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3. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

Author

Van Den Bossche, Tim, Kunath, Benoit J., Schallert, Kay, Schäpe, Stephanie S., Abraham, Paul E., Armengaud, Jean, Arntzen, Magnus Ø., Bassignani, Ariane, Benndorf, Dirk, Fuchs, Stephan, Giannone, Richard J., Griffin, Timothy J., Hagen, Live H., Halder, Rashi, Henry, Céline, Hettich, Robert L., Heyer, Robert, Jagtap, Pratik, Jehmlich, Nico, Jensen, Marlene, Juste, Catherine, Kleiner, Manuel, Langella, Olivier, Lehmann, Theresa, Leith, Emma, May, Patrick, Mesuere, Bart, Miotello, Guylaine, Peters, Samantha L., Pible, Olivier, Queiros, Pedro T., Reichl, Udo, Renard, Bernhard Y., Schiebenhoefer, Henning, Sczyrba, Alexander, Tanca, Alessandro, Trappe, Kathrin, Trezzi, Jean-Pierre, Uzzau, Sergio, Verschaffelt, Pieter, von Bergen, Martin, Wilmes, Paul, Wolf, Maximilian, Martens, Lennart, and Muth, Thilo

Published
2021
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5. The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes

Author

Van Den Bossche, Tim, Arntzen, Magnus Ø., Becher, Dörte, Benndorf, Dirk, Eijsink, Vincent G. H., Henry, Céline, Jagtap, Pratik D., Jehmlich, Nico, Juste, Catherine, Kunath, Benoit J., Mesuere, Bart, Muth, Thilo, Pope, Phillip B., Seifert, Jana, Tanca, Alessandro, Uzzau, Sergio, Wilmes, Paul, Hettich, Robert L., and Armengaud, Jean

Published
2021
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6. Synergistic convergence of microbiota-specific systemic IgG and secretory IgA

Author

Fadlallah, Jehane, Sterlin, Delphine, Fieschi, Claire, Parizot, Christophe, Dorgham, Karim, El Kafsi, Hela, Autaa, Gaëlle, Ghillani-Dalbin, Pascale, Juste, Catherine, Lepage, Patricia, Malphettes, Marion, Galicier, Lionel, Boutboul, David, Clément, Karine, André, Sébastien, Marquet, Florian, Tresallet, Christophe, Mathian, Alexis, Miyara, Makoto, Oksenhendler, Eric, Amoura, Zahir, Yssel, Hans, Larsen, Martin, and Gorochov, Guy

Published
2019
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8. Faecalibacterium duncaniae A2-165 regulates the expression of butyrate synthesis, ferrous iron uptake, and stress-response genes based on acetate consumption

Author

Verstraeten, Sophie, primary, Layec, Séverine, additional, Auger, Sandrine, additional, Juste, Catherine, additional, Henry, Céline, additional, Charif, Sawiya, additional, Jaszczyszyn, Yan, additional, Sokol, Harry, additional, Beney, Laurent, additional, Langella, Philippe, additional, Thomas, Muriel, additional, and Huillet, Eugénie, additional

Published
2023
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9. Faecalibacterium duncaniae A2-165 regulates the expression of butyrate synthesis, ferrous iron uptake, and stress-response genes based on acetate level in early-stationary cultures.

Author

Verstraeten, Sophie, primary, Layec, Séverine, additional, Auger, Sandrine, additional, Juste, Catherine, additional, Henry, Céline, additional, Charif, Sawiya, additional, Jaszczyszyn, Yan, additional, Sokol, Harry, additional, Beney, Laurent, additional, Langella, Philippe, additional, Thomas, Muriel, additional, and Huillet, Eugénie, additional

Published
2023
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11. Faecalibacterium duncaniae A2-165 regulates the expression of butyrate synthesis, ferrous iron uptake, and stress-response genes based on acetate level in early-stationary cultures

