, Alexandre, Melo Minardi, Raquel, Mʼrini, Christine, Muller, Jean, Oozeer, Raish, Parkhill, Julian, Renault, Pierre, Rescigno, Maria, Sanchez, Nicolas, Sunagawa, Shinichi, Torrejon, Antonio, Turner, Keith, Vandemeulebrouck, Gaetana, Varela, Encarna, Winogradsky, Yohanan, Zeller, Georg, Weissenbach, Jean, Ehrlich, S. Dusko, and Bork, Peer

Published
2011
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12. A human gut microbial gene catalogue established by metagenomic sequencing

Author

Qin, Junjie, Li, Ruiqiang, Raes, Jeroen, Arumugam, Manimozhiyan, Burgdorf, Kristoffer Solvsten, Manichanh, Chaysavanh, Nielsen, Trine, Pons, Nicolas, Levenez, Florence, Yamada, Takuji, Mende, Daniel R., Li, Junhua, Xu, Junming, Li, Shaochuan, Li, Dongfang, Cao, Jianjun, Wang, Bo, Liang, Huiqing, Zheng, Huisong, Xie, Yinlong, Tap, Julien, Lepage, Patricia, Bertalan, Marcelo, Batto, Jean-Michel, Hansen, Torben, Le Paslier, Denis, Linneberg, Allan, Nielsen, Bjørn H., Pelletier, Eric, Renault, Pierre, Sicheritz-Ponten, Thomas, Turner, Keith, Zhu, Hongmei, Yu, Chang, Li, Shengting, Jian, Min, Zhou, Yan, Li, Yingrui, Zhang, Xiuqing, Li, Songgang, Qin, Nan, Yang, Huanming, Wang, Jian, Brunak, Søren, Doré, Joel, Guarner, Francisco, Kristiansen, Karsten, Pedersen, Oluf, Parkhill, Julian, Weissenbach, Jean, Antolin, Maria, Artiguenave, François, Blottiere, Hervé, Borruel, Natalia, Bruls, Thomas, Casellas, Francesc, Chervaux, Christian, Cultrone, Antonella, Delorme, Christine, Denariaz, Gérard, Dervyn, Rozenn, Forte, Miguel, Friss, Carsten, van de Guchte, Maarten, Guedon, Eric, Haimet, Florence, Jamet, Alexandre, Juste, Catherine, Kaci, Ghalia, Kleerebezem, Michiel, Knol, Jan, Kristensen, Michel, Layec, Severine, Le Roux, Karine, Leclerc, Marion, Maguin, Emmanuelle, Minardi, Raquel Melo, Oozeer, Raish, Rescigno, Maria, Sanchez, Nicolas, Tims, Sebastian, Torrejon, Toni, Varela, Encarna, de Vos, Willem, Winogradsky, Yohanan, Zoetendal, Erwin, Bork, Peer, Ehrlich, Dusko S., and Wang, Jun

Published
2010
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15. Gene inactivation in Lactococcus lactis: histidine biosynthesis

Author

Delorme, Christine, Godon, Jean-Jacques, Ehrlich, S. Dusko, and Renault, Pierre

Subjects
Histidine -- Influence, Bacteria -- Growth, Biological sciences
Abstract

Inactivation in histidine (his) genes (his CGDBH) of Lactococcus lactis IL1403 of E. coli mutants takes place through mutations of type frameshift and nonsense and is caused by the non-occurrence of transcription. IL1403 his operon can be inactivated from three different angles related to repression, promoter inactivation or transcript processing and structural gene inactivation, due to the presence of histidine. This results in the inhibition of branched-chain amino acid (BCAA) synthesis and impairment of other amino acids. The histidine operon contains server histidine biosynthetic genes (his A to his G) and three unrelated open reading frames (ORFs), among which three genes his A, his B and his G are found to be inactive. Adaptation to milk by lactococcus strains results in histidine auxotrophy.

