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2. Inducing novel endosymbioses by implanting bacteria in fungi

Author

Giger, Gabriel H., Ernst, Chantal, Richter, Ingrid, Gassler, Thomas, Field, Christopher M., Sintsova, Anna, Kiefer, Patrick, Gäbelein, Christoph G., Guillaume–Gentil, Orane, Scherlach, Kirstin, Bortfeld-Miller, Miriam, Zambelli, Tomaso, Sunagawa, Shinichi, Künzler, Markus, Hertweck, Christian, and Vorholt, Julia A.

Published
2024
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4. The NEREA Augmented Observatory: an integrative approach to marine coastal ecology

Author

Campese, Lucia, Russo, Luca, Abagnale, Maria, Alberti, Adriana, Bachi, Giancarlo, Balestra, Cecilia, Bellardini, Daniele, Buondonno, Angela, Cardini, Ulisse, Carotenuto, Ylenia, Checcucci, Giovanni, Chiusano, Maria Luisa, D’Ambra, Isabella, d’Ippolito, Giuliana, Di Capua, Iole, Donnarumma, Vincenzo, Fontana, Angelo, Furia, Marta, Galarza-Verkovitch, Denisse, Gallia, Roberto, Labadie, Karine, Leone, Serena, Licandro, Priscilla, Longo, Antonio, Maselli, Maira, Merquiol, Louise, Murano, Carola, Oliveira, Pedro H., Passarelli, Augusto, Percopo, Isabella, Perdereau, Aude, Piredda, Roberta, Raffini, Francesca, Roncalli, Vittoria, Ruscheweyh, Hans-Joachim, Russo, Ennio, Saggiomo, Maria, Santinelli, Chiara, Sarno, Diana, Sunagawa, Shinichi, Tramontano, Ferdinando, Trano, Anna Chiara, Uttieri, Marco, Wincker, Patrick, Zampicinini, Gianpaolo, Casotti, Raffaella, Conversano, Fabio, D’Alelio, Domenico, Iudicone, Daniele, Margiotta, Francesca, and Montresor, Marina

Published
2024
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5. Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters

Author

Villena-Alemany, Cristian, Mujakić, Izabela, Fecskeová, Livia K., Woodhouse, Jason, Auladell, Adrià, Dean, Jason, Hanusová, Martina, Socha, Magdalena, Gazulla, Carlota R., Ruscheweyh, Hans-Joachim, Sunagawa, Shinichi, Silva Kavagutti, Vinicius, Andrei, Adrian-Ştefan, Grossart, Hans-Peter, Ghai, Rohit, Koblížek, Michal, and Piwosz, Kasia

Published
2024
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8. 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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9. Salmonella Typhimurium screen identifies shifts in mixed-acid fermentation during gut colonization

Author

Nguyen, Bidong D., Sintsova, Anna, Schubert, Christopher, Sichert, Andreas, Scheidegger, Clio, Näf, Jana, Huttman, Julien, Lentsch, Verena, Keys, Tim, Rutschmann, Christoph, Christen, Philipp, Kiefer, Patrick, Keller, Philipp, Barthel, Manja, Cuenca, Miguelangel, Christen, Beat, Sauer, Uwe, Slack, Emma, Vorholt, Julia A., Sunagawa, Shinichi, and Hardt, Wolf-Dietrich

Published
2024
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10. Critical Assessment of Metagenome Interpretation: the second round of challenges

