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3. Functional and evolutionary significance of unknown genes from uncultivated taxa

Author

Rodríguez del Río, Álvaro, Giner-Lamia, Joaquín, Cantalapiedra, Carlos P., Botas, Jorge, Deng, Ziqi, Hernández-Plaza, Ana, Munar-Palmer, Martí, Santamaría-Hernando, Saray, Rodríguez-Herva, José J., Ruscheweyh, Hans-Joachim, Paoli, Lucas, Schmidt, Thomas S. B., Sunagawa, Shinichi, Bork, Peer, López-Solanilla, Emilia, Coelho, Luis Pedro, and Huerta-Cepas, Jaime

Published
2024
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5. Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide

Author

Andrikopoulos, Petros, Aron-Wisnewsky, Judith, Chakaroun, Rima, Myridakis, Antonis, Forslund, Sofia K., Nielsen, Trine, Adriouch, Solia, Holmes, Bridget, Chilloux, Julien, Vieira-Silva, Sara, Falony, Gwen, Salem, Joe-Elie, Andreelli, Fabrizio, Belda, Eugeni, Kieswich, Julius, Chechi, Kanta, Puig-Castellvi, Francesc, Chevalier, Mickael, Le Chatelier, Emmanuelle, Olanipekun, Michael T., Hoyles, Lesley, Alves, Renato, Helft, Gerard, Isnard, Richard, Køber, Lars, Coelho, Luis Pedro, Rouault, Christine, Gauguier, Dominique, Gøtze, Jens Peter, Prifti, Edi, Froguel, Philippe, Zucker, Jean-Daniel, Bäckhed, Fredrik, Vestergaard, Henrik, Hansen, Torben, Oppert, Jean-Michel, Blüher, Matthias, Nielsen, Jens, Raes, Jeroen, Bork, Peer, Yaqoob, Muhammad M., Stumvoll, Michael, Pedersen, Oluf, Ehrlich, S. Dusko, Clément, Karine, and Dumas, Marc-Emmanuel

Published
2023
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6. Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs?

Author

Bengtsson-Palme, Johan, Abramova, Anna, Berendonk, Thomas U., Coelho, Luis Pedro, Forslund, Sofia K., Gschwind, Rémi, Heikinheimo, Annamari, Jarquín-Díaz, Víctor Hugo, Khan, Ayaz Ali, Klümper, Uli, Löber, Ulrike, Nekoro, Marmar, Osińska, Adriana D., Ugarcina Perovic, Svetlana, Pitkänen, Tarja, Rødland, Ernst Kristian, Ruppé, Etienne, Wasteson, Yngvild, Wester, Astrid Louise, and Zahra, Rabaab

Published
2023
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7. Microbially Produced Imidazole Propionate Is Associated With Heart Failure and Mortality

Author

Alves, Renato, Amouyal, Chloe, Andersson Galijatovic, Ehm Astrid, Andreelli, Fabrizio, Barthelemy, Olivier, Bastard, Jean-Philippe, Batisse, Jean-Paul, Berland, Magalie, Bittar, Randa, Blüher, Matthias, Bork, Peer, Bourron, Olivier, Camus, Mickael, Cassuto, Dominique, Ciangura, Cecile, Coelho, Luis Pedro, Collet, Jean-Philippe, Dumas, Marc-Emmanuel, Ehrlich, S. Dusko, Engelbrechtsen, Line, Fezeu, Leopold, Forslund, Sofia, Fromentin, Sebastien, Galan, Pilar, Giral, Philippe, Gøtze, Jens Peter, Hansen, Torben, Hansen, Tue H., Hartemann, Agnes, Hartmann, Bolette, Hercberg, Serge, Holmes, Bridget, Holst, Jens Juul, Hornbak, Malene, Hoyles, Lesley, Hulot, Jean-Sebastien, Jaqueminet, Sophie, Kerneis, Mathieu, Khemis, Jean, Kozlowski, Ruby, Pedersen, Helle Krogh, Kuhn, Michael, Mannerås-Holm, Louise, Marko, Lajos, Martinez-Gili Robin Massey, Laura, Maziers, Nicolas, Medina-Stamminger, Jonathan, Moitinho-Silva, Lucas, Montalescot, Gilles, Moutel, Sandrine, Neves, Ana Luisa, Olanipekun, Michael, Oppert, Jean-Michel, Poitou, Christine, Pousset, Francoise, Pouzoulet, Laurence, Rouault, Christine, Silvain, Johanne, Vestergaard, Henrik, Molinaro, Antonio, Nemet, Ina, Bel Lassen, Pierre, Chakaroun, Rima, Nielsen, Trine, Aron-Wisnewsky, Judith, Bergh, Per-Olof, Li, Lin, Henricsson, Marcus, Køber, Lars, Isnard, Richard, Helft, Gerard, Stumvoll, Michael, Pedersen, Oluf, Smith, J. Gustav, Tang, W.H. Wilson, Clément, Karine, Hazen, Stanley L., and Bäckhed, Fredrik

Published
2023
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8. Drivers and determinants of strain dynamics following fecal microbiota transplantation

Author

Schmidt, Thomas S. B., Li, Simone S., Maistrenko, Oleksandr M., Akanni, Wasiu, Coelho, Luis Pedro, Dolai, Sibasish, Fullam, Anthony, Glazek, Anna M., Hercog, Rajna, Herrema, Hilde, Jung, Ferris, Kandels, Stefanie, Orakov, Askarbek, Thielemann, Roman, von Stetten, Moritz, Van Rossum, Thea, Benes, Vladimir, Borody, Thomas J., de Vos, Willem M., Ponsioen, Cyriel Y., Nieuwdorp, Max, and Bork, Peer

Published
2022
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9. A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer

Author

Swiss National Science Foundation, Shanghai Municipal Natural Science Foundation, Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), European Commission, Dmitrijeva, Marija [0000-0002-8561-6490], Tackmann, Janko [0000-0003-1467-2863], Matias Rodrigues, João Frederico [0000-0001-8413-9920], Huerta-Cepas, Jaime [0000-0003-4195-5025], Coelho, Luis Pedro [0000-0002-9280-7885], von Mering, Christian [0000-0001-7734-9102], Dmitrijeva, Marija, Tackmann, Janko, Matias Rodrigues, João Frederico, Huerta-Cepas, Jaime, Coelho, Luis Pedro, von Mering, Christian, Swiss National Science Foundation, Shanghai Municipal Natural Science Foundation, Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), European Commission, Dmitrijeva, Marija [0000-0002-8561-6490], Tackmann, Janko [0000-0003-1467-2863], Matias Rodrigues, João Frederico [0000-0001-8413-9920], Huerta-Cepas, Jaime [0000-0003-4195-5025], Coelho, Luis Pedro [0000-0002-9280-7885], von Mering, Christian [0000-0001-7734-9102], Dmitrijeva, Marija, Tackmann, Janko, Matias Rodrigues, João Frederico, Huerta-Cepas, Jaime, Coelho, Luis Pedro, and von Mering, Christian