Published
1993

16. Gene inactivation in Lactococcus lactis: branched-chain amino acid biosynthesis

Author

Godon, Jean-Jacques, Delorme, Christine, Bardowski, Jacek, Chopin, Marie-Christine, Ehrlich, S. Dusko, and Renault, Pierre

Subjects
Branched chain amino acids -- Research, Bacteria -- Genetic aspects, Biological sciences
Abstract

Mutations in the leu genes adversely affect the amino acid biosynthesis in Lactococcus lactis at the molecular level. L. lactis dairy fermentation strains, when introduced in milk, ultilize lactose through a phosphotransferase system and cause the degradation of casein. he strains are incapacitated to synthesize branched-chain amino acids (BCAA) and histidine. Leu operon and his operon of the strain L. lactis evolve at different rates.

Published
1993

18. Histidine biosynthesis genes in Lactococcus lactis subsp. lactis

Author

Delorme, Christine, Ehrlich, S. Dusko, and Renault, Pierre

Subjects
Histidine -- Genetic aspects, Microbiological synthesis -- Research, Lactic acid -- Physiological aspects, Biological sciences
Abstract

The organization of a cluster of genes involved in histidine biosynthesis in Lactococcus lactis subsp. lactis NCDO2118 was reported. Complementation studies in Bacillus subtilis and Escherichia coli indicated that eight genes (hisA, hisB, hisC, hisD, hisF, hisG, hisIE and hisH) are present within an 11-kb region. Moreover, two other genes specify proteins homologous to the 3'-aminoglycoside phosphotransferases annd histidyl-tRNA synthetases, but do not possess the corresponding functions.

Published
1992

19. 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

21. Identification of New Factors Modulating Adhesion Abilities of the Pioneer Commensal Bacterium Streptococcus salivarius

Author

Couvigny, Benoit, primary, Kulakauskas, Saulius, additional, Pons, Nicolas, additional, Quinquis, Benoit, additional, Abraham, Anne-Laure, additional, Meylheuc, Thierry, additional, Delorme, Christine, additional, Renault, Pierre, additional, Briandet, Romain, additional, Lapaque, Nicolas, additional, and Guédon, Eric, additional

Published
2018
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23. Emergence of a cell wall protease in the Streptococcus thermophilus population

Author

Delorme, Christine, Bartholini, Claire, Bolotine, Alexander, Ehrlich, S. Dusko, and Renault, Pierre

Subjects
Evolution -- Research, Genomics -- Research, Proteases -- Research, Streptococcus -- Genetic aspects, Streptococcus -- Physiological aspects, Biological sciences
Abstract

A multilocus sequence typing approach has showed that Streptococcus thermophilus has diverged from its potential ancestors of the salivarius group and has displayed a low level of allelic variability, confirming its emergence. The studies have supported an evolutionary scheme of Streptococcus thermophilus where gene acquisition and selection by food producers are determining factors.

Published
2010

24. [i]Streptococcus thermophilus[/i] strains reduce expression of NF-κB in human intestinal epithelial cells

Author

Chuat, Victoria, Bobet, Sophie, Lapaque, Nicolas, Blottiere, Herve, Lortal, Sylvie, Valence-Bertel, Florence, Delorme, Christine, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, inflammation, HT-29, intestin, anti-inflammatoire, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Streptococcus thermophilus, immuno-modulation, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, NF-κB
Abstract

The increase of inflammatory bowel diseases (IBD) is a major health concern in western countries. 11 Some commensal or ingested bacteria, such as some species of Lactobacillus and Bifidobacterium, are 12 known to reduce gut inflammation. In this context, species from the salivarius group have been shown 13 to reduce the immune response by inhibiting the inflammatory pathways. 14The salivarius group harbours three species: Streptococcus salivarius, Streptococcus thermophilus and 15 Streptococcus vestibularis. S. salivarius, one of the earliest colonizers of the oral cavity and digestive 16 tract, exhibits in vitro and in vivo anti-inflammatory effects. We have demonstrated that S. salivarius 17 strains can significantly reduce the IL-8 secretion and the activation of the NF-κB pathway in several 18 intestinal epithelial cells (1). NF-kB is a transcriptional factor playing a central role in human 19 inflammatory response, and especially in IBD. Immuno-modulation properties are linked to active 20 compounds released during the growth of S. salivarius. This anti-inflammatory potential was 21 confirmed by an inhibition of inflammation in mouse models of colitis (2). 22In this work, we investigated the immuno-modulatory effects of S. thermophilus, another species of 23 the salivarius group. This species is widely used in dairy production. Some studies have already 24 described positive effects of commercial S. thermophilus strains on inflammatory response. We 25 analyzed the effect of commercial strains and strains isolated from traditional dairy products on the 26 NF-κB expression in human cells. Immuno-modulation properties of cell free supernatants and live 27 S. thermophilus strains were assessed on TNFα-induced NF-κB activation in HT-29 cells. The step of 28 the NF-κB pathway modulated by S. thermophilus strains in the HT-29 cell model was analyzed by 29 Western-blot. The anti-inflammatory properties and its GRAS (Generally Recognized As Safe) status 30 enable S. thermophilus strains to be considered as potential probiotics.