Author

Verstraeten, Sophie, Layec, Séverine, Auger, Sandrine, Juste, Catherine, Henry, Céline, Charif, Sawiya, Jaszczyszyn, Yan, Sokol, Harry, Beney, Laurent, Langella, Philippe, Thomas, Muriel, Huillet, Eugénie, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), CEA- Saclay (CEA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, Procédés Microbiologiques et Biotechnologiques (PMB), Procédés Alimentaires et Microbiologiques [Dijon] (PAM), Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut Agro Dijon, 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)-Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut Agro Dijon, 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
FeoB transporter, Metaproteomics, Faecalibacterium duncaniae A2-165, early stationary phase, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, RNA-Seq, acetate, butyrate, Faecalibacterium
Abstract

Background Faecalibacterium prausnitzii, a promising next-generation probiotic, is one of the most abundant acetate-consuming, butyrate-producing bacteria in the healthy human gut. However, little is known about the gene expression strategies used by this bacterium to adapt to the availability of acetate in the human gut. Result We first established a growth model of F. duncaniae A2-165 (previously known as F. prausnitzii A2-165) using batch cultures, under high- and low-acetate conditions. Over late exponential and early stationary phases, the bacteria displayed a growth deficiency and a low butyrate production in low- compared with high-acetate conditions. Using RNA-seq, we compared expression patterns between early stationary and late exponential phases in high- and low-acetate conditions and between high- and low-acetate conditions in the early stationary phase. Functional classification of the low-acetate transcriptome revealed the specific activation of a general stress response, including upregulation of chaperones, toxin-antitoxin type II systems and downregulation of numerous protein synthesis genes. We observed two distinct import system transcriptomes, under low and high-acetate conditions, suggesting major adaptation responses to nutrient-deprived conditions of the early-stationary growth phase. Specifically, in high-acetate conditions, the feoAABC operon encoding one FeoB ferrous iron transporter was strongly activated but not the feoAB gene encoding the second FeoB transporter of F. duncaniae A2-165. This strong activation in early-stationary phase under high-acetate conditions suggested that (i) the level of extracellular ferrous iron is low (ii) FeoAABC system is required for ferrous iron uptake, in this iron-poor environment. Using RT-PCR, we demonstrated that excess ferrous iron represses feoB expression (i.e feoAABC operon) but not feoAB expression in high-acetate conditions. Finally, we conducted an integrated analysis of a healthy human fecal metaproteome, in which we were able to detect FeoB peptides from both genus Faecalibacterium and strain A2-165. Conclusion We characterized two early-stationary lifestyles of F. duncaniae A2-165 at the transcriptional level, related to acetate consumption and butyrate production. We characterized the regulation of feoAABC operon encoding an high-affinity ferrous iron transporter that may play a major role in iron homeostasis and butyrate synthesis in iron-poor and acetate-rich conditions in F. duncaniae A2-165.

Published
2023
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16. The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes

Author

Fonds National de la Recherche - FnR ; ERC-CoG 863664 [sponsor], Van den Bossche, Tim, Arntzen, Magnus, Becher, Dörte, Benndorf, Dirk, Eijsink, Vincent, Henry, Céline, Jagtap, Pratik, Jehmlich, Nico, Juste, Catherine, Kunath, Benoît, Mesuere, Bart, Muth, Thilo, Pope, Phillip, Seifert, Jana, Tanca, Alessandro, Uzzau, Sergio, Wilmes, Paul, Hettich, Robert, Armengaud, Jean, Fonds National de la Recherche - FnR ; ERC-CoG 863664 [sponsor], Van den Bossche, Tim, Arntzen, Magnus, Becher, Dörte, Benndorf, Dirk, Eijsink, Vincent, Henry, Céline, Jagtap, Pratik, Jehmlich, Nico, Juste, Catherine, Kunath, Benoît, Mesuere, Bart, Muth, Thilo, Pope, Phillip, Seifert, Jana, Tanca, Alessandro, Uzzau, Sergio, Wilmes, Paul, Hettich, Robert, and Armengaud, Jean