Author

Meyer, Fernando, Fritz, Adrian, Deng, Zhi-Luo, Koslicki, David, Lesker, Till Robin, Gurevich, Alexey, Robertson, Gary, Alser, Mohammed, Antipov, Dmitry, Beghini, Francesco, Bertrand, Denis, Brito, Jaqueline J, Brown, C Titus, Buchmann, Jan, Buluç, Aydin, Chen, Bo, Chikhi, Rayan, Clausen, Philip TLC, Cristian, Alexandru, Dabrowski, Piotr Wojciech, Darling, Aaron E, Egan, Rob, Eskin, Eleazar, Georganas, Evangelos, Goltsman, Eugene, Gray, Melissa A, Hansen, Lars Hestbjerg, Hofmeyr, Steven, Huang, Pingqin, Irber, Luiz, Jia, Huijue, Jørgensen, Tue Sparholt, Kieser, Silas D, Klemetsen, Terje, Kola, Axel, Kolmogorov, Mikhail, Korobeynikov, Anton, Kwan, Jason, LaPierre, Nathan, Lemaitre, Claire, Li, Chenhao, Limasset, Antoine, Malcher-Miranda, Fabio, Mangul, Serghei, Marcelino, Vanessa R, Marchet, Camille, Marijon, Pierre, Meleshko, Dmitry, Mende, Daniel R, Milanese, Alessio, Nagarajan, Niranjan, Nissen, Jakob, Nurk, Sergey, Oliker, Leonid, Paoli, Lucas, Peterlongo, Pierre, Piro, Vitor C, Porter, Jacob S, Rasmussen, Simon, Rees, Evan R, Reinert, Knut, Renard, Bernhard, Robertsen, Espen Mikal, Rosen, Gail L, Ruscheweyh, Hans-Joachim, Sarwal, Varuni, Segata, Nicola, Seiler, Enrico, Shi, Lizhen, Sun, Fengzhu, Sunagawa, Shinichi, Sørensen, Søren Johannes, Thomas, Ashleigh, Tong, Chengxuan, Trajkovski, Mirko, Tremblay, Julien, Uritskiy, Gherman, Vicedomini, Riccardo, Wang, Zhengyang, Wang, Ziye, Wang, Zhong, Warren, Andrew, Willassen, Nils Peder, Yelick, Katherine, You, Ronghui, Zeller, Georg, Zhao, Zhengqiao, Zhu, Shanfeng, Zhu, Jie, Garrido-Oter, Ruben, Gastmeier, Petra, Hacquard, Stephane, Häußler, Susanne, Khaledi, Ariane, Maechler, Friederike, Mesny, Fantin, Radutoiu, Simona, Schulze-Lefert, Paul, Smit, Nathiana, and Strowig, Till

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Networking and Information Technology R&D (NITRD), Archaea, Metagenome, Metagenomics, Reproducibility of Results, Sequence Analysis, DNA, Software, Technology, Medical and Health Sciences, Developmental Biology, Biological sciences
Abstract

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.

Published
2022

13. Ocean-wide comparisons of mesopelagic planktonic community structures

Author

Rigonato, Janaina, Budinich, Marko, Murillo, Alejandro A., Brandão, Manoela C., Pierella Karlusich, Juan J., Soviadan, Yawouvi Dodji, Gregory, Ann C., Endo, Hisashi, Kokoszka, Florian, Vik, Dean, Henry, Nicolas, Frémont, Paul, Labadie, Karine, Zayed, Ahmed A., Dimier, Céline, Picheral, Marc, Searson, Sarah, Poulain, Julie, Kandels, Stefanie, Pesant, Stéphane, Karsenti, Eric, Bork, Peer, Bowler, Chris, de Vargas, Colomban, Eveillard, Damien, Gehlen, Marion, Iudicone, Daniele, Lombard, Fabien, Ogata, Hiroyuki, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Wincker, Patrick, Chaffron, Samuel, and Jaillon, Olivier

Published
2023
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14. Multi-omics determination of metabolome diversity in natural coral populations in the Pacific Ocean

Author

Reddy, Maggie M., Goossens, Corentine, Zhou, Yuxiang, Chaib, Slimane, Raviglione, Delphine, Nicolè, Florence, Hume, Benjamin C. C., Forcioli, Didier, Agostini, Sylvain, Boissin, Emilie, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Douville, Eric, Flores, Michel, Furla, Paola, Galand, Pierre E., Gilson, Eric, Lombard, Fabien, Pesant, Stéphane, Reynaud, Stéphanie, Sullivan, Matthew B., Sunagawa, Shinichi, Troublé, Romain, Thurber, Rebecca Vega, Wincker, Patrick, Zoccola, Didier, Voolstra, Christian R., Allemand, Denis, Planes, Serge, Thomas, Olivier P., and Banaigs, Bernard