Published
2016

25. 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

26. Divergence of genomic sequences between Lactococcus lactis subsp. lactis andLactococcus lactis subsp. cremoris

Author

Godon, Jean-Jacques, Delorme,Christine, Ehrlich, S. Dusko, and Renault, Pierre

Subjects
Genomes -- Research, Bacteria -- Analysis, Hybridization -- Methods, Biological sciences
Abstract

New means of examining the relation between the Lactoccus lactis subspecies cremoris and lactis are presented. Southern hybridization analysis using cloned chromosomal genes as probes was used to assess the bacteria. It was found that two distinctgroups are formed by the two subspecies while a 20 to 30% sequence divergence is estimated between the two. This DNA homology is the basis for the call for anew classification between the groups.

Published
1992

27. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

Author

Forslund, Kristoffer, Hildebrand, Falk, Nielsen, Trine, Falony, Gwen, Le Chatelier, Emmanuelle, Sunagawa, Shinichi, Prifti, Edi, Vieira-Silva, Sara, Gudmundsdottir, Valborg, Pedersen, Helle Krogh, Arumugam, Manimozhiyan, Kristiansen, Karsten, Voigt, Anita Yvonne, Vestergaard, Henrik, Hercog, Rajna, Costea, Paul Igor, Kultima, Jens Roat, Li, Junhua, Jorgensen, Torben, Levenez, Florence, Dore, Joel, Consortium, MetaHit, Nielsen, H. Bjorn, Brunak, Soren, Raes, Jeroen, Hansen, Torben, Wang, Jun, Ehrlich, Dusko S, Bork, Peer, Pedersen, Oluf, Almeida, Mathieu, Batto, Jean-Michel, Blottiere, Hervé H, 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, Structural and Computational Biology Unit, European Molecular Biology Laboratory [Hamburg] (EMBL), VIB Center for the Biology of Disease, Université Catholique de Louvain = Catholic University of Louvain (UCL), Department of Bioscience Engineering, Vrije Universiteit Brussel (VUB), 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), Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), 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) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark [Lyngby] (DTU), Department of Biology [Copenhagen], Faculty of Science [Copenhagen], Molecular Medicine Partnership Unit, Heidelberg University, Department of Applied Tumor Biology, Institute of Pathology, Beijing Genomics Institute [Shenzhen] (BGI), Faculty of Medicine, Aalborg University [Denmark] (AAU), Research Centre for Prevention and Health, Capital Region of Denmark, Department of Public Health [Copenhagen], 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, Faculty of Health Sciences, University of Southern Denmark (SDU), Macau University of Science and Technology (MUST), Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong (HKU), Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy’s Hospital, King‘s College London, Max Delbrück Center for Molecular Medicine [Berlin] (MDC), Helmholtz-Gemeinschaft = Helmholtz Association, Department of Bioinformatics, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), Génie et Microbiologie des Procédés Alimentaires (GMPA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Département Microbiologie et Chaîne Alimentaire (MICA), Metagenopolis grant ANR-11-DPBS-0001, European Research Council 268985, European Union 600375, Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care (LuCamp), Novo Nordisk Foundation NNF14CC0001, European Molecular Biology Laboratory (EMBL), Novo Nordisk Foundation, Innovation Fund Denmark through the MicrobDiab project, European Project: 201052, Faculty of Sciences and Bioengineering Sciences, Department of Bio-engineering Sciences, Microbiology, Université Catholique de Louvain, Vrije Universiteit [Brussels] (VUB), 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], University of Heidelberg, Beijing Genomics Institute, Max Delbrück Center for Molecular Medicine, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, and Julius-Maximilians-Universität Würzburg (JMU)

