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52. The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

Author

Flundas, Dimitrios, Binder, Manfred, Riley, Robert, Barry, Kerrie, Blanchette, Robert A., Henrissat, Bernard, Martínez, Angel T., Otillar, Robert, Spatafora, Joseph W., Yadav, Jagjit S., Aerts, Andrea, Benoit, Isabelle, Boyd, Alex, Carlson, Alexis, Copeland, Alex, Coutinho, Pedro M., de Vries, Ronald P., Ferreira, Patricia, Findley, Keisha, Foster, Brian, Gaskell, Jill, Glotzer, Dylan, Górecki, Paweł, Heitman, Joseph, Hesse, Cedar, Hori, Chiaki, Igarashi, Kiyohiko, Jurgens, Joel A., Kallen, Nathan, Kersten, Phil, Kohler, Annegret, Kües, Ursula, Kumar, T. K. Arun, Kuo, Alan, LaButti, Kurt, Larrondo, Luis F., Lindquist, Erika, Ling, Albee, Lombard, Vincent, Lucas, Susan, Lundell, Taina, Martin, Rachael, McLaughlin, David J., Morgenstern, Ingo, Morin, Emanuelle, Murat, Claude, Nagy, Laszlo G., Nolan, Matt, Ohm, Robin A., Patyshakuliyeva, Aleksandrina, Rokas, Antonis, Ruiz-Dueñas, Francisco J., Sabat, Grzegorz, Salamov, Asaf, Samejima, Masahiro, Schmutz, Jeremy, Slot, Jason C., St. John, Franz, Stenlid, Jan, Sun, Hui, Sun, Sheng, Syed, Khajamohiddin, Tsang, Adrian, Wiebenga, Ad, Young, Darcy, Pisabarro, Antonio, Eastwood, Daniel C., Martin, Francis, Cullen, Dan, Grigoriev, Igor V., and Hibbett, David S.

Published
2012
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55. Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida

Author

40627634, 50323746, Kamikawa, Ryoma, Mochizuki, Takako, Sakamoto, Mika, Tanizawa, Yasuhiro, Nakayama, Takuro, Onuma, Ryo, Cenci, Ugo, Moog, Daniel, Speak, Samuel, Sarkozi, Krisztina, Toseland, Andrew, van Oosterhout, Cock, Oyama, Kaori, Kato, Misako, Kume, Keitaro, Kayama, Motoki, Azuma, Tomonori, Ishii, Ken-ichiro, Miyashita, Hideaki, Henrissat, Bernard, Lombard, Vincent, Win, Joe, Kamoun, Sophien, Kashiyama, Yuichiro, Mayama, Shigeki, Miyagishima, Shin-ya, Tanifuji, Goro, Mock, Thomas, Nakamura, Yasukazu, 40627634, 50323746, Kamikawa, Ryoma, Mochizuki, Takako, Sakamoto, Mika, Tanizawa, Yasuhiro, Nakayama, Takuro, Onuma, Ryo, Cenci, Ugo, Moog, Daniel, Speak, Samuel, Sarkozi, Krisztina, Toseland, Andrew, van Oosterhout, Cock, Oyama, Kaori, Kato, Misako, Kume, Keitaro, Kayama, Motoki, Azuma, Tomonori, Ishii, Ken-ichiro, Miyashita, Hideaki, Henrissat, Bernard, Lombard, Vincent, Win, Joe, Kamoun, Sophien, Kashiyama, Yuichiro, Mayama, Shigeki, Miyagishima, Shin-ya, Tanifuji, Goro, Mock, Thomas, and Nakamura, Yasukazu

Abstract

Secondary loss of photosynthesis is observed across almost all plastid-bearing branches of the eukaryotic tree of life. However, genome-based insights into the transition from a phototroph into a secondary heterotroph have so far only been revealed for parasitic species. Free-living organisms can yield unique insights into the evolutionary consequence of the loss of photosynthesis, as the parasitic lifestyle requires specific adaptations to host environments. Here, we report on the diploid genome of the free-living diatom Nitzschia putrida (35 Mbp), a nonphotosynthetic osmotroph whose photosynthetic relatives contribute ca. 40% of net oceanic primary production. Comparative analyses with photosynthetic diatoms and heterotrophic algae with parasitic lifestyle revealed that a combination of gene loss, the accumulation of genes involved in organic carbon degradation, a unique secretome, and the rapid divergence of conserved gene families involved in cell wall and extracellular metabolism appear to have facilitated the lifestyle of a free-living secondary heterotroph.

Published
2022

56. Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota

Author

Ostrowski, Matthew P., La Rosa, Sabina Leanti, Kunath, Benoit J., Robertson, Andrew, Pereira, Gabriel, Hagen, Live H., Varghese, Neha J., Qiu, Ling, Yao, Tianming, Flint, Gabrielle, Li, James, McDonald, Sean P., Buttner, Duna, Pudlo, Nicholas A., Schnizlein, Matthew K., Young, Vincent B., Brumer, Harry, Schmidt, Thomas M., Terrapon, Nicolas, Lombard, Vincent, Henrissat, Bernard, Hamaker, Bruce, Eloe-Fadrosh, Emiley A., Tripathi, Ashootosh, Pope, Phillip B., Martens, Eric C., Ostrowski, Matthew P., La Rosa, Sabina Leanti, Kunath, Benoit J., Robertson, Andrew, Pereira, Gabriel, Hagen, Live H., Varghese, Neha J., Qiu, Ling, Yao, Tianming, Flint, Gabrielle, Li, James, McDonald, Sean P., Buttner, Duna, Pudlo, Nicholas A., Schnizlein, Matthew K., Young, Vincent B., Brumer, Harry, Schmidt, Thomas M., Terrapon, Nicolas, Lombard, Vincent, Henrissat, Bernard, Hamaker, Bruce, Eloe-Fadrosh, Emiley A., Tripathi, Ashootosh, Pope, Phillip B., and Martens, Eric C.