Published
2023
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15. Different environmental response strategies in sympatric corals from Pacific Islands

Author

Porro, Barbara, Zamoum, Thamilla, Forcioli, Didier, Gilson, Eric, Poquet, Adrien, Di Franco, Eugenio, Barnay-Verdier, Stéphanie, Lombard, Fabien, Voolstra, Christian R., Hume, Benjamin C. C., Galand, Pierre E., Moulin, Clémentine, Boissin, Emilie, Bourdin, Guillaume, Iwankow, Guillaume, Poulain, Julie, Romac, Sarah, Agostini, Sylvain, Banaigs, Bernard, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Douville, Eric, Flores, Michel, Pesant, Stéphane, Reynaud, Stéphanie, Sullivan, Matthew B., Sunagawa, Shinichi, Thomas, Olivier P., Troublé, Romain, Thurber, Rebecca Vega, Wincker, Patrick, Zoccola, Didier, Planes, Serge, Allemand, Denis, Röttinger, Eric, and Furla, Paola

Published
2023
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17. Differences in carbonate chemistry up-regulation of long-lived reef-building corals

Author

Canesi, Marine, Douville, Eric, Montagna, Paolo, Taviani, Marco, Stolarski, Jarosław, Bordier, Louise, Dapoigny, Arnaud, Coulibaly, Gninwoyo Eric Hermann, Simon, Anne-Catherine, Agelou, Mathieu, Fin, Jonathan, Metzl, Nicolas, Iwankow, Guillaume, Allemand, Denis, Planes, Serge, Moulin, Clémentine, Lombard, Fabien, Bourdin, Guillaume, Troublé, Romain, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Flores, Michel, Forcioli, Didier, Furla, Paola, Gilson, Eric, Galand, Pierre E., Pesant, Stéphane, Sunagawa, Shinichi, Thomas, Olivier P., Vega Thurber, Rebecca, Voolstra, Christian R., Wincker, Patrick, Zoccola, Didier, and Reynaud, Stéphanie

Published
2023
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19. Sea surface temperature reconstruction in the Pacific Ocean using multi-elemental proxy in Porites and Diploastrea corals: Application to Palau Archipelago

Author

Canesi, Marine, Douville, Eric, Montagna, Paolo, Bordier, Louise, Caquineau, Sandrine, Pons-Branchu, Edwige, Iwankow, Guillaume, Stolarski, Jarosław, Allemand, Denis, Planes, Serge, Moulin, Clémentine, Lombard, Fabien, Bourdin, Guillaume, Troublé, Romain, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Flores, J. Michel, Forcioli, Didier, Furla, Paola, Gilson, Eric, Galand, Pierre E., Pesant, Stéphane, Sunagawa, Shinichi, Thomas, Olivier P., Thurber, Rebecca Vega, Voolstra, Christian R., Wincker, Patrick, Zoccola, Didier, and Reynaud, Stéphanie

Published
2024
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21. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities.

Author

Acinas, Silvia G, Sánchez, Pablo, Salazar, Guillem, Cornejo-Castillo, Francisco M, Sebastián, Marta, Logares, Ramiro, Royo-Llonch, Marta, Paoli, Lucas, Sunagawa, Shinichi, Hingamp, Pascal, Ogata, Hiroyuki, Lima-Mendez, Gipsi, Roux, Simon, González, José M, Arrieta, Jesús M, Alam, Intikhab S, Kamau, Allan, Bowler, Chris, Raes, Jeroen, Pesant, Stéphane, Bork, Peer, Agustí, Susana, Gojobori, Takashi, Vaqué, Dolors, Sullivan, Matthew B, Pedrós-Alió, Carlos, Massana, Ramon, Duarte, Carlos M, and Gasol, Josep M

Subjects
Bacteria, DNA, Bacterial, Seawater, Photosynthesis, Metagenome, Carbon Cycle
Abstract

The deep sea, the largest ocean's compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.