Subjects
Male, Diabetes Mellitus, Type 2/drug therapy, endocrine system diseases, GENOMES, CLOSTRIDIUM, Biology, Microbiology, DISEASE, Article, GLUCOSE, Hypoglycemic Agents/pharmacology, Metformin/pharmacology, RNA, Ribosomal, 16S, Nondestructive testing, Forensic engineering, Hypoglycemic Agents, risk factors, Humans, Gastrointestinal Microbiome/drug effects, Metagenome/drug effects, RNA, Ribosomal, 16S/genetics, Multidisciplinary, IDENTIFICATION, SEQUENCES, business.industry, Biodiversity, CANCER, Metformin, Computational biology and bioinformatics, 3. Good health, Gastrointestinal Microbiome, METAGENOME, Diabetes Mellitus, Type 2, SP-NOV, Female, HEALTH, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

In recent years, several associations between common chronic human disorders and altered gut microbiome composition and function have been reported. In most of these reports, treatment regimens were not controlled for and conclusions could thus be confounded by the effects of various drugs on the microbiota, which may obscure microbial causes, protective factors or diagnostically relevant signals. Our study addresses disease and drug signatures in the human gut microbiome of type 2 diabetes mellitus (T2D). Two previous quantitative gut metagenomics studies of T2D patients that were unstratified for treatment yielded divergent conclusions regarding its associated gut microbial dysbiosis. Here we show, using 784 available human gut metagenomes, how antidiabetic medication confounds these results, and analyse in detail the effects of the most widely used antidiabetic drug metformin. We provide support for microbial mediation of the therapeutic effects of metformin through short-chain fatty acid production, as well as for potential microbiota-mediated mechanisms behind known intestinal adverse effects in the form of a relative increase in abundance of Escherichia species. Controlling for metformin treatment, we report a unified signature of gut microbiome shifts in T2D with a depletion of butyrate-producing taxa. These in turn cause functional microbiome shifts, in part alleviated by metformin-induced changes. Overall, the present study emphasizes the need to disentangle gut microbiota signatures of specific human diseases from those of medication. ispartof: Nature vol:528 issue:7581 pages:262-6 ispartof: location:England status: published

Published
2015

29. The commensal bacterium [i]Streptococcus salivarius[/i] inhibits PPARg activity and its target genes in human intestinal epithelial cells

Author

Couvigny, Benoit, De Wouters, Tomas, Kaci, Ghalia, Delorme, Christine, Dore, Joel, Renault, Pierre, Lapaque, Nicolas, Blottiere, Herve, Guedon, Eric, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, intestin, inflammation, réponse immunitaire, [SDV.IDA]Life Sciences [q-bio]/Food engineering, cellule épithéliale, santé humaine, Streptococcus salivarius, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

The impact of commensal bacteria in eukaryotic transcriptional regulation has increasingly been demonstrated over the last decades. A multitude of studies have shown direct effects of commensal bacteria from local transcriptional activity to systemic impact. The commensal bacterium Streptococcus salivarius is one of the early bacteria colonizing the oral and gut mucosal surfaces. It has been shown to down-regulate nuclear transcription factor (NF-кB) in human intestinal cells, a central regulator of the host mucosal immune system response to the microbiota. In order to evaluate its impact on a further important transcription factor shown to link metabolism and inflammation in the intestine, namely PPARγ (peroxisome proliferator-activated receptor), we used human intestinal epithelial cell-lines engineered to monitor PPARγ transcriptional activity in response to a wide range of S. salivarius strains. We demonstrated that different strains from this bacterial group share the property to inhibit PPARγ activation independently of the ligand used. First attempts to identify the nature of the active compounds showed that it is a low-molecular-weight, DNase-, proteases- and heat-resistant metabolite secreted by S. salivarius strains. Among PPARγ-targeted metabolic genes, I-FABP and Angptl4 expression levels were dramatically reduced in intestinal epithelial cells exposed to S. salivarius supernatant. Both gene products modulate lipid accumulation in cells and down-regulating their expression might consequently affect host health. Our study shows that species belonging to the salivarius group of streptococci impact both host inflammatory and metabolic regulation suggesting a possible role in the host homeostasis and health.