Abstract

Processed foods often include food additives such as xanthan gum, a complex polysaccharide with unique rheological properties, that has established widespread use as a stabilizer and thickening agent. Xanthan gum’s chemical structure is distinct from those of host and dietary polysaccharides that are more commonly expected to transit the gastrointestinal tract, and little is known about its direct interaction with the gut microbiota, which plays a central role in digestion of other dietary fibre polysaccharides. Here we show that the ability to digest xanthan gum is common in human gut microbiomes from industrialized countries and appears contingent on a single uncultured bacterium in the family Ruminococcaceae. Our data reveal that this primary degrader cleaves the xanthan gum backbone before processing the released oligosaccharides using additional enzymes. Some individuals harbour Bacteroides intestinalis that is incapable of consuming polymeric xanthan gum but grows on oligosaccharide products generated by the Ruminococcaceae. Feeding xanthan gum to germfree mice colonized with a human microbiota containing the uncultured Ruminococcaceae supports the idea that the additive xanthan gum can drive expansion of the primary degrader Ruminococcaceae, along with exogenously introduced B. intestinalis. Our work demonstrates the existence of a potential xanthan gum food chain involving at least two members of different phyla of gut bacteria and provides an initial framework for understanding how widespread consumption of a recently introduced food additive influences human microbiomes.

Published
2022

57. The carbohydrate-active enzyme database: functions and literature

Author

Drula, Elodie, Garron, Marie Line, Dogan, Suzan, Lombard, Vincent, Henrissat, Bernard, Terrapon, Nicolas, Drula, Elodie, Garron, Marie Line, Dogan, Suzan, Lombard, Vincent, Henrissat, Bernard, and Terrapon, Nicolas

Abstract

Thirty years have elapsed since the emergence of the classification of carbohydrate-active enzymes in sequence-based families that became the CAZy database over 20 years ago, freely available for browsing and download at www.cazy.org. In the era of large scale sequencing and high-throughput Biology, it is important to examine the position of this specialist database that is deeply rooted in human curation. The three primary tasks of the CAZy curators are (i) to maintain and update the family classification of this class of enzymes, (ii) to classify sequences newly released by GenBank and the Protein Data Bank and (iii) to capture and present functional information for each family. The CAZy website is updated once a month. Here we briefly summarize the increase in novel families and the annotations conducted during the last 8 years. We present several important changes that facilitate taxonomic navigation, and allow to download the entirety of the annotations. Most importantly we highlight the considerable amount of work that accompanies the analysis and report of biochemical data from the literature.

Published
2022

58. Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida

Author

Kamikawa, Ryoma, primary, Mochizuki, Takako, additional, Sakamoto, Mika, additional, Tanizawa, Yasuhiro, additional, Nakayama, Takuro, additional, Onuma, Ryo, additional, Cenci, Ugo, additional, Moog, Daniel, additional, Speak, Samuel, additional, Sarkozi, Krisztina, additional, Toseland, Andrew, additional, van Oosterhout, Cock, additional, Oyama, Kaori, additional, Kato, Misako, additional, Kume, Keitaro, additional, Kayama, Motoki, additional, Azuma, Tomonori, additional, Ishii, Ken-ichiro, additional, Miyashita, Hideaki, additional, Henrissat, Bernard, additional, Lombard, Vincent, additional, Win, Joe, additional, Kamoun, Sophien, additional, Kashiyama, Yuichiro, additional, Mayama, Shigeki, additional, Miyagishima, Shin-ya, additional, Tanifuji, Goro, additional, Mock, Thomas, additional, and Nakamura, Yasukazu, additional

Published
2022
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60. RETRACTED ARTICLE: Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition

Author

Million, Matthieu, Tidjani Alou, Maryam, Khelaifia, Saber, Bachar, Dipankar, Lagier, Jean-Christophe, Dione, Niokhor, Brah, Souleymane, Hugon, Perrine, Lombard, Vincent, Armougom, Fabrice, Fromonot, Julien, Robert, Catherine, Michelle, Caroline, Diallo, Aldiouma, Fabre, Alexandre, Guieu, Régis, Sokhna, Cheikh, Henrissat, Bernard, Parola, Philippe, and Raoult, Didier

Published
2016
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66. Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related microalgae

Author

Dorrell, Richard G., primary, Kuo, Alan, additional, Füssy, Zoltan, additional, Richardson, Elisabeth, additional, Salamov, Asaf, additional, Zarevski, Nikola, additional, Freyria, Nastasia J., additional, Ibarbalz, Federico M., additional, Jenkins, Jerry, additional, Karlusich, Juan Jose Pierella, additional, Steindorff, Andrei Stecca, additional, Edgar, Robyn E., additional, Handley, Lori, additional, Lail, Kathleen, additional, Lipzen, Anna, additional, Lombard, Vincent, additional, McFarlane, John, additional, Nef, Charlotte, additional, Novák Vanclová, Anna M.G., additional, Peng, Yi, additional, Plott, Chris, additional, Potvin, Marianne, additional, Vieira, Fabio Rocha Jimenez, additional, Barry, Kerrie, additional, Dacks, Joel B., additional, de Vargas, Colomban, additional, Henrissat, Bernard, additional, Pelletier, Eric, additional, Schmutz, Jeremy, additional, Wincker, Patrick, additional, Bowler, Chris, additional, Grigoriev, Igor V., additional, and Lovejoy, Connie, additional

Published
2021
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67. The Food Additive Xanthan Gum Drives Adaptation of the Human Gut Microbiota

Author

Martens, Eric, primary, Ostrowski, Matthew, additional, Rosa, Sabina La, additional, Kunath, Benoit, additional, Robertson, Andrew, additional, Pereira, Gabriel, additional, Hagan, Live, additional, Varghese, Neha, additional, Qiu, Ling, additional, Yao, Tianming, additional, Flint, Gabrielle, additional, Li, James, additional, McDonald, Sean, additional, Martin, Duna, additional, Pudlo, Nicholas, additional, Schnizlein, Matthew, additional, Brumer, Harry, additional, Schmidt, Thomas, additional, Terrapon, Nicolas, additional, Lombard, Vincent, additional, Henrissat, Bernard, additional, Hamaker, Bruce, additional, Eloe-Fadrosh, Emiley, additional, Tripathi, Ashootosh, additional, and Young, Vincent, additional