Abstract

Horizontal gene transfer, the exchange of genetic material through means other than reproduction, is a fundamental force in prokaryotic genome evolution. Genomic persistence of horizontally transferred genes has been shown to be influenced by both ecological and evolutionary factors. However, there is limited availability of ecological information about species other than the habitats from which they were isolated, which has prevented a deeper exploration of ecological contributions to horizontal gene transfer. Here we focus on transfers detected through comparison of individual gene trees to the species tree, assessing the distribution of gene-exchanging prokaryotes across over a million environmental sequencing samples. By analysing detected horizontal gene transfer events, we show distinct functional profiles for recent versus old events. Although most genes transferred are part of the accessory genome, genes transferred earlier in evolution tend to be more ubiquitous within present-day species. We find that co-occurring, interacting and high-abundance species tend to exchange more genes. Finally, we show that host-associated specialist species are most likely to exchange genes with other host-associated specialist species, whereas species found across different habitats have similar gene exchange rates irrespective of their preferred habitat. Our study covers an unprecedented scale of integrated horizontal gene transfer and environmental information, highlighting broad eco-evolutionary trends.

Published
2024

10. Functional and evolutionary significance of unknown genes from uncultivated taxa

Author

Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Fundación la Caixa, Silicon Valley Community Foundation, Swiss National Science Foundation, ETH Zurich, Rodríguez, Alvaro [0000-0003-3907-3904], Giner-Lamia, Joaquín [0000-0003-1553-8295], Cantalapiedra, Carlos P [0000-0001-5263-533X], Botas, Jorge [0000-0001-7292-8981], Hernández-Plaza, Ana [0000-0002-9844-7999], Munar-Palmer, Martí [0000-0002-8898-4483], Santamaría-Hernando, Saray [0000-0001-6763-3839], Rodríguez-Herva, José J. [0000-0001-9962-2261], Ruscheweyh, Hans-Joachim [0000-0001-7473-6086], Paoli, Lucas [0000-0003-0771-8309], Schmidt, Thomas Sebastian [0000-0001-8587-4177], Sunagawa, Shinichi [0000-0003-3065-0314], Bork, Peer [0000-0002-2627-833X], López-Solanilla, Emilia [0000-0002-8578-7433], Coelho, Luis Pedro [0000-0002-9280-7885], Huerta-Cepas, Jaime [0000-0003-4195-5025], Rodríguez, Alvaro, Giner-Lamia, Joaquín, Cantalapiedra, Carlos P, Botas, Jorge, Deng, Ziqi, Hernández-Plaza, Ana, Munar-Palmer, Martí, Santamaría-Hernando, Saray, Rodríguez-Herva, José J., Ruscheweyh, Hans-Joachim, Paoli, Lucas, Schmidt, Thomas Sebastian, Sunagawa, Shinichi, Bork, Peer, López-Solanilla, Emilia, Coelho, Luis Pedro, Huerta-Cepas, Jaime, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Fundación la Caixa, Silicon Valley Community Foundation, Swiss National Science Foundation, ETH Zurich, Rodríguez, Alvaro [0000-0003-3907-3904], Giner-Lamia, Joaquín [0000-0003-1553-8295], Cantalapiedra, Carlos P [0000-0001-5263-533X], Botas, Jorge [0000-0001-7292-8981], Hernández-Plaza, Ana [0000-0002-9844-7999], Munar-Palmer, Martí [0000-0002-8898-4483], Santamaría-Hernando, Saray [0000-0001-6763-3839], Rodríguez-Herva, José J. [0000-0001-9962-2261], Ruscheweyh, Hans-Joachim [0000-0001-7473-6086], Paoli, Lucas [0000-0003-0771-8309], Schmidt, Thomas Sebastian [0000-0001-8587-4177], Sunagawa, Shinichi [0000-0003-3065-0314], Bork, Peer [0000-0002-2627-833X], López-Solanilla, Emilia [0000-0002-8578-7433], Coelho, Luis Pedro [0000-0002-9280-7885], Huerta-Cepas, Jaime [0000-0003-4195-5025], Rodríguez, Alvaro, Giner-Lamia, Joaquín, Cantalapiedra, Carlos P, Botas, Jorge, Deng, Ziqi, Hernández-Plaza, Ana, Munar-Palmer, Martí, Santamaría-Hernando, Saray, Rodríguez-Herva, José J., Ruscheweyh, Hans-Joachim, Paoli, Lucas, Schmidt, Thomas Sebastian, Sunagawa, Shinichi, Bork, Peer, López-Solanilla, Emilia, Coelho, Luis Pedro, and Huerta-Cepas, Jaime

Abstract

Many of the Earth's microbes remain uncultured and understudied, limiting our understanding of the functional and evolutionary aspects of their genetic material, which remain largely overlooked in most metagenomic studies1. Here we analysed 149,842 environmental genomes from multiple habitats2-6 and compiled a curated catalogue of 404,085 functionally and evolutionarily significant novel (FESNov) gene families exclusive to uncultivated prokaryotic taxa. All FESNov families span multiple species, exhibit strong signals of purifying selection and qualify as new orthologous groups, thus nearly tripling the number of bacterial and archaeal gene families described to date. The FESNov catalogue is enriched in clade-specific traits, including 1,034 novel families that can distinguish entire uncultivated phyla, classes and orders, probably representing synapomorphies that facilitated their evolutionary divergence. Using genomic context analysis and structural alignments we predicted functional associations for 32.4% of FESNov families, including 4,349 high-confidence associations with important biological processes. These predictions provide a valuable hypothesis-driven framework that we used for experimental validatation of a new gene family involved in cell motility and a novel set of antimicrobial peptides. We also demonstrate that the relative abundance profiles of novel families can discriminate between environments and clinical conditions, leading to the discovery of potentially new biomarkers associated with colorectal cancer. We expect this work to enhance future metagenomics studies and expand our knowledge of the genetic repertory of uncultivated organisms.

Published
2024

11. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Author

Salazar, Guillem, Paoli, Lucas, Alberti, Adriana, Huerta-Cepas, Jaime, Ruscheweyh, Hans-Joachim, Cuenca, Miguelangel, Field, Christopher M, Coelho, Luis Pedro, Cruaud, Corinne, Engelen, Stefan, Gregory, Ann C, Labadie, Karine, Marec, Claudie, Pelletier, Eric, Royo-Llonch, Marta, Roux, Simon, Sánchez, Pablo, Uehara, Hideya, Zayed, Ahmed A, Zeller, Georg, Carmichael, Margaux, Dimier, Céline, Ferland, Joannie, Kandels, Stefanie, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Coordinators, Tara Oceans, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels-Lewis, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stephane, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B, Sunagawa, Shinichi, and Wincker, Patrick

Subjects
Genetics, Climate Action, Gene Expression Regulation, Geography, Metagenome, Microbiota, Molecular Sequence Annotation, Oceans and Seas, RNA, Messenger, Seawater, Temperature, Transcriptome, Tara Oceans Coordinators, Tara Oceans, biogeochemistry, community turnover, eco-systems biology, gene expression change, global ocean microbiome, metagenome, metatranscriptome, microbial ecology, ocean warming, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.

