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204 results on '"Ruscheweyh, Hans-Joachim"'

2. 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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3. 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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5. 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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6. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Author

Belser, Caroline, Poulain, Julie, Labadie, Karine, Gavory, Frederick, Alberti, Adriana, Guy, Julie, Carradec, Quentin, Cruaud, Corinne, da Silva, Corinne, Engelen, Stefan, Mielle, Paul, Perdereau, Aude, Samson, Gaelle, Gaz, Shahinaz, Team, Genoscope Technical, Voolstra, Christian R, Galand, Pierre E, Flores, J. Michel, Hume, Benjamin Cc, Perna, Gabriela, Ziegler, Maren, Ruscheweyh, Hans-Joachim, Boissin, Emilie, Romac, Sarah, Bourdin, Guillaume, Iwankow, Guillaume, Moulin, Clémentine, García, David A Paz, Coordinators, Tara Pacific Consortium, Scarpelli, Claude, Jacoby, E Krame, Oliveira, Pedro H, Aury, Jean-Marc, Allemand, Denis, Planes, Serge, and Wincker, Patrick

Subjects
Quantitative Biology - Quantitative Methods
Abstract

Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the host coral organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.

Published
2022

7. 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

9. 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

10. 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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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

15. 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

16. 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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17. 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

19. 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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23. mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants and isogenic strain populations

Author

Sintsova, Anna, primary, Ruscheweyh, Hans-Joachim, additional, Field, Christopher M., additional, Feer, Lilith, additional, Nguyen, Bidong D., additional, Daniel, Benjamin, additional, Hardt, Wolf-Dietrich, additional, Vorholt, Julia A., additional, and Sunagawa, Shinichi, additional

Published
2023
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24. From microbiome composition to functional engineering, one step at a time

Author

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

Published
2023
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25. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource

Author

Schmidt, Thomas S B, primary, Fullam, Anthony, additional, Ferretti, Pamela, additional, Orakov, Askarbek, additional, Maistrenko, Oleksandr M, additional, Ruscheweyh, Hans-Joachim, additional, Letunic, Ivica, additional, Duan, Yiqian, additional, Van Rossum, Thea, additional, Sunagawa, Shinichi, additional, Mende, Daniel R, additional, Finn, Robert D, additional, Kuhn, Michael, additional, Pedro Coelho, Luis, additional, and Bork, Peer, additional

Published
2023
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27. Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals

Author

Rouan, Alice, primary, Pousse, Melanie, additional, Djerbi, Nadir, additional, Porro, Barbara, additional, Bourdin, Guillaume, additional, Carradec, Quentin, additional, Hume, Benjamin CC., additional, Poulain, Julie, additional, Lê-Hoang, Julie, additional, Armstrong, Eric, additional, Agostini, Sylvain, additional, Salazar, Guillem, additional, Ruscheweyh, Hans-Joachim, additional, Aury, Jean-Marc, additional, Paz-García, David A., additional, McMinds, Ryan, additional, Giraud-Panis, Marie-Josèphe, additional, Deshuraud, Romane, additional, Ottaviani, Alexandre, additional, Morini, Lycia Die, additional, Leone, Camille, additional, Wurzer, Lia, additional, Tran, Jessica, additional, Zoccola, Didier, additional, Pey, Alexis, additional, Moulin, Clémentine, additional, Boissin, Emilie, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, de Vargas, Colomban, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, Douville, Eric, additional, Flores, Michel, additional, Reynaud, Stéphanie, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Planes, Serge, additional, Allemand, Denis, additional, Pesant, Stephane, additional, Galand, Pierre E., additional, Wincker, Patrick, additional, Sunagawa, Shinichi, additional, Röttinger, Eric, additional, Furla, Paola, additional, Voolstra, Christian R., additional, Forcioli, Didier, additional, Lombard, Fabien, additional, and Gilson, Eric, additional

Published
2023
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28. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Author

Veglia, Alex J., primary, Bistolas, Kalia S. I., additional, Voolstra, Christian R., additional, Hume, Benjamin C. C., additional, Ruscheweyh, Hans-Joachim, additional, Planes, Serge, additional, Allemand, Denis, additional, Boissin, Emilie, additional, Wincker, Patrick, additional, Poulain, Julie, additional, Moulin, Clémentine, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Galand, Pierre E., additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Sunagawa, Shinichi, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Zoccola, Didier, additional, Correa, Adrienne M. S., additional, and Vega Thurber, Rebecca L., additional