Published
2021
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68. The Food Additive Xanthan Gum Drives Adaptation of the Human Gut Microbiota

Author

Ostrowski, Matthew P., primary, La Rosa, Sabina Leanti, additional, Kunath, Benoit J., additional, Robertson, Andrew, additional, Pereira, Gabriel, additional, Hagen, Live H., additional, Varghese, Neha J., additional, Qiu, Ling, additional, Yao, Tianming, additional, Flint, Gabrielle, additional, Li, James, additional, McDonald, Sean, additional, Buttner, Duna, additional, Pudlo, Nicholas A., additional, Schnizlein, Matthew K., additional, Young, Vincent B., additional, Brumer, Harry, additional, Schmidt, Thomas, additional, Terrapon, Nicolas, additional, Lombard, Vincent, additional, Henrissat, Bernard, additional, Hamaker, Bruce, additional, Eloe-Fadrosh, Emiley A, additional, Tripathi, Ashootosh, additional, Pope, Phillip B., additional, and Martens, Eric, additional

Published
2021
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69. Density of Myrmica nests in bogs: the case of the Jouvion bog (Massif central, France)

Author

Belenguier, Luc, Kreder², Marine, Lombard, Vincent, Poussin, Mathilde, Galkovsky, Christophe, Maison du Parc, Exploitant agricole, Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Photographe, and Association Antarea

Subjects
The Auvergne region, Myrmica, Bogs, Ants, Nids, [SDE]Environmental Sciences, Density, Densité, Nests, Fourmis, Tourbières, Auvergne
Abstract

International audience; As part of a study to evaluate the conservation status of Maculinea alcon alcon stations inthe Regional natural Park of the Volcanoes of Auvergne, a study was conducted in July 2015to evaluate the density of host ant nests (Myrmica sp.) on the Jouvion peat bog. The studymethod consisted of two phases: trapping using 249 baits distributed within grids having 16m²meshes and then a search for anthills within grids where Myrmica sp. had been found in theprevious phase. A total of 194 Myrmica nests were detected. The results provide data in termsof nest density for three species: Myrmica rubra, Myrmica ruginodis and Myrmica scabrinodis, withan average of 2.13, 0.65 and 2.08 nests per 100 m2 respectively. These densities seem low incomparison with existing bibliographic data. However, the heterogeneity of inventory and densityestimation methods complicates the comparison between studies. Our results indicate that inJouvion, the overlap between the host plants and the host anthills of Maculinea alcon alcon is low,which could at least partly explain the decline of the species observed on this site since 2011.; Dans le cadre d’un travail visant à évaluer l’état de conservation des stations de Maculinea alconalcon dans le Parc naturel régional des Volcans d’Auvergne, une étude a été menée en juillet 2015pour évaluer la densité de nids de fourmis hôtes (Myrmica sp.) sur la tourbière de Jouvion. La méthoded’étude retenue comportait deux phases : un piégeage à l’aide de 249 appâts distribués au sein degrilles possédant des mailles de 16m² puis une recherche des fourmilières au sein des mailles oùdes Myrmica sp. avaient été trouvées lors de la phase précédente. Un total de 194 nids de Myrmicaa été détecté. Les résultats obtenus apportent des éléments en termes de densité de nids pourtrois espèces : Myrmica rubra, Myrmica ruginodis et Myrmica scabrinodis, avec respectivement unemoyenne de 2,13, 0,65 et 2,08 nids par 100 m2. Ces densités semblent faibles en comparaison desdonnées bibliographiques existantes. L’hétérogénéité des méthodes d’inventaires et d’estimation desdensités complique toutefois la comparaison entre études. Nos résultats indiquent qu’à Jouvion, lechevauchement entre les plantes hôtes et les fourmilières hôtes de Maculinea alcon alcon est faible,ce qui pourrait expliquer au moins en partie le déclin de l’espèce observé sur ce site depuis 2011.

Published
2020
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70. Larvae of longhorned beetles (Coleoptera; Cerambycidae) have evolved a diverse and phylogenetically conserved array of plant cell wall degrading enzymes

Author

Shin, Na Ra, primary, Shin, Seunggwan, additional, Okamura, Yu, additional, Kirsch, Roy, additional, Lombard, Vincent, additional, Svacha, Petr, additional, Denux, Olivier, additional, Augustin, Sylvie, additional, Henrissat, Bernard, additional, McKenna, Duane D., additional, and Pauchet, Yannick, additional

Published
2021
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71. Gut microbiome of capybara, the Amazon master of the grasses, harbors unprecedented enzymatic strategies for plant glycans breakdown

Author

Cabral, Lucelia, primary, Persinoti, Gabriela F., additional, Paixao, Douglas A. A., additional, Martins, Marcele P., additional, Chinaglia, Mariana, additional, Domingues, Mariane N., additional, Morais, Mariana A. B., additional, Sforca, Mauricio L., additional, Pirolla, Renan A. S., additional, Generoso, Wesley C., additional, Santos, Clelton A., additional, Maciel, Lucas F., additional, Terrapon, Nicolas, additional, Lombard, Vincent, additional, Henrissat, Bernard, additional, and Murakami, Mario T., additional

Published
2021
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72. Global and temporal state of the human gut microbiome in health and disease

Author

Shoaie, Saeed, primary, Lee, Sunjae, additional, Almeida, Mathieu, additional, Bidkhori, Gholamreza, additional, Pons, Nicolas, additional, Onate, Florian, additional, Chatelier, Emmanuelle, additional, Begum, Neelu, additional, Proffitt, Ceri, additional, Rosário, Dorinês, additional, Vaga, Stefania, additional, Park, Junseok, additional, von Feilitzen, Kalle, additional, Johansson, Fredric, additional, Meslier, Victoria, additional, Harzandi, Azadeh, additional, Etienne-Mesmin, Lucie, additional, Edwards, Lindsey, additional, Lombard, Vincent, additional, Gauthier, Franck, additional, Steves, Claire, additional, Gomez-Cabrero, David, additional, Henrissat, Bernard, additional, Lee, Doheon, additional, Shawcross, Debbie, additional, Blanquet-Diot, Stéphanie, additional, Proctor, Gordon, additional, Engstrand, Lars, additional, Mardinoglu, Adil, additional, Nielsen, Jens, additional, Ehrlich, Stanislav, additional, and Uhlen, Mathias, additional