Published
2021

22. A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directions

Author

Dittami, Simon, Arboleda, Enrique, Auguet, Jean-Christophe, Bigalke, Arite, Briand, Enora, Cárdenas, Paco, Cardini, Ulisse, Decelle, Johan, Engelen, Ashwin, Eveillard, Damien, Gachon, Claire, Griffiths, Sarah, Harder, Tilmann, Kayal, Ehsan, Kazamia, Elena, Lallier, François, Medina, Mónica, Marzinelli, Ezequiel, Morganti, Teresa, Pons, Laura, Prado, Soizic, Valverde, José Pintado, Saha, Mahasweta, Selosse, Marc-Andre, Skillings, Derek, Stock, Willem, Sunagawa, Shinichi, Toulza, Eve, Vorobev, Alexey, Leblanc, Catherine, and Not, Fabrice

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Host-microbe interactions play crucial roles in marine ecosystems, but we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help describe and understand these complex systems. It posits that a host and its associated microbiota, living together in a long-lasting relationship, form the holobiont, and have to be studied together, as a coherent biological and functional unit, in order to understand the biology, ecology and evolution of the organisms. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences with comparisons to terrestrial science whenever appropriate. A deeper understanding of such complex systems, however, will require further technological and conceptual advances. The most significant challenge will be to bridge functional research on simple and tractable model systems and global approaches. This will require scientists to work together as an (inter)active community in order to address, for instance, ecological and evolutionary questions and the roles of holobionts in biogeochemical cycles., Comment: PeerJ Preprints, Computer Science Preprints., 2019

Published
2019
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23. Import of Aspartate and Malate by DcuABC Drives H2/Fumarate Respiration to Promote Initial Salmonella Gut-Lumen Colonization in Mice

Author

Nguyen, Bidong D, Cuenca V, Miguelangel, Hartl, Johannes, Gül, Ersin, Bauer, Rebekka, Meile, Susanne, Rüthi, Joel, Margot, Céline, Heeb, Laura, Besser, Franziska, Escriva, Pau Pérez, Fetz, Céline, Furter, Markus, Laganenka, Leanid, Keller, Philipp, Fuchs, Lea, Christen, Matthias, Porwollik, Steffen, McClelland, Michael, Vorholt, Julia A, Sauer, Uwe, Sunagawa, Shinichi, Christen, Beat, and Hardt, Wolf-Dietrich

Subjects
Microbiology, Medical Microbiology, Biomedical and Clinical Sciences, Biological Sciences, Biodefense, Microbiome, Digestive Diseases, Emerging Infectious Diseases, Infectious Diseases, 2.1 Biological and endogenous factors, Administration, Oral, Animals, Aspartic Acid, Bacterial Proteins, Citric Acid Cycle, Disease Models, Animal, Escherichia coli, Feces, Female, Fumarates, Gastrointestinal Microbiome, Intestines, Malates, Male, Mice, Mice, Inbred C57BL, Mutagenesis, RNA, Ribosomal, 16S, Salmonella, Salmonella typhimurium, Sequence Analysis, DNA, Succinic Acid, infection, intestine, metabolism, mouse model, Immunology, Biochemistry and cell biology, Medical microbiology
Abstract

Initial enteropathogen growth in the microbiota-colonized gut is poorly understood. Salmonella Typhimurium is metabolically adaptable and can harvest energy by anaerobic respiration using microbiota-derived hydrogen (H2) as an electron donor and fumarate as an electron acceptor. As fumarate is scarce in the gut, the source of this electron acceptor is unclear. Here, transposon sequencing analysis along the colonization trajectory of S. Typhimurium implicates the C4-dicarboxylate antiporter DcuABC in early murine gut colonization. In competitive colonization assays, DcuABC and enzymes that convert the C4-dicarboxylates aspartate and malate into fumarate (AspA, FumABC), are required for fumarate/H2-dependent initial growth. Thus, S. Typhimurium obtains fumarate by DcuABC-mediated import and conversion of L-malate and L-aspartate. Fumarate reduction yields succinate, which is exported by DcuABC in exchange for L-aspartate and L-malate. This cycle allows S. Typhimurium to harvest energy by H2/fumarate respiration in the microbiota-colonized gut. This strategy may also be relevant for commensal E. coli diminishing the S. Typhimurium infection.