Published
2012

30. Prevalence of streptococci in the intestinal flora

Author

Almeida, Mathieu, Le Chatelier, Emmanuelle, Pons, Nicolas, Achouri, Emna, Layec, Séverine, Moumen, Bouziane, Batto, Jean-Michel, Boumezbeur, Fouad, Kennedy, Sean, Delorme, Christine, Guedon, Eric, Ehrlich, Stanislav, Renault, Pierre, MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Biomics, Centre de Recherche et Innovation Technologique (CITECH), Institut Pasteur [Paris]-Institut Pasteur [Paris], Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
streptococcusi, flore intestinale, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

absent

Published
2012

31. Genotyping of Streptococcus thermophilus strains isolated from traditional Egyptian dairy products by sequence analysis of the phosphoserine phosphatase (serB) gene with phenotypic characterizations of the strains

Author

El-Sharoud, W. M., Delorme, Christine, Darwish, M. S., Renault, Pierre, Fac Agr, Dairy Dept, Food Safety & Microbial Physiol Lab, Mansoura Univ, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Egypt-France Science and Technology Cooperation Programme (IMHOTEP) [47]

Subjects
urease, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, SAFETY ASSESSMENT, dairy products, exopolysaccharides, DIVERSITY, food and beverages, respiratory system, METABOLISM, PCR, LACTIC-ACBACTERIA, Streptococcus thermophilus, UREA, serB sequencing
Abstract

Aims: To develop a new, simplified genotyping method for examining the genetic diversity of Streptococcus thermophilus strains isolated from traditional Egyptian fermented dairy products and to characterize phenotypic traits of those strains related to their potential use in bioprocessing applications. Methods and Results: A novel, simplified approach was developed for genotyping Strep. thermophilus involving the analysis of nucleotide sequence variations within a housekeeping gene encoding the phosphoserine phosphatase (SerB). Using this method, it was possible to identify ten genotypes involving diverse serB alleles among 54 Strep. thermophilus isolates cultured from Egyptian dairy products. These isolates harboured five de novo serB alleles that have not been detected in other Strep. thermophilus strains, deposited in a multilocus sequence typing (MLST) database. To assess distinct genotypes of the organism with phenotypic traits relevant to their potential use in industry, Strep. thermophilus strains were all subjected to a series of phenotypic characterizations. The strains were found to exhibit phenotypic diversity in terms of their ability to ferment lactose and galactose, express urease activity, produce exopolysaccharides and develop acidity. Conclusions: The analysis of nucleotide sequence variations within the serB gene could serve as a suitable tool for probing diverse genotypes of Strep. thermophilus. Streptococcus thermophilus isolates associated with traditional Egyptian dairy products show high degree of genetic and phenotypic diversity. Significance and Impact of the Study: This study presents a novel, simplified procedure based on serB nucleotide sequencing for genotyping Strep. thermophilus. It also provides a pool of phenotypically diverse Strep. thermophilus cultures, from which certain strains could be selected for use in bioprocessing applications including the preparation of fermented dairy products.

Published
2012

32. Complete genome sequence of the clinical Streptococcus salivarius strain CCHSS3

Author

Delorme , Christine, Guédon , Eric, Pons , Nicolas, Cruaud , Corine, Couloux , Arnaud, Loux , Valentin, Chiapello , Helene, Poyart , Claire, Gautier , Celine, Sanchez , Nicolas, Almeida , Mathieu, Kennedy , Sean, Ehrlich , Stanislav, Gibrat , Jean-Francois, Wincker , Patrick, Renault , Pierre, MICrobiologie de l'ALImentation au Service de la Santé humaine ( MICALIS ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Unité Mathématique, Informatique et Génome ( MIG ), Institut National de la Recherche Agronomique ( INRA ), 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 ), Université Paris Descartes - Faculté de Médecine ( UPD5 Médecine ), Université Paris Descartes - Paris 5 ( UPD5 ), and Département Microbiologie et Chaîne Alimentaire ( MICA )

Subjects
sang, stomatognathic diseases, stomatognathic system, COMPLETE GENOME, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, BACTERIA, COMPLETE
Abstract

Streptococcus salivarius is a commensal species commonly found in the human oral cavity and digestive tract, although it is also associated with human infections such as meningitis, endocarditis, and bacteremia. Here, we report the complete sequence of S. salivarius strain CCHSS3, isolated from human blood.