Published
2021
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75. The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

Author

Floudas, Dimitrios, Binder, Manfred, Riley, Robert, Barry, Kerrie, Blanchette, Robert A., Henrissat, Bernard, Martínez, Angel T., Otillar, Robert, Spatafora, Joseph W., Yadav, Jagjit S., Aerts, Andrea, Benoit, Isabelle, Boyd, Alex, Carlson, Alexis, Copeland, Alex, Coutinho, Pedro M., de Vries, Ronald P., Ferreira, Patricia, Findley, Keisha, Foster, Brian, Gaskell, Jill, Glotzer, Dylan, Górecki, Paweł, Heitman, Joseph, Hesse, Cedar, Hori, Chiaki, Igarashi, Kiyohiko, Jurgens, Joel A., Kallen, Nathan, Kersten, Phil, Kohler, Annegret, Kües, Ursula, Kumar, Arun T. K., Kuo, Alan, LaButti, Kurt, Larrondo, Luis F., Lindquist, Erika, Ling, Albee, Lombard, Vincent, Lucas, Susan, Lundell, Taina, Martin, Rachael, McLaughlin, David J., Morgenstern, Ingo, Morin, Emanuelle, Murat, Claude, Nagy, Laszlo G., Nolan, Matt, Ohm, Robin A., Patyshakuliyeva, Aleksandrina, Rokas, Antonis, Ruiz-Dueñas, Francisco J., Sabat, Grzegorz, Salamov, Asaf, Samejima, Masahiro, Schmutz, Jeremy, Slot, Jason C., John, Franz St., Stenlid, Jan, Sun, Hui, Sun, Sheng, Syed, Khajamohiddin, Tsang, Adrian, Wiebenga, Ad, Young, Darcy, Pisabarro, Antonio, Eastwood, Daniel C., Martin, Francis, Cullen, Dan, Grigoriev, Igor V., and Hibbett, David S.

Published
2012
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76. Genome evolution of a non-parasitic secondary heterotroph, the diatom Nitzschia putrida

Author

Kamikawa, Ryoma, primary, Mochizuki, Takako, additional, Sakamoto, Mika, additional, Tanizawa, Yasuhiro, additional, Nakayama, Takuro, additional, Onuma, Ryo, additional, Cenci, Ugo, additional, Moog, Daniel, additional, Speak, Samuel, additional, Sarkozi, Krisztina, additional, Toseland, Andrew, additional, van Oosterhout, Cock, additional, Oyama, Kaori, additional, Kato, Misako, additional, Kume, Keitaro, additional, Kayama, Motoki, additional, Azuma, Tomonori, additional, Ishii, Ken-ichiro, additional, Miyashita, Hideaki, additional, Henrissat, Bernard, additional, Lombard, Vincent, additional, Win, Joe, additional, Kamoun, Sophien, additional, Kashiyama, Yuichiro, additional, Mayama, Shigeki, additional, Miyagishima, Shin-ya, additional, Tanifuji, Goro, additional, Mock, Thomas, additional, and Nakamura, Yasukazu, additional

Published
2021
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77. Gut Microbiome of the Amazon Master of the Grasses Harbors Unprecedented Enzymatic Strategies for Plant Glycans Breakdown

Author

Cabral, Lucelia, primary, Persinoti, Gabriela F, additional, Paixao, Douglas A, additional, Martins, Marcele P, additional, Chinaglia, Mariana, additional, Domingues, Mariane N, additional, Morais, Mariana AB, additional, Sforca, Mauricio L, additional, Pirolla, Renan A. S., additional, Generoso, Wesley C, additional, Santos, Clelton A, additional, Maciel, Lucas F, additional, terrapon, Nicolas, additional, Lombard, Vincent, additional, Henrissat, Bernard, additional, and Murakami, Mario, additional

Published
2020
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78. α-Galactosidase and Sucrose-Kinase Relationships in a Bi-functional AgaSK Enzyme Produced by the Human Gut Symbiont Ruminococcus gnavus E1

Author

Lafond, Mickael, primary, Tauzin, Alexandra S., additional, Bruel, Laetitia, additional, Laville, Elisabeth, additional, Lombard, Vincent, additional, Esque, Jérémy, additional, André, Isabelle, additional, Vidal, Nicolas, additional, Pompeo, Frédérique, additional, Quinson, Nathalie, additional, Perrier, Josette, additional, Fons, Michel, additional, Potocki-Veronese, Gabrielle, additional, and Giardina, Thierry, additional

Published
2020
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79. Discovery of fungal oligosaccharide-oxidising flavo-enzymes with previously unknown substrates, redox-activity profiles and interplay with LPMOs

Author

Momeni, Majid Haddad, primary, Fredslund, Folmer, additional, Bissaro, Bastien, additional, Raji, Olanrewaju, additional, Vuong, Thu, additional, Meier, Sebastian, additional, Nielsen, Tine, additional, Lombard, Vincent, additional, Guigliarelli, Bruno, additional, Biaso, Frédéric, additional, Haon, Mireille, additional, Grisel, Sacha, additional, Henrissat, Bernard, additional, Welner, Ditte, additional, Master, Emma, additional, Berrin, Jean-Guy, additional, and Hachem, Maher Abou, additional

Published
2020
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80. Analysis of the diversity of the glycoside hydrolase family 130 in mammal gut microbiomes reveals a novel mannoside-phosphorylase function

Author

Li, Ao, primary, Laville, Elisabeth, additional, Tarquis, Laurence, additional, Lombard, Vincent, additional, Ropartz, David, additional, Terrapon, Nicolas, additional, Henrissat, Bernard, additional, Guieysse, David, additional, Esque, Jeremy, additional, Durand, Julien, additional, Morgavi, Diego P., additional, and Potocki-Veronese, Gabrielle, additional

Published
2020
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81. Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