Published
2019

12. Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Author

Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J, Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G, Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R, Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sébastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima‐Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Néou, Mario B, Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean‐Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, Remo, Speich, Sabrina, Sprovieri, Mario, Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Kandels‐Lewis, Stefanie, Searson, Sarah, Dimier, Céline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, Vargas, Colomban, Follows, Michael J, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B, Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, d'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, d'Alcalà, Maurizio Ribera, Wincker, Patrick, Bowler, Chris, Iudicone, Daniele, Gorsky, Gabriel, and Jaillon, Olivier

Subjects
Genetics, Life Below Water, Atmospheric Sciences, Geochemistry, Oceanography, Meteorology & Atmospheric Sciences
Abstract

Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment.

Published
2019

15. Quest for Orthologs in the Era of Biodiversity Genomics.

Author

Langschied, Felix, Bordin, Nicola, Cosentino, Salvatore, Fuentes-Palacios, Diego, Glover, Natasha, Hiller, Michael, Hu, Yanhui, Huerta-Cepas, Jaime, Coelho, Luis Pedro, Iwasaki, Wataru, Majidian, Sina, Manzano-Morales, Saioa, Persson, Emma, Richards, Thomas A, Gabaldón, Toni, Sonnhammer, Erik, Thomas, Paul D, Dessimoz, Christophe, and Ebersberger, Ingo

Subjects
COMPARATIVE genetics, GENE families, ALTERNATIVE RNA splicing, NON-coding RNA, COMPARATIVE genomics
Abstract

The era of biodiversity genomics is characterized by large-scale genome sequencing efforts that aim to represent each living taxon with an assembled genome. Generating knowledge from this wealth of data has not kept up with this pace. We here discuss major challenges to integrating these novel genomes into a comprehensive functional and evolutionary network spanning the tree of life. In summary, the expanding datasets create a need for scalable gene annotation methods. To trace gene function across species, new methods must seek to increase the resolution of ortholog analyses, e.g. by extending analyses to the protein domain level and by accounting for alternative splicing. Additionally, the scope of orthology prediction should be pushed beyond well-investigated proteomes. This demands the development of specialized methods for the identification of orthologs to short proteins and noncoding RNAs and for the functional characterization of novel gene families. Furthermore, protein structures predicted by machine learning are now readily available, but this new information is yet to be integrated with orthology-based analyses. Finally, an increasing focus should be placed on making orthology assignments adhere to the findable, accessible, interoperable, and reusable (FAIR) principles. This fosters green bioinformatics by avoiding redundant computations and helps integrating diverse scientific communities sharing the need for comparative genetics and genomics information. It should also help with communicating orthology-related concepts in a format that is accessible to the public, to counteract existing misinformation about evolution. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Microbiome and metabolome features of the cardiometabolic disease spectrum

Author

Fromentin, Sebastien, Forslund, Sofia K., Chechi, Kanta, Aron-Wisnewsky, Judith, Chakaroun, Rima, Nielsen, Trine, Tremaroli, Valentina, Ji, Boyang, Prifti, Edi, Myridakis, Antonis, Chilloux, Julien, Andrikopoulos, Petros, Fan, Yong, Olanipekun, Michael T., Alves, Renato, Adiouch, Solia, Bar, Noam, Talmor-Barkan, Yeela, Belda, Eugeni, Caesar, Robert, Coelho, Luis Pedro, Falony, Gwen, Fellahi, Soraya, Galan, Pilar, Galleron, Nathalie, Helft, Gerard, Hoyles, Lesley, Isnard, Richard, Le Chatelier, Emmanuelle, Julienne, Hanna, Olsson, Lisa, Pedersen, Helle Krogh, Pons, Nicolas, Quinquis, Benoit, Rouault, Christine, Roume, Hugo, Salem, Joe-Elie, Schmidt, Thomas S. B., Vieira-Silva, Sara, Li, Peishun, Zimmermann-Kogadeeva, Maria, Lewinter, Christian, Søndertoft, Nadja B., Hansen, Tue H., Gauguier, Dominique, Gøtze, Jens Peter, Køber, Lars, Kornowski, Ran, Vestergaard, Henrik, Hansen, Torben, Zucker, Jean-Daniel, Hercberg, Serge, Letunic, Ivica, Bäckhed, Fredrik, Oppert, Jean-Michel, Nielsen, Jens, Raes, Jeroen, Bork, Peer, Stumvoll, Michael, Segal, Eran, Clément, Karine, Dumas, Marc-Emmanuel, Ehrlich, S. Dusko, and Pedersen, Oluf

Published
2022
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17. Towards the biogeography of prokaryotic genes

Author

Coelho, Luis Pedro, Alves, Renato, del Río, Álvaro Rodríguez, Myers, Pernille Neve, Cantalapiedra, Carlos P., Giner-Lamia, Joaquín, Schmidt, Thomas Sebastian, Mende, Daniel R., Orakov, Askarbek, Letunic, Ivica, Hildebrand, Falk, Van Rossum, Thea, Forslund, Sofia K., Khedkar, Supriya, Maistrenko, Oleksandr M., Pan, Shaojun, Jia, Longhao, Ferretti, Pamela, Sunagawa, Shinichi, Zhao, Xing-Ming, Nielsen, Henrik Bjørn, Huerta-Cepas, Jaime, and Bork, Peer

Published
2022
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18. Combinatorial, additive and dose-dependent drug–microbiome associations

Author

Forslund, Sofia K., Chakaroun, Rima, Zimmermann-Kogadeeva, Maria, Markó, Lajos, Aron-Wisnewsky, Judith, Nielsen, Trine, Moitinho-Silva, Lucas, Schmidt, Thomas S. B., Falony, Gwen, Vieira-Silva, Sara, Adriouch, Solia, Alves, Renato J., Assmann, Karen, Bastard, Jean-Philippe, Birkner, Till, Caesar, Robert, Chilloux, Julien, Coelho, Luis Pedro, Fezeu, Leopold, Galleron, Nathalie, Helft, Gerard, Isnard, Richard, Ji, Boyang, Kuhn, Michael, Le Chatelier, Emmanuelle, Myridakis, Antonis, Olsson, Lisa, Pons, Nicolas, Prifti, Edi, Quinquis, Benoit, Roume, Hugo, Salem, Joe-Elie, Sokolovska, Nataliya, Tremaroli, Valentina, Valles-Colomer, Mireia, Lewinter, Christian, Søndertoft, Nadja B., Pedersen, Helle Krogh, Hansen, Tue H., Gøtze, Jens Peter, Køber, Lars, Vestergaard, Henrik, Hansen, Torben, Zucker, Jean-Daniel, Hercberg, Serge, Oppert, Jean-Michel, Letunic, Ivica, Nielsen, Jens, Bäckhed, Fredrik, Ehrlich, S. Dusko, Dumas, Marc-Emmanuel, Raes, Jeroen, Pedersen, Oluf, Clément, Karine, Stumvoll, Michael, and Bork, Peer