Published
2011

33. Tina wooden vat biofilms used in Sicilian PDO Ragusano cheese provide a new cluster of Streptococcus thermophilus strains

Author

Valence-Bertel, Florence, Delorme, Christine, Pediliggieri, I., Madec, Marie-Noelle, Chuat, Victoria, Parayre-Breton, Sandrine, Carpino, S., Campo, S., Renault, Pierre, Lortal, Sylvie, Licitra, G., Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Consorzio Ricerca Filiera Lattiero Casearia (CORFILAC), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
strptococcus thermophilus, contamination, sicile, bactérie lactique, [SDV.IDA]Life Sciences [q-bio]/Food engineering, conservation, food and beverages, technologie fromagère, fromage, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

Cette publication est également parue dans la revue "Journal of Animal Science", Vol.89, E-Suppl.1.; In the Sicilian PDO Ragusano cheese making, raw milk is placed in a wooden vat called a Tina. As no starter is added, lactic acid is produced by milk flora and flora released from the Tina biofilm. The aim of this work was to assess the safety and efficiency of this natural inoculation system. From 15 Tinas' biofilms, bacteria total counts varied from 10(3) to 10(6) CFU/cm(2), with the predominance of thermophilic lactic acid bacteria. Low counts of yeasts and moulds were found in a few Tinas. Salmonella, Listeria monocytogenes, Escherichia coli O157:H7 were totally absent, as assessed by conventional plating and the Bax detection system after enrichment, highlighting the safety of the system. From four Tinas out of the 15, micropieces of wood were observed by confocal and scanning electron microscopy. The biofilm entrapped in a matrix covered almost entirely the surface of the wood. Polysaccharides were detected in the four Tinas. In three of the latter, cocci were predominant in the ecosystem whereas in the other one, cocci, bacilli, yeasts and moulds were observed. Fifty litres of microfiltrated milk (

Published
2011

34. Metagenomics of the intestinal microbiota: potential applications

Author

Dusko, Ehrlich S., Antolin, Maria, Artiquenave, François, Arumugam, Manimozhiyan, Batto, Jean-Michel, Bertalan, Marcelo, Blottiere, Hervé M., Bork, Peer, Borruel, Natalia, Brechot, Christian, Brunak, Soren, Bruls, Thomas, Burgdorf, Kristoffer Solvsten, Cao, Jianjun, Casellas, Francesc, Chervaux, Christian, Colombel, Jean Frédérique, Cultrone, Antonella, Doré, Joel, Delorme, Christine, Denariaz, Gérard, Dervyn, Rozenn, Forte, Miguel, Friss, Carsten, Guarner, Francisco, Van De Guchte, Maarten, Guedon, Eric, Haimet, Florence, Hansen, Torben, Jamet, Alexandre, Jian, Min, Juste, Catherine, Kaci, Ghalia, Kleerebezem, Michiel, Knol, Jan, Kristiansen, Karsten, Layec, Severine, Le Roux, Karine, Marion, Leclerc, Le Paslier, Denis, Levenez, Florence, Li, Dong, Li, Jun, Li, Shaochuan, Li, Songgang, Li, Shengting, Yingrui, Li, Liang, Huiqing, Mende, Daniel R., Maguin, Emmanuelle, Manichanh, Chaysavanh, Minardi, Raquel Melo, Mrini, Christine, Nielsen, H. Bjorn, Nielsen, Trine, Oozeer, Raish, Parkhill, Julian, Pons, Nicolas, Pedersen, Oluf, Pelletier, Eric, Qin, Junjie, Raes, Jeroen, Renault, Pierre, Rescigno, Maria, Li, Ruiqiang, Sanchez, Nicolas, Sicheritz-Ponten, Thomas, Sebastian, Tims, Torrejon, Antonio, Turner, Keith, Encarna, Varela, Wang, Bo, Wang, Jian, Wang, Jun, Weissenbach, Jean, Winogradsky, Yohanan, Xie, Ying, Xu, Junming, Yamada, Takuji, Yang, Huanming, Yu, Chang, Zheng, Huisong, Zhang, Xiuqing, Zhu, Hongmei, Zhou, Yan, Zoetendal, Erwin G, De Vos, Willem, and Department of Bio-engineering Sciences