Published
2021

17. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

Author

Fonds National de la Recherche - FnR [sponsor], ERC-CoG 863664 [sponsor], Van Den Bossche, Tim, Kunath, Benoît, Schallert, Kay, Schäpe, Stephanie S., Abraham, Paul E., Armengaud, Jean, Arntzen, Magnus Ø., Bassignani, Ariane, Benndorf, Dirk, Fuchs, Stephan, Giannone, Richard J., Griffin, Timothy J., Hagen, Live H., Halder, Rashi, Henry, Céline, Hettich, Robert L., Heyer, Robert, Jagtap, Pratik, Jehmlich, Nico, Jensen, Marlene, Juste, Catherine, Kleiner, Manuel, Langella, Olivier, Lehmann, Theresa, Leith, Emma, May, Patrick, Mesuere, Bart, Miotello, Guylaine, Peters, Samantha L., Pible, Olivier, Teixeira Queiros, Pedro, Reichl, Udo, Renard, Bernhard Y., Schiebenhoefer, Henning, Sczyrba, Alexander, Tanca, Alessandro, Trappe, Kathrin, Trezzi, Jean-Pierre, Uzzau, Sergio, Verschaffelt, Pieter, von Bergen, Martin, Wilmes, Paul, Wolf, Maximilian, Martens, Lennart, Muth, Thilo, Fonds National de la Recherche - FnR [sponsor], ERC-CoG 863664 [sponsor], Van Den Bossche, Tim, Kunath, Benoît, Schallert, Kay, Schäpe, Stephanie S., Abraham, Paul E., Armengaud, Jean, Arntzen, Magnus Ø., Bassignani, Ariane, Benndorf, Dirk, Fuchs, Stephan, Giannone, Richard J., Griffin, Timothy J., Hagen, Live H., Halder, Rashi, Henry, Céline, Hettich, Robert L., Heyer, Robert, Jagtap, Pratik, Jehmlich, Nico, Jensen, Marlene, Juste, Catherine, Kleiner, Manuel, Langella, Olivier, Lehmann, Theresa, Leith, Emma, May, Patrick, Mesuere, Bart, Miotello, Guylaine, Peters, Samantha L., Pible, Olivier, Teixeira Queiros, Pedro, Reichl, Udo, Renard, Bernhard Y., Schiebenhoefer, Henning, Sczyrba, Alexander, Tanca, Alessandro, Trappe, Kathrin, Trezzi, Jean-Pierre, Uzzau, Sergio, Verschaffelt, Pieter, von Bergen, Martin, Wilmes, Paul, Wolf, Maximilian, Martens, Lennart, and Muth, Thilo

Abstract

Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.

Published
2021

18. Bacterial protein signals are associated with Crohn’s disease

Author

Juste, Catherine, Kreil, David P, Beauvallet, Christian, Guillot, Alain, Vaca, Sebastian, Carapito, Christine, Mondot, Stanislas, Sykacek, Peter, Sokol, Harry, Blon, Florence, Lepercq, Pascale, Levenez, Florence, Valot, Benoît, Carré, Wilfrid, Loux, Valentin, Pons, Nicolas, David, Olivier, Schaeffer, Brigitte, Lepage, Patricia, Martin, Patrice, Monnet, Véronique, Seksik, Philippe, Beaugerie, Laurent, Ehrlich, S Dusko, Gibrat, Jean-François, Van Dorsselaer, Alain, and Doré, Joël

Published
2014
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20. Perturbed Microbiota/Immune Homeostasis in Multiple Sclerosis