Published
2021
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20. Ubiquity of inverted ’gelatinous’ ecosystem pyramids in the global ocean

Author

Lombard, Fabien, Guidi, Lionel, Brandão, Manoela C., Coelho Luis, Pedro, Colin, Sébastien, Dolan, John Richard, Elineau, Amanda, Gasol, Josep M, Grondin, Pierre Luc, Henry, Nicolas, Ibarbalz, Federico M, Jalabert, Laetitia, Loreau, Michel, Martini, Séverine, Mériguet, Zoé, Picheral, Marc, Pierella Karlusich, Juan José, Pepperkok, Rainer, Romagnan, Jean-baptiste, Zinger, Lucie, Stemmann, Lars, Acinas, Silvia G, Lee, Karp-boss, Boss, Emmanuel, Sullivan, Matthew B., De Vargas, Colomban, Bowler, Chris, Karsenti, Eric, Gorsky, Gabriel, Lombard, Fabien, Guidi, Lionel, Brandão, Manoela C., Coelho Luis, Pedro, Colin, Sébastien, Dolan, John Richard, Elineau, Amanda, Gasol, Josep M, Grondin, Pierre Luc, Henry, Nicolas, Ibarbalz, Federico M, Jalabert, Laetitia, Loreau, Michel, Martini, Séverine, Mériguet, Zoé, Picheral, Marc, Pierella Karlusich, Juan José, Pepperkok, Rainer, Romagnan, Jean-baptiste, Zinger, Lucie, Stemmann, Lars, Acinas, Silvia G, Lee, Karp-boss, Boss, Emmanuel, Sullivan, Matthew B., De Vargas, Colomban, Bowler, Chris, Karsenti, Eric, and Gorsky, Gabriel

Abstract

Summary paragraph Plankton are essential in marine ecosystems. However, our knowledge of overall community structure is sparse due to inconsistent sampling across their very large organismal size range. Here we use diverse imaging methods to establish complete plankton inventories of organisms spanning five orders of magnitude in size. Plankton community size and trophic structure variation validate a long-held theoretical link between organism size-spectra and ecosystem trophic structures. We found that predator/grazer biomass and biovolume unexpectedly exceed that of primary producers at most (55%) locations, likely due to our better quantification of gelatinous organisms. Bottom- heavy ecosystems (the norm on land) appear to be rare in the ocean. Collectively, gelatinous organisms represent 30% of the total biovolume (8-9% of carbon) of marine plankton communities from tropical to polar ecosystems. Communities can be split into three extreme typologies: diatom/copepod-dominated in eutrophic blooms, rhizarian/chaetognath-dominated in oligotrophic tropical oceans, and gelatinous-dominated elsewhere. While plankton taxonomic composition changes with latitude, functional and trophic structures mostly depend on the amount of prey available for each trophic level. Given future projections of oligotrophication of marine ecosystems, our findings suggest that rhizarian and gelatinous organisms will increasingly dominate the apex position of planktonic ecosystems, leading to significant changes in the ocean’s carbon cycle.

Published
2024
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22. Plankton networks driving carbon export in the oligotrophic ocean

Author

Guidi, Lionel, Chaffron, Samuel, Bittner, Lucie, Eveillard, Damien, Larhlimi, Abdelhalim, Roux, Simon, Darzi, Youssef, Audic, Stephane, Berline, Léo, Brum, Jennifer R, Coelho, Luis Pedro, Espinoza, Julio Cesar Ignacio, Malviya, Shruti, Sunagawa, Shinichi, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Poulain, Julie, Searson, Sarah, Stemmann, Lars, Not, Fabrice, Hingamp, Pascal, Speich, Sabrina, Follows, Mick, Karp-Boss, Lee, Boss, Emmanuel, Ogata, Hiroyuki, Pesant, Stephane, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G, Bork, Peer, de Vargas, Colomban, Iudicone, Daniele, Sullivan, Matthew B, Raes, Jeroen, Karsenti, Eric, Bowler, Chris, and Gorsky, Gabriel

Subjects
Aquatic Organisms, Carbon, Chlorophyll, Dinoflagellida, Ecosystem, Expeditions, Genes, Bacterial, Genes, Viral, Geography, Oceans and Seas, Photosynthesis, Plankton, Seawater, Synechococcus, Tara Oceans coordinators, General Science & Technology
Abstract

The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.

Published
2016

23. Functional and evolutionary significance of unknown genes from uncultivated taxa

Author

Rodríguez del Río, Álvaro, primary, Giner-Lamia, Joaquín, additional, Cantalapiedra, Carlos P., additional, Botas, Jorge, additional, Deng, Ziqi, additional, Hernández-Plaza, Ana, additional, Munar-Palmer, Martí, additional, Santamaría-Hernando, Saray, additional, Rodríguez-Herva, José J., additional, Ruscheweyh, Hans-Joachim, additional, Paoli, Lucas, additional, Schmidt, Thomas S. B., additional, Sunagawa, Shinichi, additional, Bork, Peer, additional, López-Solanilla, Emilia, additional, Coelho, Luis Pedro, additional, and Huerta-Cepas, Jaime, additional

Published
2023
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25. Mahotas: Open source software for scriptable computer vision

Author

Coelho, Luis Pedro

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Software Engineering
Abstract

Mahotas is a computer vision library for Python. It contains traditional image processing functionality such as filtering and morphological operations as well as more modern computer vision functions for feature computation, including interest point detection and local descriptors. The interface is in Python, a dynamic programming language, which is very appropriate for fast development, but the algorithms are implemented in C++ and are tuned for speed. The library is designed to fit in with the scientific software ecosystem in this language and can leverage the existing infrastructure developed in that language. Mahotas is released under a liberal open source license (MIT License) and is available from (http://github.com/luispedro/mahotas) and from the Python Package Index (http://pypi.python.org/pypi/mahotas).