Published
2020

24. 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

25. Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Author

Gregory, Ann C, Zayed, Ahmed A, Conceição-Neto, Nádia, Temperton, Ben, Bolduc, Ben, Alberti, Adriana, Ardyna, Mathieu, Arkhipova, Ksenia, Carmichael, Margaux, Cruaud, Corinne, Dimier, Céline, Domínguez-Huerta, Guillermo, Ferland, Joannie, Kandels, Stefanie, Liu, Yunxiao, Marec, Claudie, Pesant, Stéphane, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Tremblay, Jean-Éric, Vik, Dean, 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, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Culley, Alexander I, Dutilh, Bas E, and Roux, Simon

Subjects
Genetics, Infection, Life Below Water, Aquatic Organisms, Biodiversity, DNA Viruses, DNA, Viral, Metagenome, Water Microbiology, Tara Oceans Coordinators, community ecology, diversity gradients, marine biology, metagenomics, population ecology, species, viruses, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.

Published
2019

26. 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

27. Biosynthetic potential of the global ocean microbiome

Author

Paoli, Lucas, Ruscheweyh, Hans-Joachim, Forneris, Clarissa C., Hubrich, Florian, Kautsar, Satria, Bhushan, Agneya, Lotti, Alessandro, Clayssen, Quentin, Salazar, Guillem, Milanese, Alessio, Carlström, Charlotte I., Papadopoulou, Chrysa, Gehrig, Daniel, Karasikov, Mikhail, Mustafa, Harun, Larralde, Martin, Carroll, Laura M., Sánchez, Pablo, Zayed, Ahmed A., Cronin, Dylan R., Acinas, Silvia G., Bork, Peer, Bowler, Chris, Delmont, Tom O., Gasol, Josep M., Gossert, Alvar D., Kahles, André, Sullivan, Matthew B., Wincker, Patrick, Zeller, Georg, Robinson, Serina L., Piel, Jörn, and Sunagawa, Shinichi

Published
2022
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28. 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

30. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Author

Sunagawa, Shinichi, Acinas, Silvia G., Bork, Peer, Karsenti, Eric, Bowler, Chris, Sardet, Christian, Stemmann, Lars, de Vargas, Colomban, Wincker, Patrick, Lescot, Magali, Babin, Marcel, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Jaillon, Olivier, Kandels, Stefanie, Iudicone, Daniele, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B., Not, Fabrice, Lee, Karp-Boss, Boss, Emmanuel, Cochrane, Guy, Follows, Michael, Poulton, Nicole, Raes, Jeroen, Sieracki, Mike, Speich, Sabrina, Delmont, Tom O., Gaia, Morgan, Hinsinger, Damien D., Frémont, Paul, Vanni, Chiara, Fernandez-Guerra, Antonio, Eren, A. Murat, Kourlaiev, Artem, d'Agata, Leo, Clayssen, Quentin, Villar, Emilie, Labadie, Karine, Cruaud, Corinne, Poulain, Julie, Da Silva, Corinne, Wessner, Marc, Noel, Benjamin, Aury, Jean-Marc, and Pelletier, Eric

Published
2022
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31. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author

Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-Bum, Malmstrom, Rex R, Martinez-Garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-Espino, David, Petit, Marie-Agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-Valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, and Eloe-Fadrosh, Emiley A

Subjects
Microbiology, Biological Sciences, Genetics, Human Genome, Databases, Genetic, Genome, Viral, Genomics, Virus Cultivation, Viruses
Abstract

We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.

Published
2019

34. 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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36. Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean

Author

Royo-Llonch, Marta, Sánchez, Pablo, Ruiz-González, Clara, Salazar, Guillem, Pedrós-Alió, Carlos, Sebastián, Marta, Labadie, Karine, Paoli, Lucas, M. Ibarbalz, Federico, Zinger, Lucie, Churcheward, Benjamin, Chaffron, Samuel, Eveillard, Damien, Karsenti, Eric, Sunagawa, Shinichi, Wincker, Patrick, Karp-Boss, Lee, Bowler, Chris, and Acinas, Silvia G.

Published
2021
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37. Enterotypes in the landscape of gut microbial community composition.