Author

Hagen, Live H., primary, Brooke, Charles G., additional, Shaw, Claire A., additional, Norbeck, Angela D., additional, Piao, Hailan, additional, Arntzen, Magnus Ø., additional, Olson, Heather M., additional, Copeland, Alex, additional, Isern, Nancy, additional, Shukla, Anil, additional, Roux, Simon, additional, Lombard, Vincent, additional, Henrissat, Bernard, additional, O’Malley, Michelle A., additional, Grigoriev, Igor V., additional, Tringe, Susannah G., additional, Mackie, Roderick I., additional, Pasa-Tolic, Ljiljana, additional, Pope, Phillip B., additional, and Hess, Matthias, additional

Published
2020
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82. A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment

Author

Li, Junhua, primary, Zhong, Huanzi, primary, Ramayo-Caldas, Yuliaxis, primary, Terrapon, Nicolas, primary, Lombard, Vincent, primary, Potocki-Veronese, Gabrielle, primary, Estellé, Jordi, primary, Popova, Milka, primary, Yang, Ziyi, primary, Zhang, Hui, primary, Li, Fang, primary, Tang, Shanmei, primary, Yang, Fangming, primary, Chen, Weineng, primary, Chen, Bing, primary, Li, Jiyang, primary, Guo, Jing, primary, Martin, Cécile, primary, Maguin, Emmanuelle, primary, Xu, Xun, primary, Yang, Huanming, primary, Wang, Jian, primary, Madsen, Lise, primary, Kristiansen, Karsten, primary, Henrissat, Bernard, primary, Ehrlich, Stanislav D, primary, and Morgavi, Diego P, primary

Published
2020
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84. Engineered fibre enables targeted activation of butyrate-producing microbiota in the distal gut

Author

Michalak, Leszek, Gaby, John Christian, Lagos, Leidy, Rosa, Sabina Leanti La, Terrapon, Nicolas, Lombard, Vincent, Henrissat, Bernard, Arntzen, Magnus Ø., Hagen, Live Heldal, Dröge, Johannes, Øverland, Margareth, Pope, Phillip B., and Westereng, Bjørge

Abstract

Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have engineered an acetylated galactoglucomannan (AcGGM) fibre from spruce trees to match unique enzymatic capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut commensals. The accuracy of AcGGM was tested in an applied pig feeding trial, which resolved 355 metagenome-assembled genomes together with quantitative metaproteomes. In AcGGM-fed pigs, both target populations differentially expressed AcGGM-specific polysaccharide utilization loci, including novel, mannan-specific esterases that are critical to its deconstruction. We additionally observed a “butterfly effect”, whereby numerous metabolic changes and interdependent cross-feeding pathways were detected in neighboring non-mannolytic populations that produce short-chain fatty acids. Our findings show that intricate structural features and acetylation patterns of dietary fibre can be customized to specific bacterial populations, with the possibility to create greater modulatory effects at large.

Published
2019
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85. A subfamily roadmap of the evolutionarily diverse glycoside hydrolase family 16 (GH16)GH16 subfamilies

Author

Viborg, Alexander Holm, Terrapon, Nicolas, Lombard, Vincent, Michel, Gurvan, Czjzek, Mirjam, Henrissat, Bernard, and Brumer, Harry

Abstract

Glycoside hydrolase family (GH) 16 comprises a large and taxonomically diverse family of glycosidases and transglycosidases that adopt a common β-jelly-roll fold and are active on a range of terrestrial and marine polysaccharides. Presently, broadly insightful sequence–function correlations in GH16 are hindered by a lack of a systematic subfamily structure. To fill this gap, we have used a highly scalable protein sequence similarity network analysis to delineate nearly 23,000 GH16 sequences into 23 robust subfamilies, which are strongly supported by hidden Markov model and maximum likelihood molecular phylogenetic analyses. Subsequent evaluation of over 40 experimental three-dimensional structures has highlighted key tertiary structural differences, predominantly manifested in active-site loops, that dictate substrate specificity across the GH16 evolutionary landscape. As for other large GH families (i.e. GH5, GH13, and GH43), this new subfamily classification provides a roadmap for functional glycogenomics that will guide future bioinformatics and experimental structure–function analyses. The GH16 subfamily classification is publicly available in the CAZy database. The sequence similarity network workflow used here, SSNpipe, is freely available from GitHub.

Published
2019

86. EMBL Nucleotide Sequence Database in 2006

Author

Kulikova, Tamara, Akhtar, Ruth, Aldebert, Philippe, Althorpe, Nicola, Andersson, Mikael, Baldwin, Alastair, Bates, Kirsty, Bhattacharyya, Sumit, Bower, Lawrence, Browne, Paul, Castro, Matias, Cochrane, Guy, Duggan, Karyn, Eberhardt, Ruth, Faruque, Nadeem, Hoad, Gemma, Kanz, Carola, Lee, Charles, Leinonen, Rasko, Lin, Quan, Lombard, Vincent, Lopez, Rodrigo, Lorenc, Dariusz, McWilliam, Hamish, Mukherjee, Gaurab, Nardone, Francesco, Pastor, Maria Pilar Garcia, Plaister, Sheila, Sobhany, Siamak, Stoehr, Peter, Vaughan, Robert, Wu, Dan, Zhu, Weimin, and Apweiler, Rolf

Published
2007

87. EMBL Nucleotide Sequence Database: developments in 2005

Author

Cochrane, Guy, Aldebert, Philippe, Althorpe, Nicola, Andersson, Mikael, Baker, Wendy, Baldwin, Alastair, Bates, Kirsty, Bhattacharyya, Sumit, Browne, Paul, van den Broek, Alexandra, Castro, Matias, Duggan, Karyn, Eberhardt, Ruth, Faruque, Nadeem, Gamble, John, Kanz, Carola, Kulikova, Tamara, Lee, Charles, Leinonen, Rasko, Lin, Quan, Lombard, Vincent, Lopez, Rodrigo, McHale, Michelle, McWilliam, Hamish, Mukherjee, Gaurab, Nardone, Francesco, Pastor, Maria Pilar Garcia, Sobhany, Siamak, Stoehr, Peter, Tzouvara, Katerina, Vaughan, Robert, Wu, Dan, Zhu, Weimin, and Apweiler, Rolf