Author

Sterlin, Delphine, primary, Larsen, Martin, additional, Fadlallah, Jehane, additional, Parizot, Christophe, additional, Vignes, Marina, additional, Autaa, Gaëlle, additional, Dorgham, Karim, additional, Juste, Catherine, additional, Lepage, Patricia, additional, Aboab, Jennifer, additional, Vicart, Savine, additional, Maillart, Elisabeth, additional, Gout, Olivier, additional, Lubetzki, Catherine, additional, Deschamps, Romain, additional, Papeix, Caroline, additional, and Gorochov, Guy, additional

Published
2021
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22. Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows

Author

Van Den Bossche, Tim, primary, Kunath, Benoit J., additional, Schallert, Kay, additional, Schäpe, Stephanie S., additional, Abraham, Paul E., additional, Armengaud, Jean, additional, Arntzen, Magnus Ø., additional, Bassignani, Ariane, additional, Benndorf, Dirk, additional, Fuchs, Stephan, additional, Giannone, Richard J., additional, Griffin, Timothy J., additional, Hagen, Live H., additional, Halder, Rashi, additional, Henry, Céline, additional, Hettich, Robert L., additional, Heyer, Robert, additional, Jagtap, Pratik, additional, Jehmlich, Nico, additional, Jensen, Marlene, additional, Juste, Catherine, additional, Kleiner, Manuel, additional, Langella, Olivier, additional, Lehmann, Theresa, additional, Leith, Emma, additional, May, Patrick, additional, Mesuere, Bart, additional, Miotello, Guylaine, additional, Peters, Samantha L., additional, Pible, Olivier, additional, Queiros, Pedro T., additional, Reichl, Udo, additional, Renard, Bernhard Y., additional, Schiebenhoefer, Henning, additional, Sczyrba, Alexander, additional, Tanca, Alessandro, additional, Trappe, Kathrin, additional, Trezzi, Jean-Pierre, additional, Uzzau, Sergio, additional, Verschaffelt, Pieter, additional, von Bergen, Martin, additional, Wilmes, Paul, additional, Wolf, Maximilian, additional, Martens, Lennart, additional, and Muth, Thilo, additional

Published
2021
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24. Benefits of Iterative Searches of Large Databases to Interpret Large Human Gut Metaproteomic Data Sets

Author

Bassignani, Ariane, primary, Plancade, Sandra, additional, Berland, Magali, additional, Blein-Nicolas, Melisande, additional, Guillot, Alain, additional, Chevret, Didier, additional, Moritz, Chloé, additional, Huet, Sylvie, additional, Rizkalla, Salwa, additional, Clément, Karine, additional, Doré, Joël, additional, Langella, Olivier, additional, and Juste, Catherine, additional

Published
2021
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25. Dietary intervention impact on gut microbial gene richness

Author

Cotillard, Aurélie, Kennedy, Sean P., Kong, Ling Chun, Prifti, Edi, Pons, Nicolas, Le Chatelier, Emmanuelle, Almeida, Mathieu, Quinquis, Benoit, Levenez, Florence, Galleron, Nathalie, Gougis, Sophie, Rizkalla, Salwa, Batto, Jean-Michel, Renault, Pierre, Doré, Joel, Zucker, Jean-Daniel, Clément, Karine, Ehrlich, Stanislav Dusko, Blottière, Hervé, Leclerc, Marion, Juste, Catherine, de Wouters, Tomas, Lepage, Patricia, Fouqueray, Charlene, Basdevant, Arnaud, Henegar, Cornelieu, Godard, Cindy, Fondacci, Marine, Rohia, Alili, Hajduch, Froogh, Weissenbach, Jean, Pelletier, Eric, Le Paslier, Denis, Gauchi, Jean-Pierre, Gibrat, Jean-François, Loux, Valentin, Carré, Wilfrid, Maguin, Emmanuelle, van de Guchte, Maarten, Jamet, Alexandre, Boumezbeur, Fouad, and Layec, Séverine

Published
2013
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26. 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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27. 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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28. Correction: Human IgA bind a diverse array of commensal bacteria