Author

Costea, Paul I, Hildebrand, Falk, Arumugam, Manimozhiyan, Bäckhed, Fredrik, Blaser, Martin J, Bushman, Frederic D, de Vos, Willem M, Ehrlich, S Dusko, Fraser, Claire M, Hattori, Masahira, Huttenhower, Curtis, Jeffery, Ian B, Knights, Dan, Lewis, James D, Ley, Ruth E, Ochman, Howard, O'Toole, Paul W, Quince, Christopher, Relman, David A, Shanahan, Fergus, Sunagawa, Shinichi, Wang, Jun, Weinstock, George M, Wu, Gary D, Zeller, Georg, Zhao, Liping, Raes, Jeroen, Knight, Rob, and Bork, Peer

Subjects
Gastrointestinal Tract, Animals, Humans, Bacteria, RNA, Ribosomal, 16S, Bacterial Typing Techniques, Biodiversity, Metagenome, Metagenomics, Gastrointestinal Microbiome, Human Genome, Genetics, Clinical Research, Microbiology, Medical Microbiology
Abstract

Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.

Published
2018

40. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.

Author

Roux, Simon, Brum, Jennifer R, Dutilh, Bas E, Sunagawa, Shinichi, Duhaime, Melissa B, Loy, Alexander, Poulos, Bonnie T, Solonenko, Natalie, Lara, Elena, Poulain, Julie, Pesant, Stéphane, Kandels-Lewis, Stefanie, Dimier, Céline, Picheral, Marc, Searson, Sarah, Cruaud, Corinne, Alberti, Adriana, Duarte, Carlos M, Gasol, Josep M, Vaqué, Dolors, Tara Oceans Coordinators, Bork, Peer, Acinas, Silvia G, Wincker, Patrick, and Sullivan, Matthew B

Subjects
Tara Oceans Coordinators, Viruses, Sulfur, DNA, Viral, Ecology, Ecosystem, Seawater, Genes, Viral, Genome, Viral, Expeditions, Oceans and Seas, Metagenome, Metagenomics, Nitrogen Cycle, Geographic Mapping, Datasets as Topic, General Science & Technology
Abstract

Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting 'global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.

Published
2016

41. 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

42. Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.

Author

Cornejo-Castillo, Francisco M, Cabello, Ana M, Salazar, Guillem, Sánchez-Baracaldo, Patricia, Lima-Mendez, Gipsi, Hingamp, Pascal, Alberti, Adriana, Sunagawa, Shinichi, Bork, Peer, de Vargas, Colomban, Raes, Jeroen, Bowler, Chris, Wincker, Patrick, Zehr, Jonathan P, Gasol, Josep M, Massana, Ramon, and Acinas, Silvia G

Subjects
Phytoplankton, Cyanobacteria, Genomics, Seawater, Nitrogen Fixation, Symbiosis, Atlantic Ocean, Biological Evolution, Haptophyta, Genetics, Human Genome
Abstract

The unicellular cyanobacterium UCYN-A, one of the major contributors to nitrogen fixation in the open ocean, lives in symbiosis with single-celled phytoplankton. UCYN-A includes several closely related lineages whose partner fidelity, genome-wide expression and time of evolutionary divergence remain to be resolved. Here we detect and distinguish UCYN-A1 and UCYN-A2 lineages in symbiosis with two distinct prymnesiophyte partners in the South Atlantic Ocean. Both symbiotic systems are lineage specific and differ in the number of UCYN-A cells involved. Our analyses infer a streamlined genome expression towards nitrogen fixation in both UCYN-A lineages. Comparative genomics reveal a strong purifying selection in UCYN-A1 and UCYN-A2 with a diversification process ∼91 Myr ago, in the late Cretaceous, after the low-nutrient regime period occurred during the Jurassic. These findings suggest that UCYN-A diversified in a co-evolutionary process, wherein their prymnesiophyte partners acted as a barrier driving an allopatric speciation of extant UCYN-A lineages.