Published
2006

88. Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Author

Molecular Microbiology, Sub Molecular Microbiology, Miyauchi, Shingo, Kiss, Enikő, Kuo, Alan, Drula, Elodie, Kohler, Annegret, Sánchez-García, Marisol, Morin, Emmanuelle, Andreopoulos, Bill, Barry, Kerrie W., Bonito, Gregory, Buée, Marc, Carver, Akiko, Chen, Cindy, Cichocki, Nicolas, Clum, Alicia, Culley, David, Crous, Pedro W., Fauchery, Laure, Girlanda, Mariangela, Hayes, Richard D., Kéri, Zsófia, LaButti, Kurt, Lipzen, Anna, Lombard, Vincent, Magnuson, Jon, Maillard, François, Murat, Claude, Nolan, Matt, Ohm, Robin A., Pangilinan, Jasmyn, Pereira, Maíra de Freitas, Perotto, Silvia, Peter, Martina, Pfister, Stephanie, Riley, Robert, Sitrit, Yaron, Stielow, J. Benjamin, Szöllősi, Gergely, Žifčáková, Lucia, Štursová, Martina, Spatafora, Joseph W., Tedersoo, Leho, Vaario, Lu Min, Yamada, Akiyoshi, Yan, Mi, Wang, Pengfei, Xu, Jianping, Bruns, Tom, Baldrian, Petr, Vilgalys, Rytas, Dunand, Christophe, Henrissat, Bernard, Grigoriev, Igor V., Hibbett, David, Nagy, László G., Martin, Francis M., Molecular Microbiology, Sub Molecular Microbiology, Miyauchi, Shingo, Kiss, Enikő, Kuo, Alan, Drula, Elodie, Kohler, Annegret, Sánchez-García, Marisol, Morin, Emmanuelle, Andreopoulos, Bill, Barry, Kerrie W., Bonito, Gregory, Buée, Marc, Carver, Akiko, Chen, Cindy, Cichocki, Nicolas, Clum, Alicia, Culley, David, Crous, Pedro W., Fauchery, Laure, Girlanda, Mariangela, Hayes, Richard D., Kéri, Zsófia, LaButti, Kurt, Lipzen, Anna, Lombard, Vincent, Magnuson, Jon, Maillard, François, Murat, Claude, Nolan, Matt, Ohm, Robin A., Pangilinan, Jasmyn, Pereira, Maíra de Freitas, Perotto, Silvia, Peter, Martina, Pfister, Stephanie, Riley, Robert, Sitrit, Yaron, Stielow, J. Benjamin, Szöllősi, Gergely, Žifčáková, Lucia, Štursová, Martina, Spatafora, Joseph W., Tedersoo, Leho, Vaario, Lu Min, Yamada, Akiyoshi, Yan, Mi, Wang, Pengfei, Xu, Jianping, Bruns, Tom, Baldrian, Petr, Vilgalys, Rytas, Dunand, Christophe, Henrissat, Bernard, Grigoriev, Igor V., Hibbett, David, Nagy, László G., and Martin, Francis M.

Published
2020

89. A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment

Author

Li, Junhua, Zhong, Huanzi, Ramayo-Caldas, Yuliaxis, Terrapon, Nicolas, Lombard, Vincent, Potocki-Veronese, Gabrielle, Estellé, Jordi, Popova, Milka, Yang, Ziyi, Zhang, Hui, Li, Fang, Tang, Shanmei, Yang, Fangming, Chen, Weineng, Chen, Bing, Li, Jiyang, Guo, Jing, Martin, Cécile, Maguin, Emmanuelle, Xu, Xun, Yang, Huanming, Wang, Jian, Madsen, Lise, Kristiansen, Karsten, Henrissat, Bernard, Ehrlich, Stanislav D., Morgavi, Diego P., Li, Junhua, Zhong, Huanzi, Ramayo-Caldas, Yuliaxis, Terrapon, Nicolas, Lombard, Vincent, Potocki-Veronese, Gabrielle, Estellé, Jordi, Popova, Milka, Yang, Ziyi, Zhang, Hui, Li, Fang, Tang, Shanmei, Yang, Fangming, Chen, Weineng, Chen, Bing, Li, Jiyang, Guo, Jing, Martin, Cécile, Maguin, Emmanuelle, Xu, Xun, Yang, Huanming, Wang, Jian, Madsen, Lise, Kristiansen, Karsten, Henrissat, Bernard, Ehrlich, Stanislav D., and Morgavi, Diego P.

Abstract

BACKGROUND: The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen. RESULTS: Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e., 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes. CONCLUSIONS: These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.

Published
2020

90. The EMBL Nucleotide Sequence Database

Author

Kanz, Carola, Aldebert, Philippe, Althorpe, Nicola, Baker, Wendy, Baldwin, Alastair, Bates, Kirsty, Browne, Paul, van den Broek, Alexandra, Castro, Matias, Cochrane, Guy, Duggan, Karyn, Eberhardt, Ruth, Faruque, Nadeem, Gamble, John, Diez, Federico Garcia, Harte, Nicola, Kulikova, Tamara, Lin, Quan, Lombard, Vincent, Lopez, Rodrigo, Mancuso, Renato, McHale, Michelle, Nardone, Francesco, Silventoinen, Ville, Sobhany, Siamak, Stoehr, Peter, Tuli, Mary Ann, Tzouvara, Katerina, Vaughan, Robert, Wu, Dan, Zhu, Weimin, and Apweiler, Rolf

Published
2005

92. The EMBL Nucleotide Sequence Database

Author

Kulikova, Tamara, Aldebert, Philippe, Althorpe, Nicola, Baker, Wendy, Bates, Kirsty, Browne, Paul, van den Broek, Alexandra, Cochrane, Guy, Duggan, Karyn, Eberhardt, Ruth, Faruque, Nadeem, Garcia-Pastor, Maria, Harte, Nicola, Kanz, Carola, Leinonen, Rasko, Lin, Quan, Lombard, Vincent, Lopez, Rodrigo, Mancuso, Renato, McHale, Michelle, Nardone, Francesco, Silventoinen, Ville, Stoehr, Peter, Stoesser, Guenter, Tuli, Mary Ann, Tzouvara, Katerina, Vaughan, Robert, Wu, Dan, Zhu, Weimin, and Apweiler, Rolf