Author

Sterlin, Delphine, primary, Fadlallah, Jehane, additional, Adams, Olivia, additional, Fieschi, Claire, additional, Parizot, Christophe, additional, Dorgham, Karim, additional, Rajkumar, Asok, additional, Autaa, Gaëlle, additional, El-Kafsi, Hela, additional, Charuel, Jean-Luc, additional, Juste, Catherine, additional, Jönsson, Friederike, additional, Candela, Thomas, additional, Wardemann, Hedda, additional, Aubry, Alexandra, additional, Capito, Carmen, additional, Brisson, Hélène, additional, Tresallet, Christophe, additional, Cummings, Richard D., additional, Larsen, Martin, additional, Yssel, Hans, additional, von Gunten, Stephan, additional, and Gorochov, Guy, additional

Published
2020
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29. 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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35. Human IgA binds a diverse array of commensal bacteria

Author

Sterlin, Delphine, primary, Fadlallah, Jehane, additional, Adams, Olivia, additional, Fieschi, Claire, additional, Parizot, Christophe, additional, Dorgham, Karim, additional, Rajkumar, Asok, additional, Autaa, Gaëlle, additional, El-Kafsi, Hela, additional, Charuel, Jean-Luc, additional, Juste, Catherine, additional, Jönsson, Friederike, additional, Candela, Thomas, additional, Wardemann, Hedda, additional, Aubry, Alexandra, additional, Capito, Carmen, additional, Brisson, Hélène, additional, Tresallet, Christophe, additional, Cummings, Richard D., additional, Larsen, Martin, additional, Yssel, Hans, additional, von Gunten, Stephan, additional, and Gorochov, Guy, additional

Published
2019
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36. An iterative workflow for mining the human intestinal metaproteome

Author

Beauvallet Christian, Galan Pilar, Boeren Sjef, de Been Mark, Doré Joël, Juste Catherine, Kolmeder Carolin, Rooijers Koos, de Vos Willem M, and Schaap Peter J

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Peptide spectrum matching (PSM) is the standard method in shotgun proteomics data analysis. It relies on the availability of an accurate and complete sample proteome that is used to make interpretation of the spectra feasible. Although this procedure has proven to be effective in many proteomics studies, the approach has limitations when applied on complex samples of microbial communities, such as those found in the human intestinal tract. Metagenome studies have indicated that the human intestinal microbiome contains over 100 times more genes than the human genome and it has been estimated that this ecosystem contains over 5000 bacterial species. The genomes of the vast majority of these species have not yet been sequenced and hence their proteomes remain unknown. To enable data analysis of shotgun proteomics data using PSM, and circumvent the lack of a defined matched metaproteome, an iterative workflow was developed that is based on a synthetic metaproteome and the developing metagenomic databases that are both representative for but not necessarily originating from the sample of interest. Results Two human fecal samples for which metagenomic data had been collected, were analyzed for their metaproteome using liquid chromatography-mass spectrometry and used to benchmark the developed iterative workflow to other methods. The results show that the developed method is able to detect over 3,000 peptides per fecal sample from the spectral data by circumventing the lack of a defined proteome without naive translation of matched metagenomes and cross-species peptide identification. Conclusions The developed iterative workflow achieved an approximate two-fold increase in the amount of identified spectra at a false discovery rate of 1% and can be applied in metaproteomic studies of the human intestinal tract or other complex ecosystems.

Published
2011
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38. Oral treatment with Lactococcus lactis expressing Staphylococcus hyicus lipase enhances lipid digestion in pigs with induced pancreatic insufficiency

Author

Drouault, Sophie, Juste, Catherine, Marteau, Philippe, Renault, Pierre, and Corthier, Gerard

Subjects
Microbiological research -- Analysis, Lactococcus -- Genetic aspects, Gene expression -- Physiological aspects, Staphylococcus -- Genetic aspects, Lipase -- Genetic aspects, Lipids -- Genetic aspects, Pancreatic insufficiency -- Causes of, Biological sciences
Abstract

Research has been conducted on genetically engineered Lactococcus lactis cells. The effectiveness of these cells expressing Staphylococcus hyicus bacterial lipase and their role in lipid digestion in pigs with pancreatic insufficiency have been investigated and are discussed.