Published
2016

43. A cryptic plasmid is among the most numerous genetic elements in the human gut

Author

Fogarty, Emily C, Schechter, Matthew S, Lolans, Karen, Sheahan, Madeline L, Veseli, Iva, Moore, Ryan M, Kiefl, Evan, Moody, Thomas, Rice, Phoebe A, Yu, Michael K, Mimee, Mark, Chang, Eugene B, Ruscheweyh, Hans-Joachim, Sunagawa, Shinichi, Mclellan, Sandra L, Willis, Amy D, Comstock, Laurie E, Eren, A Murat, Fogarty, Emily C, Schechter, Matthew S, Lolans, Karen, Sheahan, Madeline L, Veseli, Iva, Moore, Ryan M, Kiefl, Evan, Moody, Thomas, Rice, Phoebe A, Yu, Michael K, Mimee, Mark, Chang, Eugene B, Ruscheweyh, Hans-Joachim, Sunagawa, Shinichi, Mclellan, Sandra L, Willis, Amy D, Comstock, Laurie E, and Eren, A Murat

Abstract

Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry “cryptic” plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales, and although it does not appear to impact bacterial host fitness in vivo, it can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an alternative approach to track human colonic inflammatory states.

Published
2024

44. From microbiome composition to functional engineering, one step at a time

Author

Burz, Sebastian Dan, Causevic, Senka, Dal Co, Alma, Dmitrijeva, Marija, Engel, Philipp, Garrido-Sanz, Daniel, Greub, Gilbert, Hapfelmeier, Siegfried, Hardt, Wolf-Dietrich, Hatzimanikatis, Vassily, Heiman, Clara Margot, Herzog, Mathias Klaus-Maria, Hockenberry, Alyson, Keel, Christoph, Keppler, Andreas, Lee, Soon-Jae, Luneau, Julien, Malfertheiner, Lukas, Mitri, Sara, Ngyuen, Bidong, Oftadeh, Omid, Pacheco, Alan R., Peaudecerf, Francois, Resch, Gregory, Ruscheweyh, Hans-Joachim, Sahin, Asli, Sanders, Ian R., Slack, Emma, Sunagawa, Shinichi, Tackmann, Janko, Tecon, Robin, Ugolini, Giovanni Stefano, Vacheron, Jordan, van der Meer, Jan Roelof, Vayena, Evangelia, Vonaesch, Pascale, Vorholt, Julia A., Burz, Sebastian Dan, Causevic, Senka, Dal Co, Alma, Dmitrijeva, Marija, Engel, Philipp, Garrido-Sanz, Daniel, Greub, Gilbert, Hapfelmeier, Siegfried, Hardt, Wolf-Dietrich, Hatzimanikatis, Vassily, Heiman, Clara Margot, Herzog, Mathias Klaus-Maria, Hockenberry, Alyson, Keel, Christoph, Keppler, Andreas, Lee, Soon-Jae, Luneau, Julien, Malfertheiner, Lukas, Mitri, Sara, Ngyuen, Bidong, Oftadeh, Omid, Pacheco, Alan R., Peaudecerf, Francois, Resch, Gregory, Ruscheweyh, Hans-Joachim, Sahin, Asli, Sanders, Ian R., Slack, Emma, Sunagawa, Shinichi, Tackmann, Janko, Tecon, Robin, Ugolini, Giovanni Stefano, Vacheron, Jordan, van der Meer, Jan Roelof, Vayena, Evangelia, Vonaesch, Pascale, and Vorholt, Julia A.

Abstract

Communities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.

Published
2024
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45. Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters

Author

National Science Centre (Poland), Czech Science Foundation, Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72], Villena-Alemany, Cristian, Mujaki, Izabela, Fecskeová, Livia K., Woodhouse, Jason, Auladell Martin, Adria, Dean, Jason, Hanusová, Martina, Gazulla, Carlota R., Ruscheweyh, Hans-Joachim, Sunagawa, Shinichi, Silva Kavagutti, Vinicius, Andrei, Adrian‑Ştefan, Grossart, Hans-Peter, Ghai, Rohit, Koblížek, Michal, Piwosz, Kasia, National Science Centre (Poland), Czech Science Foundation, Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72], Villena-Alemany, Cristian, Mujaki, Izabela, Fecskeová, Livia K., Woodhouse, Jason, Auladell Martin, Adria, Dean, Jason, Hanusová, Martina, Gazulla, Carlota R., Ruscheweyh, Hans-Joachim, Sunagawa, Shinichi, Silva Kavagutti, Vinicius, Andrei, Adrian‑Ştefan, Grossart, Hans-Peter, Ghai, Rohit, Koblížek, Michal, and Piwosz, Kasia