Published
2012
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27. Recovery of gut microbiota of healthy adults following antibiotic exposure

Author

Palleja, Albert, Mikkelsen, Kristian H., Forslund, Sofia K., Kashani, Alireza, Allin, Kristine H., Nielsen, Trine, Hansen, Tue H., Liang, Suisha, Feng, Qiang, Zhang, Chenchen, Pyl, Paul Theodor, Coelho, Luis Pedro, Yang, Huanming, Wang, Jian, Typas, Athanasios, Nielsen, Morten F., Nielsen, Henrik Bjorn, Bork, Peer, Wang, Jun, Vilsbøll, Tina, Hansen, Torben, Knop, Filip K., Arumugam, Manimozhiyan, and Pedersen, Oluf

Published
2018
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28. Structure and function of the global topsoil microbiome

Author

Bahram, Mohammad, Hildebrand, Falk, Forslund, Sofia K., Anderson, Jennifer L., Soudzilovskaia, Nadejda A., Bodegom, Peter M., Bengtsson-Palme, Johan, Anslan, Sten, Coelho, Luis Pedro, Harend, Helery, Huerta-Cepas, Jaime, Medema, Marnix H., Maltz, Mia R., Mundra, Sunil, Olsson, Pål Axel, Pent, Mari, Põlme, Sergei, Sunagawa, Shinichi, Ryberg, Martin, Tedersoo, Leho, and Bork, Peer

Published
2018
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30. ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics

Author

Gschwind, Rémi, Ugarcina Perovic, Svetlana, Weiss, Maja, Petitjean, Marie, Lao, Julie, Coelho, Luis Pedro, Ruppé, Etienne, Gschwind, Rémi, Ugarcina Perovic, Svetlana, Weiss, Maja, Petitjean, Marie, Lao, Julie, Coelho, Luis Pedro, and Ruppé, Etienne

Abstract

Metagenomics can be used to monitor the spread of antibiotic resistance genes (ARGs). ARGs found in databases such as ResFinder and CARD primarily originate from culturable and pathogenic bacteria, while ARGs from non-culturable and non-pathogenic bacteria remain understudied. Functional metagenomics is based on phenotypic gene selection and can identify ARGs from non-culturable bacteria with a potentially low identity shared with known ARGs. In 2016, the ResFinderFG v1.0 database was created to collect ARGs from functional metagenomics studies. Here, we present the second version of the database, ResFinderFG v2.0, which is available on the Center of Genomic Epidemiology web server. It comprises 3913 ARGs identified by functional metagenomics from 50 carefully curated datasets. We assessed its potential to detect ARGs in comparison to other popular databases in gut, soil and water (marine + freshwater) Global Microbial Gene Catalogues. ResFinderFG v2.0 allowed for the detection of ARGs that were not detected using other databases. These included ARGs conferring resistance to beta-lactams, cycline, phenicol, glycopeptide/cycloserine and trimethoprim/sulfonamide. Thus, ResFinderFG v2.0 can be used to identify ARGs differing from those found in conventional databases and therefore improve the description of resistomes.

Published
2023

32. Microbial abundance, activity and population genomic profiling with mOTUs2

Author

Milanese, Alessio, Mende, Daniel R, Paoli, Lucas, Salazar, Guillem, Ruscheweyh, Hans-Joachim, Cuenca, Miguelangel, Hingamp, Pascal, Alves, Renato, Costea, Paul I, Coelho, Luis Pedro, Schmidt, Thomas S. B., Almeida, Alexandre, Mitchell, Alex L, Finn, Robert D., Huerta-Cepas, Jaime, Bork, Peer, Zeller, Georg, and Sunagawa, Shinichi

Published
2019
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33. Towards standards for human fecal sample processing in metagenomic studies

Author

Costea, Paul I, Zeller, Georg, Sunagawa, Shinichi, Pelletier, Eric, Alberti, Adriana, Levenez, Florence, Tramontano, Melanie, Driessen, Marja, Hercog, Rajna, Jung, Ferris-Elias, Kultima, Jens Roat, Hayward, Matthew R, Coelho, Luis Pedro, Allen-Vercoe, Emma, Bertrand, Laurie, Blaut, Michael, Brown, Jillian R M, Carton, Thomas, Cools-Portier, Stéphanie, Daigneault, Michelle, Derrien, Muriel, Druesne, Anne, de Vos, Willem M, Finlay, B Brett, Flint, Harry J, Guarner, Francisco, Hattori, Masahira, Heilig, Hans, Luna, Ruth Ann, van Hylckama Vlieg, Johan, Junick, Jana, Klymiuk, Ingeborg, Langella, Philippe, Le Chatelier, Emmanuelle, Mai, Volker, Manichanh, Chaysavanh, Martin, Jennifer C, Mery, Clémentine, Morita, Hidetoshi, O'Toole, Paul W, Orvain, Céline, Patil, Kiran Raosaheb, Penders, John, Persson, Søren, Pons, Nicolas, Popova, Milena, Salonen, Anne, Saulnier, Delphine, Scott, Karen P, Singh, Bhagirath, Slezak, Kathleen, Veiga, Patrick, Versalovic, James, Zhao, Liping, Zoetendal, Erwin G, Ehrlich, S Dusko, Dore, Joel, and Bork, Peer

Published
2017
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37. Structured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature

Author

Coelho, Luís Pedro, Ahmed, Amr, Arnold, Andrew, Kangas, Joshua, Sheikh, Abdul-Saboor, Xing, Eric P., Cohen, William W., Murphy, Robert F., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Blaschke, Christian, editor, and Shatkay, Hagit, editor

Published
2010
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38. Principles of Bioimage Informatics: Focus on Machine Learning of Cell Patterns

Author

Coelho, Luis Pedro, Glory-Afshar, Estelle, Kangas, Joshua, Quinn, Shannon, Shariff, Aabid, Murphy, Robert F., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Blaschke, Christian, editor, and Shatkay, Hagit, editor

Published
2010
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39. Towards the biogeography of prokaryotic genes