Subjects
xxx
Abstract

A major challenge in the human metagenomics field is to identify associations of the bacterial genes and human phenotypes and act to modulate microbial populations in order to improve human health and wellbeing. MetaHIT project addresses this ambitious challenge by developing and integrating a number of necessary approaches within the context of the gut microbiome. Among the first results is the establishment of a broad catalog of the human gut microbial genes, which was achieved by an original application of the new generation sequencing technology. The catalog contains 3.3 million non-redundant genes, 150-fold more than the human genome equivalent and includes a large majority of the gut metagenomic sequences determined across three continents, Europe, America and Asia. Its content corresponds to some 1000 bacterial species, which likely represent a large fraction of species associated with humankind intestinal tract. The catalog enables development of the gene profiling approaches aiming to detect associations of bacterial genes and phenotypes. These should lead to the speedy development of diagnostic and prognostic tools and open avenues to reasoned approaches to the modulation of the individual's microbiota in order to optimize health and well-being.

Published
2010

38. Réseau de régulation de la transcription des gènes du système protéolytique de Lactococcus lactis

Author

Guedon, E., Martin, C., Gobert, F.X., Ehrlich, S.D., Renault, P., Delorme, Christine, Unité de recherche Génétique Microbienne (UGM), Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, LACTOCOCCUS LACTIS, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2000

39. Enterotypes of the human gut microbiome:[Plus]Corrigendum [Plus]Addendum

Author

Arumugam, Manimozhiyan, Raes, Jeroen, Pelletier, Eric, Le Paslier, Denis, Yamada, Takuji, Mende, Daniel R, Fernandes, Gabriel R, Tap, Julien, Bruls, Thomas, Batto, Jean-Michel, dos Santos, Marcelo Bertalan Quintanilha, Borruel, Natalia, Casellas, Francesc, Fernandez, Leyden, Gautier, Laurent, Hansen, Torben, Hattori, Masahira, Hayashi, Tetsuya, Kleerebezem, Michiel, Kurokawa, Ken, Leclerc, Marion, Levenez, Florence, Manichanh, Chaysavanh, Nielsen, H Bjørn, Nielsen, Trine, Pons, Nicolas, Poulain, Julie, Qin, Junjie, Sicheritz-Ponten, Thomas, Tims, Sebastian, Torrents, David, Ugarte, Edgardo, Zoetendal, Erwin G, Wang, Jun, Guarner, Francisco, Pedersen, Oluf, de Vos, Willem M, Brunak, Søren, Doré, Joel, Antolín, María, Artiguenave, François, Blottiere, Hervé M, Almeida, Mathieu, Brechot, Christian, Cara, Carlos, Chervaux, Christian, Cultrone, Antonella, Delorme, Christine, Denariaz, Gérard, Kristiansen, Karsten, Arumugam, Manimozhiyan, Raes, Jeroen, Pelletier, Eric, Le Paslier, Denis, Yamada, Takuji, Mende, Daniel R, Fernandes, Gabriel R, Tap, Julien, Bruls, Thomas, Batto, Jean-Michel, dos Santos, Marcelo Bertalan Quintanilha, Borruel, Natalia, Casellas, Francesc, Fernandez, Leyden, Gautier, Laurent, Hansen, Torben, Hattori, Masahira, Hayashi, Tetsuya, Kleerebezem, Michiel, Kurokawa, Ken, Leclerc, Marion, Levenez, Florence, Manichanh, Chaysavanh, Nielsen, H Bjørn, Nielsen, Trine, Pons, Nicolas, Poulain, Julie, Qin, Junjie, Sicheritz-Ponten, Thomas, Tims, Sebastian, Torrents, David, Ugarte, Edgardo, Zoetendal, Erwin G, Wang, Jun, Guarner, Francisco, Pedersen, Oluf, de Vos, Willem M, Brunak, Søren, Doré, Joel, Antolín, María, Artiguenave, François, Blottiere, Hervé M, Almeida, Mathieu, Brechot, Christian, Cara, Carlos, Chervaux, Christian, Cultrone, Antonella, Delorme, Christine, Denariaz, Gérard, and Kristiansen, Karsten

Abstract

Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.