Published
2004

93. The EMBL Nucleotide Sequence Database: major new developments

Author

Stoesser, Guenter, Baker, Wendy, van den Broek, Alexandra, Garcia-Pastor, Maria, Kanz, Carola, Kulikova, Tamara, Leinonen, Rasko, Lin, Quan, Lombard, Vincent, Lopez, Rodrigo, Mancuso, Renato, Nardone, Francesco, Stoehr, Peter, Tuli, Mary Ann, Tzouvara, Katerina, and Vaughan, Robert

Published
2003

94. The EMBL Nucleotide Sequence Database

Author

Stoesser, Guenter, Baker, Wendy, van den Broek, Alexandra, Camon, Evelyn, Garcia-Pastor, Maria, Kanz, Carola, Kulikova, Tamara, Leinonen, Rasko, Lin, Quan, Lombard, Vincent, Lopez, Rodrigo, Redaschi, Nicole, Stoehr, Peter, Tuli, Mary Ann, Tzouvara, Katerina, and Vaughan, Robert

Published
2002

95. A subfamily roadmap for functional glycogenomics of the evolutionarily diverse Glycoside Hydrolase Family 16 (GH16)

Author

Viborg, Alexander Holm, Terrapon, Nicolas, Lombard, Vincent, Michel, Gurvan, Czjzek, Mirjam, Henrissat, Bernard, Brumer, Harry, University of British Columbia (UBC), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Genome Canada 10405 Ontario Genomics Genome Quebec Genome British Columbia French National Research Agency (ANR) ANR-14-CE06-0017 ANR-17-CE20-0032 Novo Nordisk Foundation French National Research Agency (ANR) ANR-10-BTBR-04, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), and ANR-17-CE20-0032,PULmarin,Criblage fonctionnel des loci impliqués dans la dégradation des polysaccharides marins(2017)

Subjects
phylogenetics, carbohydrate-active enzymes (CAZymes), [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], beta-jelly-roll fold, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], beta-sandwich, sequence similarity networks (SSN), structural biology, glycoside hydrolase, Hidden Markov Model (HMM), protein evolution, enzyme structure
Abstract

International audience; Glycoside Hydrolase Family 16 (GH16) comprises a large and taxonomically diverse family of glycosidases and transglycosidases that adopt a common beta-jelly-roll fold and are active on a range of terrestrial and marine polysaccharides. Presently, broadly insightful sequence-function correlations in GH16 are hindered by a lack of a systematic subfamily structure. To fill this gap, we have used a highly scalable protein Sequence Similarity Network (SSN) analysis to delineate nearly 23,000 GH16 sequences into 23 robust subfamilies, which are strongly supported by Hidden Markov Model (HMM) and Maximum Likelihood (ML) molecular phylogenetic analyses. Subsequent evaluation of over 40 experimental three-dimensional structures has highlighted key tertiary structural differences, predominantly manifested in active-site loops, which dictate substrate specificity across the GH16 evolutionary landscape. As for other large GH families (i.e. GH5, GH13, and GH43), this new subfamily classification provides a roadmap for functional glycogenomics that will guide future bioinformatics and experimental structure-function analyses. The GH16 subfamily classification is publicly available in the CAZy database via URL www.cazy.org/GH16.html. The SSN workflow used here is available via URL https://github.com/ahvdk/SSNpipe/.

Published
2019
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96. Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