Author

European Commission, European Research Council, Helmut Horten Foundation, National Key Research and Development Program (China), Shanghai Municipal Education Commission, International Development Research Centre (Canada), Fundación la Caixa, Agencia Estatal de Investigación (España), Innovation Fund Denmark, Coelho, Luis Pedro [0000-0002-9280-7885], Alves, Renato [0000-0002-7212-0234], Del Río, Álvaro Rodríguez [0000-0003-3907-3904], Myers, Pernille Neve [0000-0002-1824-3305], Cantalapiedra, Carlos P [0000-0001-5263-533X], Giner-Lamia, Joaquín [0000-0003-1553-8295], Mende, Daniel R. [0000-0001-6831-4557], Orakov, Askarbek [0000-0001-6823-5269], Letunic, Ivica [0000-0003-3560-4288], Hildebrand, Falk [0000-0002-0078-8948], Van Rossum, Thea [0000-0002-3598-5001], Forslund, Sofia K [0000-0003-4285-6993], Khedkar, Supriya [0000-0001-6606-2202], Maistrenko, Oleksandr M [0000-0003-1961-7548], Pan, Shaojun [0000-0002-5270-5614], Jia, Longhao [0000-0002-3490-840X], Ferretti, Pamela [0000-0002-1707-9013], Sunagawa, Shinichi [0000-0003-3065-0314], Nielsen, Henrik Bjørn [0000-0003-2281-5713], Huerta-Cepas, Jaime [0000-0003-4195-5025], Bork, Peer [0000-0002-2627-833X], Coelho, Luis Pedro, Alves, Renato, Del Río, Álvaro Rodríguez, Myers, Pernille Neve, Cantalapiedra, Carlos P, Giner-Lamia, Joaquín, Schmidt, Thomas Sebastian, Mende, Daniel R., Orakov, Askarbek, Letunic, Ivica, Hildebrand, Falk, Van Rossum, Thea, Forslund, Sofía K., Khedkar, Supriya, Maistrenko, Oleksandr M., Pan, Shaojun, Jia, Longhao, Ferretti, Pamela, Sunagawa, Shinichi, Zhao, Xing-Ming, Nielsen, Henrik Bjørn, Huerta-Cepas, Jaime, Bork, Peer, European Commission, European Research Council, Helmut Horten Foundation, National Key Research and Development Program (China), Shanghai Municipal Education Commission, International Development Research Centre (Canada), Fundación la Caixa, Agencia Estatal de Investigación (España), Innovation Fund Denmark, Coelho, Luis Pedro [0000-0002-9280-7885], Alves, Renato [0000-0002-7212-0234], Del Río, Álvaro Rodríguez [0000-0003-3907-3904], Myers, Pernille Neve [0000-0002-1824-3305], Cantalapiedra, Carlos P [0000-0001-5263-533X], Giner-Lamia, Joaquín [0000-0003-1553-8295], Mende, Daniel R. [0000-0001-6831-4557], Orakov, Askarbek [0000-0001-6823-5269], Letunic, Ivica [0000-0003-3560-4288], Hildebrand, Falk [0000-0002-0078-8948], Van Rossum, Thea [0000-0002-3598-5001], Forslund, Sofia K [0000-0003-4285-6993], Khedkar, Supriya [0000-0001-6606-2202], Maistrenko, Oleksandr M [0000-0003-1961-7548], Pan, Shaojun [0000-0002-5270-5614], Jia, Longhao [0000-0002-3490-840X], Ferretti, Pamela [0000-0002-1707-9013], Sunagawa, Shinichi [0000-0003-3065-0314], Nielsen, Henrik Bjørn [0000-0003-2281-5713], Huerta-Cepas, Jaime [0000-0003-4195-5025], Bork, Peer [0000-0002-2627-833X], Coelho, Luis Pedro, Alves, Renato, Del Río, Álvaro Rodríguez, Myers, Pernille Neve, Cantalapiedra, Carlos P, Giner-Lamia, Joaquín, Schmidt, Thomas Sebastian, Mende, Daniel R., Orakov, Askarbek, Letunic, Ivica, Hildebrand, Falk, Van Rossum, Thea, Forslund, Sofía K., Khedkar, Supriya, Maistrenko, Oleksandr M., Pan, Shaojun, Jia, Longhao, Ferretti, Pamela, Sunagawa, Shinichi, Zhao, Xing-Ming, Nielsen, Henrik Bjørn, Huerta-Cepas, Jaime, and Bork, Peer

Abstract

Microbial genes encode the majority of the functional repertoire of life on earth. However, despite increasing efforts in metagenomic sequencing of various habitats1,2,3, little is known about the distribution of genes across the global biosphere, with implications for human and planetary health. Here we constructed a non-redundant gene catalogue of 303 million species-level genes (clustered at 95% nucleotide identity) from 13,174 publicly available metagenomes across 14 major habitats and use it to show that most genes are specific to a single habitat. The small fraction of genes found in multiple habitats is enriched in antibiotic-resistance genes and markers for mobile genetic elements. By further clustering these species-level genes into 32 million protein families, we observed that a small fraction of these families contain the majority of the genes (0.6% of families account for 50% of the genes). The majority of species-level genes and protein families are rare. Furthermore, species-level genes, and in particular the rare ones, show low rates of positive (adaptive) selection, supporting a model in which most genetic variability observed within each protein family is neutral or nearly neutral.

Published
2021

42. Dotted Suffix Trees A Structure for Approximate Text Indexing

Author

Coelho, Luís Pedro, Oliveira, Arlindo L., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Crestani, Fabio, editor, Ferragina, Paolo, editor, and Sanderson, Mark, editor

Published
2006
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44. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

Author

European Commission, EMBO, Maistrenko, Oleksandr M. [0000-0003-1961-7548], Mende, Daniel R. [0000-0001-6831-4557], Hildebrand, Falk [0000-0002-0078-8948], Schmidt, Thomas Sebastian [0000-0001-8587-4177], Li, Simone S. [0000-0002-0073-3656], Rodrigues, Joao Frederico Matias [0000-0001-8413-9920], von Mering, Christian [0000-0001-7734-9102], Coelho, Luis Pedro [0000-0002-9280-7885], Huerta-Cepas, Jaime [0000-0003-4195-5025], Sunagawa, Shinichi [0000-0003-3065-0314], Bork, Peer [0000-0002-2627-833X], Maistrenko, Oleksandr M., Mende, Daniel R., Luetge, Mechthild, Hildebrand, Falk, Schmidt, Thomas Sebastian, Li, Simone S., Rodrigues, Joao Frederico Matias, von Mering, Christian, Coelho, Luis Pedro, Huerta-Cepas, Jaime, Sunagawa, Shinichi, Bork, Peer, European Commission, EMBO, Maistrenko, Oleksandr M. [0000-0003-1961-7548], Mende, Daniel R. [0000-0001-6831-4557], Hildebrand, Falk [0000-0002-0078-8948], Schmidt, Thomas Sebastian [0000-0001-8587-4177], Li, Simone S. [0000-0002-0073-3656], Rodrigues, Joao Frederico Matias [0000-0001-8413-9920], von Mering, Christian [0000-0001-7734-9102], Coelho, Luis Pedro [0000-0002-9280-7885], Huerta-Cepas, Jaime [0000-0003-4195-5025], Sunagawa, Shinichi [0000-0003-3065-0314], Bork, Peer [0000-0002-2627-833X], Maistrenko, Oleksandr M., Mende, Daniel R., Luetge, Mechthild, Hildebrand, Falk, Schmidt, Thomas Sebastian, Li, Simone S., Rodrigues, Joao Frederico Matias, von Mering, Christian, Coelho, Luis Pedro, Huerta-Cepas, Jaime, Sunagawa, Shinichi, and Bork, Peer

Abstract

Microbial organisms inhabit virtually all environments and encompass a vast biological diversity. The pangenome concept aims to facilitate an understanding of diversity within defined phylogenetic groups. Hence, pangenomes are increasingly used to characterize the strain diversity of prokaryotic species. To understand the interdependence of pangenome features (such as the number of core and accessory genes) and to study the impact of environmental and phylogenetic constraints on the evolution of conspecific strains, we computed pangenomes for 155 phylogenetically diverse species (from ten phyla) using 7,000 high-quality genomes to each of which the respective habitats were assigned. Species habitat ubiquity was associated with several pangenome features. In particular, core-genome size was more important for ubiquity than accessory genome size. In general, environmental preferences had a stronger impact on pangenome evolution than phylogenetic inertia. Environmental preferences explained up to 49% of the variance for pangenome features, compared with 18% by phylogenetic inertia. This observation was robust when the dataset was extended to 10,100 species (59 phyla). The importance of environmental preferences was further accentuated by convergent evolution of pangenome features in a given habitat type across different phylogenetic clades. For example, the soil environment promotes expansion of pangenome size, while host-associated habitats lead to its reduction. Taken together, we explored the global principles of pangenome evolution, quantified the influence of habitat, and phylogenetic inertia on the evolution of pangenomes and identified criteria governing species ubiquity and habitat specificity.