Published
2002

39. 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
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40. Microbial ecology perturbation in human IgA deficiency

Author

Fadlallah, Jehane, primary, El Kafsi, Hela, additional, Sterlin, Delphine, additional, Juste, Catherine, additional, Parizot, Christophe, additional, Dorgham, Karim, additional, Autaa, Gaëlle, additional, Gouas, Doriane, additional, Almeida, Mathieu, additional, Lepage, Patricia, additional, Pons, Nicolas, additional, Le Chatelier, Emmanuelle, additional, Levenez, Florence, additional, Kennedy, Sean, additional, Galleron, Nathalie, additional, de Barros, Jean-Paul Pais, additional, Malphettes, Marion, additional, Galicier, Lionel, additional, Boutboul, David, additional, Mathian, Alexis, additional, Miyara, Makoto, additional, Oksenhendler, Eric, additional, Amoura, Zahir, additional, Doré, Joel, additional, Fieschi, Claire, additional, Ehrlich, S. Dusko, additional, Larsen, Martin, additional, and Gorochov, Guy, additional

Published
2018
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41. Method for preparing a fecal microbiota sample

Author

Juste, Catherine, Dore, Joel, Lepage, Patricia, Maillet, Christel, Rabot, Sylvie, Fonseca, Fernanda, Blottiere, Herve, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génie et Microbiologie des Procédés Alimentaires (GMPA), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

Subjects
PCT/FR2016/050958, [SDV]Life Sciences [q-bio], Method, fecal microbiota sample
Abstract

Plusieurs dépôts: D015 FR (3035328A1), 2016: US (US20180099012A1) EP (EP3285784A1) WO (WO2016170285A1) AU (AU2016252209A1) JP (JP2018514228A) CA (CA2983192A1) CN (CN107530280A), 2018 IL (IL259888D0); Method for preparing a fecal microbiota sample

Published
2016

42. 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
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43. Bacteroides sp. strain D8, the first cholesterol-reducing bacterium isolated from human feces

Author

Gerard, Philippe, Lepercq, Pascale, Leclerc, Marion, Gavini, Francoise, Raibaud, Pierre, and Juste, Catherine

Subjects
Anaerobic bacteria -- Physiological aspects, Anaerobic bacteria -- Genetic aspects, Nucleotide sequencing -- Usage, Scanning electron microscopes -- Observations, Bacteriology -- Cultures and culture media, Bacteriology -- Research, Biological sciences
Abstract

The first isolation and characterization of a cholesterol-reducing bacterium of human origin, strain D8, which is closely related to the newly described species of Bacteroides dorei is reported.

Published
2007

44. 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
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46. Method of preparing a faecal microniota sample

Author

Juste, Catherine, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Université Paris Saclay (COmUE)

Subjects
[SDV]Life Sciences [q-bio]
Published
2015

47. Quality control of microbiota metagenomics by k-mer analysis

Author

Plaza Onate, Florian, Batto, Jean-Michel, Juste, Catherine, Fadlallah, Jehane, Fougeroux, Cyrielle, Gouas, Doriane, Pons, Nicolas, Kennedy, Sean, Levenez, Florence, Dore, Joel, Dusko Ehrlich, S., Gorochov, Guy, Larsen, Martin, INRA US1367 MetaGenoPolis, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Service d'immunologie [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], Centre d'Immunologie et de Maladies Infectieuses (CIMI), 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), MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), Service d'Immunologie [CHU Pitié-Salpétrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), The study was funded by INSERM, the University Pierre et Marie Curie ËMERGENCE' program, Fondation pour l’Aide a la Recherche sur la Sclerose En Plaques (ARSEP), ARTHRITIS Fondation COURTIN and Agence nationale de la recherché (ANR)., The authors acknowledge the funding agencies and the volunteers providing samples for the study., Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and Administateur, HAL Sorbonne Université