Abstract

Background: Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centers. Despite their substantial contribution to bacterial biomass, microbial food webs, and carbon cycle, their phenology in freshwater lakes remains unknown. Hence, we investigated seasonal variations of AAP abundance and community composition biweekly across 3 years in a temperate, meso-oligotrophic freshwater lake. Results: AAP bacteria displayed a clear seasonal trend with a spring maximum following the bloom of phytoplankton and a secondary maximum in autumn. As the AAP bacteria represent a highly diverse assemblage of species, we followed their seasonal succession using the amplicon sequencing of the pufM marker gene. To enhance the accuracy of the taxonomic assignment, we developed new pufM primers that generate longer amplicons and compiled the currently largest database of pufM genes, comprising 3633 reference sequences spanning all phyla known to contain AAP species. With this novel resource, we demonstrated that the majority of the species appeared during specific phases of the seasonal cycle, with less than 2% of AAP species detected during the whole year. AAP community presented an indigenous freshwater nature characterized by high resilience and heterogenic adaptations to varying conditions of the freshwater environment. Conclusions: Our findings highlight the substantial contribution of AAP bacteria to the carbon flow and ecological dynamics of lakes and unveil a recurrent and dynamic seasonal succession of the AAP community. By integrating this information with the indicator of primary production (Chlorophyll-a) and existing ecological models, we show that AAP bacteria play a pivotal role in the recycling of dissolved organic matter released during spring phytoplankton bloom. We suggest a potential role of AAP bacteria within the context of the PEG model and thei

Published
2024

47. Tara Oceans: towards global ocean ecosystems biology

Author

Sunagawa, Shinichi, Acinas, Silvia G., Bork, Peer, Bowler, Chris, Eveillard, Damien, Gorsky, Gabriel, Guidi, Lionel, Iudicone, Daniele, Karsenti, Eric, Lombard, Fabien, Ogata, Hiroyuki, Pesant, Stephane, Sullivan, Matthew B., Wincker, Patrick, and de Vargas, Colomban

Published
2020
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49. Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes)

Author

Heras, Joseph, McClintock, Kelly, Sunagawa, Shinichi, and Aguilar, Andres

Subjects
Bioinformatics, Orthologs, Positive selection, Reproductive genes, Untranslated region, Zona pellucida
Abstract

Background: The genetic mechanisms of speciation and adaptation in the marine environment are not well understood. The rockfish genus Sebastes provides a unique model system for studying adaptive evolution because of the extensive diversity found within this group, which includes morphology, ecology, and a broad range of life spans. Examples of adaptive radiations within marine ecosystems are considered an anomaly due to the absence of geographical barriers and the presence of gene flow. Using marine rockfishes, we identified signatures of natural selection from transcriptomes developed from gonadal tissue of two rockfish species (Sebastes goodei and S. saxicola). We predicted orthologous transcript pairs, and estimated their distributions of nonsynonymous (Ka) and synonymous (Ks) substitution rates. Results: We identified 144 genes out of 1079 orthologous pairs under positive selection, of which 11 are functionally annotated to reproduction based on gene ontologies (GOs). One orthologous pair of the zona pellucida gene family, which is known for its role in the selection of sperm by oocytes, out of ten was identified to be evolving under positive selection. In addition to our results in the protein coding-regions of transcripts, we found substitution rates in 3' and 5' UTRs to be significantly lower than Ks substitution rates implying negative selection in these regions. Conclusions: We were able to identify a series of candidate genes that are useful for the assessment of the critical genes that diverged and are responsible for the radiation within this genus. Genes associated with longevity hold potential for understanding the molecular mechanisms that have contributed to the radiation within this genus.

Published
2015

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