Published
2020

45. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

Author

European Commission, Comunidad de Madrid, Agencia Estatal de Investigación (España), Mende, Daniel R. [0000-0001-6831-4557], Letunic, Ivica [0000-0003-3560-4288], Maistrenko, Oleksandr M. [0000-0003-1961-7548], Schmidt, Thomas Sebastian [0000-0001-8587-4177], Milanese, Alessio [0000-0002-7050-2239], Paoli, Lucas [0000-0003-0771-8309], Orakov, Askarbek [0000-0001-6823-5269], Forslund, Sofía K. [0000-0003-4285-6993], Sunagawa, Shinichi [0000-0003-3065-0314], Zeller, Georg [0000-0003-1429-7485], Huerta-Cepas, Jaime [0000-0003-4195-5025], Coelho, Luis Pedro [0000-0002-9280-7885], Bork, Peer [0000-0002-2627-833X], Mende, Daniel R., Letunic, Ivica, Maistrenko, Oleksandr M., Schmidt, Thomas Sebastian, Milanese, Alessio, Paoli, Lucas, Hernández-Plaza, Ana, Orakov, Askarbek, Forslund, Sofía K., Sunagawa, Shinichi, Zeller, Georg, Huerta-Cepas, Jaime, Coelho, Luis Pedro, Bork, Peer, European Commission, Comunidad de Madrid, Agencia Estatal de Investigación (España), Mende, Daniel R. [0000-0001-6831-4557], Letunic, Ivica [0000-0003-3560-4288], Maistrenko, Oleksandr M. [0000-0003-1961-7548], Schmidt, Thomas Sebastian [0000-0001-8587-4177], Milanese, Alessio [0000-0002-7050-2239], Paoli, Lucas [0000-0003-0771-8309], Orakov, Askarbek [0000-0001-6823-5269], Forslund, Sofía K. [0000-0003-4285-6993], Sunagawa, Shinichi [0000-0003-3065-0314], Zeller, Georg [0000-0003-1429-7485], Huerta-Cepas, Jaime [0000-0003-4195-5025], Coelho, Luis Pedro [0000-0002-9280-7885], Bork, Peer [0000-0002-2627-833X], Mende, Daniel R., Letunic, Ivica, Maistrenko, Oleksandr M., Schmidt, Thomas Sebastian, Milanese, Alessio, Paoli, Lucas, Hernández-Plaza, Ana, Orakov, Askarbek, Forslund, Sofía K., Sunagawa, Shinichi, Zeller, Georg, Huerta-Cepas, Jaime, Coelho, Luis Pedro, and Bork, Peer

Abstract

Microbiology depends on the availability of annotated microbial genomes for many applications. Comparative genomics approaches have been a major advance, but consistent and accurate annotations of genomes can be hard to obtain. In addition, newer concepts such as the pan-genome concept are still being implemented to help answer biological questions. Hence, we present proGenomes2, which provides 87 920 high-quality genomes in a user-friendly and interactive manner. Genome sequences and annotations can be retrieved individually or by taxonomic clade. Every genome in the database has been assigned to a species cluster and most genomes could be accurately assigned to one or multiple habitats. In addition, general functional annotations and specific annotations of antibiotic resistance genes and single nucleotide variants are provided. In short, proGenomes2 provides threefold more genomes, enhanced habitat annotations, updated taxonomic and functional annotation and improved linkage to the NCBI BioSample database. The database is available at http://progenomes.embl.de/.

Published
2020

46. Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism

Author

Belda, Eugeni, Voland, Lise, Tremaroli, Valentina, Falony, Gwen, Adriouch, Solia, Assmann, Karen E., Prifti, Edi, Aron-Wisnewsky, Judith, Debédat, Jean, Le Roy, Tiphaine, Nielsen, Trine, Amouya, Chloé, André, Sébastien, Andreelli,, Fabrizio, Blüher, Matthias Blüher, Chakaroun, Rima, Chilloux, Julien, Coelho, Luis Pedro, Dao, Maria Carlota, Das, Promi, Fellahi, Soraya, Forslund, Sofia, Galleron, Nathalie, Hansen, Tue, Holmes, Bridget, Ji, Boyang, Krogh Pedersen, Helle, Le, Phuong, Le Chatelier, Emmanuelle, Lewinter, Christian, Mannerås-Holm, Louise, Marquet, Florian, Myridakis, Antonis, Pelloux, Veronique, Pons, Nicolas, Quinquis, Benoit, Rouault, Christine, Roume, Hugo, Salem, Joe-Elie, Sokolovska, Nataliya, Søndertoft, Nadja B, Touch, Sothea, Vieira-Silva, Sara, Consortium, MetaCardis, Galan, Pilar, Holst, Jens, Gøtze, Jens Peter, Køber, Lars, Vestergaard, Henrik, Hansen, Torben, Hercberg, Serge, Oppert, Jean-Michel, Nielsen, Jens, Letunic, Ivica, Dumas, Marc-Emmanuel, Stumvol, Michael, Pedersen, Oluf Borbye, Bork, Peer, Dusko Ehrlich, Stanislav, Zucker, Jens-Daniel, Bäckhed, Fredrik, Raes, Jeroen, Clément, Karine, Belda, Eugeni, Voland, Lise, Tremaroli, Valentina, Falony, Gwen, Adriouch, Solia, Assmann, Karen E., Prifti, Edi, Aron-Wisnewsky, Judith, Debédat, Jean, Le Roy, Tiphaine, Nielsen, Trine, Amouya, Chloé, André, Sébastien, Andreelli,, Fabrizio, Blüher, Matthias Blüher, Chakaroun, Rima, Chilloux, Julien, Coelho, Luis Pedro, Dao, Maria Carlota, Das, Promi, Fellahi, Soraya, Forslund, Sofia, Galleron, Nathalie, Hansen, Tue, Holmes, Bridget, Ji, Boyang, Krogh Pedersen, Helle, Le, Phuong, Le Chatelier, Emmanuelle, Lewinter, Christian, Mannerås-Holm, Louise, Marquet, Florian, Myridakis, Antonis, Pelloux, Veronique, Pons, Nicolas, Quinquis, Benoit, Rouault, Christine, Roume, Hugo, Salem, Joe-Elie, Sokolovska, Nataliya, Søndertoft, Nadja B, Touch, Sothea, Vieira-Silva, Sara, Consortium, MetaCardis, Galan, Pilar, Holst, Jens, Gøtze, Jens Peter, Køber, Lars, Vestergaard, Henrik, Hansen, Torben, Hercberg, Serge, Oppert, Jean-Michel, Nielsen, Jens, Letunic, Ivica, Dumas, Marc-Emmanuel, Stumvol, Michael, Pedersen, Oluf Borbye, Bork, Peer, Dusko Ehrlich, Stanislav, Zucker, Jens-Daniel, Bäckhed, Fredrik, Raes, Jeroen, and Clément, Karine

Abstract

Gut microbiota is a key component in obesity and type 2 diabetes, yet mechanisms and metabolites central to this interaction remain unclear. We examined the human gut microbiome’s functional composition in healthy metabolic state and the most severe states of obesity and type 2 diabetes within the MetaCardis cohort. We focused on the role of B vitamins and B7/B8 biotin for regulation of host metabolic state, as these vitamins influence both microbial function and host metabolism and inflammation.