Subjects
Sample size limits, Quality control, Sampling bias, Metagenomics, Next generation sequencing, MESH: Bacteria/genetics, MESH: Quality Control, Médecine humaine et pathologie, MESH: Metagenomics/standards, MESH: Genome, Bacterial, Sensitivity and Specificity, Feces, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Cluster Analysis, Humans, MESH: Gastrointestinal Tract/microbiology, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, MESH: Humans, Bacteria, Methodology Article, Microbiota, MESH: Feces/microbiology, MESH: Metagenome, MESH: Microbiota, MESH: Cluster Analysis, MESH: Sensitivity and Specificity, MESH: Metagenomics/methods, Gastrointestinal Tract, MESH: Bacteria/classification, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Metagenome, Human health and pathology, Genome, Bacterial, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Biotechnology
Abstract

Background The biological and clinical consequences of the tight interactions between host and microbiota are rapidly being unraveled by next generation sequencing technologies and sophisticated bioinformatics, also referred to as microbiota metagenomics. The recent success of metagenomics has created a demand to rapidly apply the technology to large case–control cohort studies and to studies of microbiota from various habitats, including habitats relatively poor in microbes. It is therefore of foremost importance to enable a robust and rapid quality assessment of metagenomic data from samples that challenge present technological limits (sample numbers and size). Here we demonstrate that the distribution of overlapping k-mers of metagenome sequence data predicts sequence quality as defined by gene distribution and efficiency of sequence mapping to a reference gene catalogue. Results We used serial dilutions of gut microbiota metagenomic datasets to generate well-defined high to low quality metagenomes. We also analyzed a collection of 52 microbiota-derived metagenomes. We demonstrate that k-mer distributions of metagenomic sequence data identify sequence contaminations, such as sequences derived from “empty” ligation products. Of note, k-mer distributions were also able to predict the frequency of sequences mapping to a reference gene catalogue not only for the well-defined serial dilution datasets, but also for 52 human gut microbiota derived metagenomic datasets. Conclusions We propose that k-mer analysis of raw metagenome sequence reads should be implemented as a first quality assessment prior to more extensive bioinformatics analysis, such as sequence filtering and gene mapping. With the rising demand for metagenomic analysis of microbiota it is crucial to provide tools for rapid and efficient decision making. This will eventually lead to a faster turn-around time, improved analytical quality including sample quality metrics and a significant cost reduction. Finally, improved quality assessment will have a major impact on the robustness of biological and clinical conclusions drawn from metagenomic studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1406-7) contains supplementary material, which is available to authorized users.

Published
2015
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48. A Data Integration Multi-Omics Approach to Study Calorie Restriction-Induced Changes in Insulin Sensitivity.

Author

Dao, Maria Carlota, Sokolovska, Nataliya, Brazeilles, Rémi, Affeldt, Séverine, Pelloux, Véronique, Prifti, Edi, Chilloux, Julien, Verger, Eric O., Kayser, Brandon D., Aron-Wisnewsky, Judith, Ichou, Farid, Pujos-Guillot, Estelle, Hoyles, Lesley, Juste, Catherine, Doré, Joël, Dumas, Marc-Emmanuel, Rizkalla, Salwa W., Holmes, Bridget A., Zucker, Jean-Daniel, and Clément, Karine

Subjects
INSULIN resistance, LOW-calorie diet, GENE expression, ENDOPLASMIC reticulum, BRANCHED chain amino acids
Abstract