Author

Seeleuthner, Yoann, Mondy, Samuel, Lombard, Vincent, Carradec, Quentin, Pelletier, Eric, Wessner, Marc, Leconte, Jade, Mangot, Jean-François, Poulain, Julie, Labadie, Karine, Logares, Ramiro, Sunagawa, Shinichi, de Berardinis, Véronique, Salanoubat, Marcel, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Pesant, Stéphane, Poulton, Nicole, Stepanauskas, Ramunas, Bork, Peer, Bowler, Chris, Hingamp, Pascal, Sullivan, Matthew, Iudicone, Daniele, Massana, Ramon, Aury, Jean-Marc, Henrissat, Bernard, Karsenti, Eric, Jaillon, Olivier, Sieracki, Mike, de Vargas, Colomban, Wincker, Patrick, Acinas, Silvia G., Boss, Emmanuel, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Karp-Boss, Lee, Krzic, Uros, Not, Fabrice, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Weissenbach, Jean, Velayoudon, Didier, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), European Molecular Biology Laboratory [Heidelberg] (EMBL), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), Department of Oceanography [Honolulu], University of Hawai‘i [Mānoa] (UHM), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Data Publisher for Earth and Environmental Science (PANGAEA), University of Bremen, Bigelow Laboratory for Ocean Sciences, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Ohio State University [Columbus] (OSU), Stazione Zoologica Anton Dohrn (SZN), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia, National Science Foundation [Arlington] (NSF), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), University of Maine, Department of Earth, Atmospheric and Planetary Sciences [MIT, Cambridge] (EAPS), Massachusetts Institute of Technology (MIT), Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), University College Dublin [Dublin] (UCD), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Université de Brest (UBO), DVIP Consulting, CNRS [GDR3280], European Molecular Biology Laboratory (EMBL), Genoscope/CEA, French Governement 'Investissement d'Avenir' programs Oceanomics [ANR-11-BTBR-0008], FRANCE GENOMIQUE [ANR-10-INBS-09], MEMO LIFE [ANR-10-LABX-54], PSL* Research University [ANR-11-IDEX-0001-02], Fund for Scientific Research-Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR [PHYTBACK/ANR-2010-1709-01, POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCS-GENM-217, ARA-GIRUS/ANR-09-PCS-GENM-218], EU FP7 [IHMS/HEALTH-F4-2010-261376], ERC Advanced Grant Award [294823], US NSF grant [DEB-1031049], FWO, BIO5, Biosphere 2, agnes b., Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L'Orient, EDF Foundation EDF Diversiterre, FRB, Prince Albert II de Monaco Foundation, ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), ANR-10-BLAN-1709,PHYTBACK,Rétroactions écologie-climat dues à l'évolution de la taille et de la forme du phytoplancton(2010), ANR-09-BLAN-0348,POSEIDON(2009), ANR-09-GENM-0031,PROMETHEUS,Approches génomiques pour l?analyse de la biodiversité fonctionnelle des protistes océaniques de l?expédition Tara-Oceans.(2009), ANR-09-GENM-0032,TARA-GIRUS,Inventaire et ressources génétiques de virus géants à ADN dans les milieux marins sur Tara-Oceans(2009), European Project: 287589,EC:FP7:KBBE,FP7-OCEAN-2011,MICRO B3(2012), European Project: 261376,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,IHMS(2011), European Project: 294823,EC:FP7:ERC,ERC-2011-ADG_20110310,DIATOMITE(2012), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Universités, Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Rega Institute for Medical Research, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris), ANR-11-BTBR-0008/11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-IDEX-0001-02/10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), ANR-09-BLAN-0348,POSEIDON,PrOtiSts EcologIcal bioDiversity in Tara-OceaNs(2009), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Hingamp, Pascal, Biotech - Bioressources - Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques - - OCEANOMICS2011 - ANR-11-BTBR-0008 - BTBR - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Initiative d'excellence - Paris Sciences et Lettres - - PSL2010 - ANR-10-IDEX-0001 - IDEX - VALID, BLANC - Rétroactions écologie-climat dues à l'évolution de la taille et de la forme du phytoplancton - - PHYTBACK2010 - ANR-10-BLAN-1709 - BLANC - VALID, Blanc - - POSEIDON2009 - ANR-09-BLAN-0348 - Blanc - VALID, Génomique et biotechnologies végétales - Approches génomiques pour l?analyse de la biodiversité fonctionnelle des protistes océaniques de l?expédition Tara-Oceans. - - PROMETHEUS2009 - ANR-09-GENM-0031 - GENOM-BTV - VALID, Génomique et biotechnologies végétales - Inventaire et ressources génétiques de virus géants à ADN dans les milieux marins sur Tara-Oceans - - TARA-GIRUS2009 - ANR-09-GENM-0032 - GENOM-BTV - VALID, Marine Microbial Biodiversity, Bioinformatics and Biotechnology - MICRO B3 - - EC:FP7:KBBE2012-01-01 - 2015-12-31 - 287589 - VALID, International Human Microbiome Standards - IHMS - - EC:FP7:HEALTH2011-02-01 - 2015-01-31 - 261376 - VALID, Genome-enabled dissection of marine diatom ecophysiology - DIATOMITE - - EC:FP7:ERC2012-06-01 - 2017-05-31 - 294823 - VALID, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Unité de Biologie du développement et biotechnologies (JOUY BIOLOG DEVELOP BIOTECHNOL), Institut National de la Recherche Agronomique (INRA), European Molecular Biology Laboratory, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Hawai'i [Honolulu] (UH), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR)

Subjects
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDE]Environmental Sciences, fungi, [SDV.BID]Life Sciences [q-bio]/Biodiversity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ComputingMilieux_MISCELLANEOUS, Article, [SDV.BID] Life Sciences [q-bio]/Biodiversity
Abstract

Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology., The biology of many marine protists, such as stramenopiles, remains obscure. Here, the authors exploit single-cell genomics and metagenomics to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles.

Published
2018
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98. Discovery of hyperstable carbohydrate‐active enzymes through metagenomics of extreme environments

Author

Strazzulli, Andrea, primary, Cobucci‐Ponzano, Beatrice, additional, Iacono, Roberta, additional, Giglio, Rosa, additional, Maurelli, Luisa, additional, Curci, Nicola, additional, Schiano‐di‐Cola, Corinna, additional, Santangelo, Annalisa, additional, Contursi, Patrizia, additional, Lombard, Vincent, additional, Henrissat, Bernard, additional, Lauro, Federico M., additional, Fontes, Carlos M.G.A., additional, and Moracci, Marco, additional

Published
2019
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99. Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut

Author

Michalak, Leszek, primary, Gaby, John Christian, additional, Lagos, Leidy, additional, La Rosa, Sabina Leanti, additional, Hvidsten, Torgeir R., additional, Tétard-Jones, Catherine, additional, Willats, William G.T., additional, Terrapon, Nicolas, additional, Lombard, Vincent, additional, Henrissat, Bernard, additional, Dröge, Johannes, additional, Arntzen, Magnus Ø., additional, Hagen, Live Heldal, additional, Øverland, Margareth, additional, Pope, Phillip B., additional, and Westereng, Bjørge, additional

Published
2019
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100. Gut microbiome contributions to altered metabolism in a pig model of undernutrition.

Author

Hao-Wei Chang, McNulty, Nathan P., Hibberd, Matthew C., O'Donnell, David, Jiye Cheng, Lombard, Vincent, Henrissat, Bernard, Ilkayeva, Olga, Muehlbauer, Michael J., Newgard, Christopher B., Barratt, Michael J., Xi Lin, Odle, Jack, and Gordon, Jeffrey I.

Subjects
GUT microbiome, METABOLIC models, SWINE breeding, SWINE farms, ANIMAL health, MALNUTRITION, ALTERNATIVE fuels
Abstract

The concept that gut microbiome-expressed functions regulate ponderal growth has important implications for infant and child health, as well as animal health. Using an intergenerational pig model of diet restriction (DR) that produces reduced weight gain, we developed a feature-selection algorithm to identify representative characteristics distinguishing DR fecal microbiomes from those of full-fed (FF) pigs as both groups consumed a common sequence of diets during their growth cycle. Gnotobiotic mice were then colonized with DR and FF microbiomes and subjected to controlled feeding with a pig diet. DR microbiomes have reduced representation of genes that degrade dominant components of late growth-phase diets, exhibit reduced production of butyrate, a key host-accessible energy source, and are causally linked to reduced hepatic fatty acid metabolism(ß-oxidation) and the selection of alternative energy substrates. The approach described could aid in the development of guidelines for microbiome stewardship in diverse species, including farm animals, in order to support their healthy growth. [ABSTRACT FROM AUTHOR]

Published
2021
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