Published
2022

47. Impairment of gut microbial biotin metabolism and host biotin status in severe obesity:effect of biotin and prebiotic supplementation on improved metabolism

Author

Belda, Eugeni, Voland, Lise, Tremaroli, Valentina, Falony, Gwen, Adriouch, Solia, Assmann, Karen E., Prifiti, Edi, Aron-Wisnewsky, Judith, Debedat, Jean, Le Roy, Tiphaine, Nielsen, Trine, Amouyal, Chloe, Andre, Sebastien, Andreelli, Fabrizio, Blueher, Matthias, Chakaroun, Rima, Chilloux, Julien, Coelho, Luis Pedro, Dao, Maria Carlota, Das, Promi, Fellahi, Soraya, Forslund, Sofia, Galleron, Nathalie, Hansen, Tue H., Holmes, Bridget, Ji, Boyang, Pedersen, Helle Krogh, Phuong Le, Le Chatelier, Emmanuelle, Lewinter, Christian, Manneras-Holm, Louise, Marquet, Florian, Myridakis, Antonis, Pelloux, Veronique, Pons, Nicolas, Quinquis, Benoit, Rouault, Christine, Roume, Hugo, Salem, Joe-Elie, Sokolovska, Nataliya, Søndertoft, Nadja B., Touch, Sothea, Vieira-Silva, Sara, Galan, Pilar, Holst, Jens, Gøtze, Jens Peter, Køber, Lars, Vestergaard, Henrik, Hansen, Torben, Hercberg, Serge, Oppert, Jean-Michel, Nielsen, Jens, Letunic, Ivica, Dumas, Marc-Emmanuel, Stumvoll, Michael, Pedersen, Oluf Borbye, Bork, Peer, Ehrlich, Stanislav Dusko, Zucker, Jean-Daniel, Baeckhed, Fredrik, Raes, Jeroen, Clement, Karine, Belda, Eugeni, Voland, Lise, Tremaroli, Valentina, Falony, Gwen, Adriouch, Solia, Assmann, Karen E., Prifiti, Edi, Aron-Wisnewsky, Judith, Debedat, Jean, Le Roy, Tiphaine, Nielsen, Trine, Amouyal, Chloe, Andre, Sebastien, Andreelli, Fabrizio, Blueher, Matthias, Chakaroun, Rima, Chilloux, Julien, Coelho, Luis Pedro, Dao, Maria Carlota, Das, Promi, Fellahi, Soraya, Forslund, Sofia, Galleron, Nathalie, Hansen, Tue H., Holmes, Bridget, Ji, Boyang, Pedersen, Helle Krogh, Phuong Le, Le Chatelier, Emmanuelle, Lewinter, Christian, Manneras-Holm, Louise, Marquet, Florian, Myridakis, Antonis, Pelloux, Veronique, Pons, Nicolas, Quinquis, Benoit, Rouault, Christine, Roume, Hugo, Salem, Joe-Elie, Sokolovska, Nataliya, Søndertoft, Nadja B., Touch, Sothea, Vieira-Silva, Sara, Galan, Pilar, Holst, Jens, Gøtze, Jens Peter, Køber, Lars, Vestergaard, Henrik, Hansen, Torben, Hercberg, Serge, Oppert, Jean-Michel, Nielsen, Jens, Letunic, Ivica, Dumas, Marc-Emmanuel, Stumvoll, Michael, Pedersen, Oluf Borbye, Bork, Peer, Ehrlich, Stanislav Dusko, Zucker, Jean-Daniel, Baeckhed, Fredrik, Raes, Jeroen, and Clement, Karine

Published
2022

48. Drivers and determinants of strain dynamics following fecal microbiota transplantation

Author

Schmidt, Thomas S.B., Li, Simone S., Maistrenko, Oleksandr M., Akanni, Wasiu, Coelho, Luis Pedro, Dolai, Sibasish, Fullam, Anthony, Glazek, Anna M., Hercog, Rajna, Herrema, Hilde, Jung, Ferris, Kandels, Stefanie, Orakov, Askarbek, Thielemann, Roman, von Stetten, Moritz, Van Rossum, Thea, Benes, Vladimir, Borody, Thomas J., de Vos, Willem M., Ponsioen, Cyriel Y., Nieuwdorp, Max, Bork, Peer, Schmidt, Thomas S.B., Li, Simone S., Maistrenko, Oleksandr M., Akanni, Wasiu, Coelho, Luis Pedro, Dolai, Sibasish, Fullam, Anthony, Glazek, Anna M., Hercog, Rajna, Herrema, Hilde, Jung, Ferris, Kandels, Stefanie, Orakov, Askarbek, Thielemann, Roman, von Stetten, Moritz, Van Rossum, Thea, Benes, Vladimir, Borody, Thomas J., de Vos, Willem M., Ponsioen, Cyriel Y., Nieuwdorp, Max, and Bork, Peer

Abstract

Fecal microbiota transplantation (FMT) is a therapeutic intervention for inflammatory diseases of the gastrointestinal tract, but its clinical mode of action and subsequent microbiome dynamics remain poorly understood. Here we analyzed metagenomes from 316 FMTs, sampled pre and post intervention, for the treatment of ten different disease indications. We quantified strain-level dynamics of 1,089 microbial species, complemented by 47,548 newly constructed metagenome-assembled genomes. Donor strain colonization and recipient strain resilience were mostly independent of clinical outcomes, but accurately predictable using LASSO-regularized regression models that accounted for host, microbiome and procedural variables. Recipient factors and donor–recipient complementarity, encompassing entire microbial communities to individual strains, were the main determinants of strain population dynamics, providing insights into the underlying processes that shape the post-FMT gut microbiome. Applying an ecology-based framework to our findings indicated parameters that may inform the development of more effective, targeted microbiome therapies in the future, and suggested how patient stratification can be used to enhance donor microbiota colonization or the displacement of recipient microbes in clinical practice.

Published
2022

49. Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes

Author

Khedkar, Supriya, primary, Smyshlyaev, Georgy, additional, Letunic, Ivica, additional, Maistrenko, Oleksandr M, additional, Coelho, Luis Pedro, additional, Orakov, Askarbek, additional, Forslund, Sofia K, additional, Hildebrand, Falk, additional, Luetge, Mechthild, additional, Schmidt, Thomas S B, additional, Barabas, Orsolya, additional, and Bork, Peer, additional

Published
2022
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