Background: The mechanisms responsible for calorie restriction (CR)-induced improvement in insulin sensitivity (IS) have not been fully elucidated. Greater insight can be achieved through deep biological phenotyping of subjects undergoing CR, and integration of big data. Materials and Methods: An integrative approach was applied to investigate associations between change in IS and factors from host, microbiota, and lifestyle after a 6-week CR period in 27 overweight or obese adults (ClinicalTrials.gov: NCT01314690). Partial least squares regression was used to determine associations of change (week 6 – baseline) between IS markers and lifestyle factors (diet and physical activity), subcutaneous adipose tissue (sAT) gene expression, metabolomics of serum, urine and feces, and gut microbiota composition. ScaleNet, a network learning approach based on spectral consensus strategy (SCS, developed by us) was used for reconstruction of biological networks. Results: A spectrum of variables from lifestyle factors (10 nutrients), gut microbiota (10 metagenomics species), and host multi-omics (metabolic features: 84 from serum, 73 from urine, and 131 from feces; and 257 sAT gene probes) most associated with IS were identified. Biological network reconstruction using SCS, highlighted links between changes in IS, serum branched chain amino acids, sAT genes involved in endoplasmic reticulum stress and ubiquitination, and gut metagenomic species (MGS). Linear regression analysis to model how changes of select variables over the CR period contribute to changes in IS, showed greatest contributions from gut MGS and fiber intake. Conclusion: This work has enhanced previous knowledge on links between host glucose homeostasis, lifestyle factors and the gut microbiota, and has identified potential biomarkers that may be used in future studies to predict and improve individual response to weight-loss interventions. Furthermore, this is the first study showing integration of the wide range of data presented herein, identifying 115 variables of interest with respect to IS from the initial input, consisting of 9,986 variables. Clinical Trial Registration: clinicaltrials.gov (NCT01314690). [ABSTRACT FROM AUTHOR]

Published
2019
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49. Diagnostic markers for Crohn's disease

Author

Juste, Catherine, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech

Subjects
[SDV]Life Sciences [q-bio]
Published
2014

50. Nouveaux dispositifs médicaux et nouveau procédé de fabrication pour un transfert de microbiote fécal par voie rectale, sans risque, standardisé et prêt à l'emploi.

Author

Dubuisson, Jean-François, Juste, Catherine, Fonseca, Fernanda, Lepage, Patricia, Bera-Maillet, Christel, Beguet-Crespel, FabiENne, Le Roux, Karine, Burz, Sebastian, LevENez, FlorENce, Leroux, Alice, Boucinha, Lilia, Deprez, Alicia, Schwintner, Carole, Dussurgey, SébastiEN, Andrieu, Thibault, Affagard, Hervé, Blottiere, Hervé, Bourlioux, Pierre, and Dore, Joël

Abstract

Fecal microbiota transfer (FMT) consists in the administration of a fecal dilution from a healthy donor into the intestinal tract of a recipient to restore microbial diversity and confer a health benefit. FMT has been demonstrated to successfully treat recurrent Clostridium difficile infection but may also have therapeutic potential for other diseases. In France, a preparation for FMT is considered as a drug and thereby must be prepared under the responsibility of pharmacists. However, the preparation, storage and rectal administration for an efficient FMT is a big challenge for health care professionals, especially hospital pharmacists. MaaT Pharma, a French start-up company has developed patented devices (collection device, storage bag and administration system), and industrialized a manufacturing process developed by The Institut national de la recherche agronomique (Inra), to produce from raw fecal material, an active and stable therapeutic inoculum. Results presented in this study show that solutions developed by MaaT Pharma and Inra help in preserving the viability, diversity and original profile of the microbiota, at all stages, from collection of raw faeces to administration of the FMT. Thereby, MaaT Pharma is able to propose to hospital pharmacists and patients a safe, standardized, ready-to-use FMT, manufactured according to the good manufacturing practices (GMP). The next short-term objective is to propose an oral form product as an alternative to rectal administration for appropriate patients. [ABSTRACT FROM AUTHOR]

Published
2018
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