Published
2011

40. 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

41. Evaluation de la diversité de l'expression génétique chez les lactocoques : développement d'un outil et son application aux peptidases

Author

Guedon, E., Renault, P., Ehrlich, S.D., Delorme, Christine, Unité de recherche Génétique Microbienne (UGM), Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration

Subjects
[SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, LACTOCOCCUS LACTIS, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
1998

42. Régulations métaboliques de Lactococcus lactis en culture pure ou mixte dans le lait

Author

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

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, LACTOCOCCUS LACTIS, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
1998

43. 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

44. 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

45. New insights in the molecular biology and physiology of Streptococcus thermophilus revealed by comparative genomics.

Author

UCL - SC/BIOL - Département de biologie, Hols, Pascal, Hancy, Frédéric, Fontaine, Laetitia, Grossiord, Benoît, Prozzi, Deborah, Leblond-Bourget, Nathalie, Decaris, Bernard, Bolotin, Alexander, Delorme, Christine, Dusko Ehrlich, S, Guédon, Eric, Monnet, Véronique, Renault, Pierre, Kleerebezem, Michiel, UCL - SC/BIOL - Département de biologie, Hols, Pascal, Hancy, Frédéric, Fontaine, Laetitia, Grossiord, Benoît, Prozzi, Deborah, Leblond-Bourget, Nathalie, Decaris, Bernard, Bolotin, Alexander, Delorme, Christine, Dusko Ehrlich, S, Guédon, Eric, Monnet, Véronique, Renault, Pierre, and Kleerebezem, Michiel

Abstract

Streptococcus thermophilus is a major dairy starter used for the manufacture of yoghurt and cheese. The access to three genome sequences, comparative genomics and multilocus sequencing analyses suggests that this species recently emerged and is still undergoing a process of regressive evolution towards a specialised bacterium for growth in milk. Notably, S. thermophilus has maintained a well-developed nitrogen metabolism whereas its sugar catabolism has been subjected to a high level of degeneracy due to a paucity of carbon sources in milk. Furthermore, while pathogenic streptococci are recognised for a high capacity to expose proteins at their cell surface in order to achieve cell adhesion or to escape the host immune system, S. thermophilus has nearly lost this unique feature as well as many virulence-related functions. Although gene decay is obvious in S. thermophilus genome evolution, numerous small genomic islands, which were probably acquired by horizontal gene transfer, comprise important industrial phenotypic traits such as polysaccharide biosynthesis, bacteriocin production, restriction-modification systems or oxygen tolerance.

Published
2005

47. Complete Genome Sequence of the Commensal Streptococcus salivarius Strain JIM8777

Author

Guédon, Eric, primary, Delorme, Christine, additional, Pons, Nicolas, additional, Cruaud, Corinne, additional, Loux, Valentin, additional, Couloux, Arnaud, additional, Gautier, Céline, additional, Sanchez, Nicolas, additional, Layec, Séverine, additional, Galleron, Nathalie, additional, Almeida, Mathieu, additional, van de Guchte, Maarten, additional, Kennedy, Sean P., additional, Ehrlich, S. Dusko, additional, Gibrat, Jean-François, additional, Wincker, Patrick, additional, and Renault, Pierre, additional

Published
2011
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49. Conjugal transfer of the determinants for bacteriocin (lacticin 481) production and immunity in Lactococcus lactis subsp.lactis CNRZ 481

Author

Piard, J.C., Delorme, Christine, Novel, M., DESMAZEAUD, M., NOVEL, G., Institut National de la Recherche Agronomique (INRA), Unité de recherche Génétique Microbienne (UGM), and ProdInra, Migration

Subjects
[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, LACTOCOCCUS LACTIS, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
1993

50. Genetique et evaluation du potentiel industriel des souches

Author

Renault, P., Delorme, Christine, Godon, Jean-Jacques, Ehrlich, S.D., Unité de recherche Génétique Microbienne (UGM), Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, LACTOCOCCUS LACTIS, BIOLOGIE MOLECULAIRE, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
1993

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