Published
2023
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29. Diversity of the Pacific Ocean coral reef microbiome

Author

Galand, Pierre E., primary, Ruscheweyh, Hans-Joachim, additional, Salazar, Guillem, additional, Hochart, Corentin, additional, Henry, Nicolas, additional, Hume, Benjamin C. C., additional, Oliveira, Pedro H., additional, Perdereau, Aude, additional, Labadie, Karine, additional, Belser, Caroline, additional, Boissin, Emilie, additional, Romac, Sarah, additional, Poulain, Julie, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Moulin, Clémentine, additional, Armstrong, Eric J., additional, Paz-García, David A., additional, Ziegler, Maren, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Zoccola, Didier, additional, Voolstra, Christian R., additional, Thurber, Rebecca Vega, additional, Sunagawa, Shinichi, additional, Wincker, Patrick, additional, Allemand, Denis, additional, and Planes, Serge, additional

Published
2023
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30. Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Author

Hochart, Corentin, primary, Paoli, Lucas, additional, Ruscheweyh, Hans-Joachim, additional, Salazar, Guillem, additional, Boissin, Emilie, additional, Romac, Sarah, additional, Poulain, Julie, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Moulin, Clémentine, additional, Ziegler, Maren, additional, Porro, Barbara, additional, Armstrong, Eric J., additional, Hume, Benjamin C. C., additional, Aury, Jean-Marc, additional, Pogoreutz, Claudia, additional, Paz-García, David A., additional, Nugues, Maggy M., additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Wincker, Patrick, additional, Zoccola, Didier, additional, Allemand, Denis, additional, Planes, Serge, additional, Thurber, Rebecca Vega, additional, Voolstra, Christian R., additional, Sunagawa, Shinichi, additional, and Galand, Pierre E., additional

Published
2023
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31. mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations.

Author

Sintsova, Anna, Ruscheweyh, Hans-Joachim, Field, Christopher M, Feer, Lilith, Nguyen, Bidong D, Daniel, Benjamin, Hardt, Wolf-Dietrich, Vorholt, Julia A, and Sunagawa, Shinichi

Subjects
*TRANSPOSONS, *DNA analysis, *WEB-based user interfaces, *GENETIC barcoding, *POPULATION dynamics, *SOURCE code, *DNA insertion elements
Abstract

Motivation DNA barcoding has become a powerful tool for assessing the fitness of strains in a variety of studies, including random transposon mutagenesis screens, attenuation of site-directed mutants, and population dynamics of isogenic strain pools. However, the statistical analysis, visualization, and contextualization of the data resulting from such experiments can be complex and require bioinformatic skills. Results Here, we developed mBARq, a user-friendly tool designed to simplify these steps for diverse experimental setups. The tool is seamlessly integrated with an intuitive web app for interactive data exploration via the STRING and KEGG databases to accelerate scientific discovery. Availability and implementation The tool is implemented in Python. The source code is freely available (https://github.com/MicrobiologyETHZ/mbarq) and the web app can be accessed at: https://microbiomics.io/tools/mbarq-app. [ABSTRACT FROM AUTHOR]

Published
2024
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32. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.

Author

Schmidt, Thomas S B, Fullam, Anthony, Ferretti, Pamela, Orakov, Askarbek, Maistrenko, Oleksandr M, Ruscheweyh, Hans-Joachim, Letunic, Ivica, Duan, Yiqian, Van Rossum, Thea, Sunagawa, Shinichi, Mende, Daniel R, Finn, Robert D, Kuhn, Michael, Pedro Coelho, Luis, and Bork, Peer

Published
2024
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33. Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Author

Hochart, Corentin, Paoli, Lucas, Ruscheweyh, Hans-Joachim, Salazar, Guillem, Boissin, Emilie, Romac, Sarah, Poulain, Julie, Hume, Benjamin C. C., Pogoreutz, Claudia, and Voolstra, Christian R.

Subjects
Multidisciplinary, ddc:570, General Physics and Astronomy, General Chemistry, General Biochemistry, Genetics and Molecular Biology
Abstract

Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera ( Pocillopora , Porites , Millepora ) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae . These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora , appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites . Millepora is more rarely associated to Endozoicomonadaceae . Our results show that different coral genera exhibit distinct strategies of host- Endozoicomonadaceae associations that are defined at the bacteria lineage level. published

Published
2023

34. mOTUs database

Author

Milanese, Alessio, Ruscheweyh, Hans-Joachim, Mende, Daniel, Zeller, Georg, and Sunagawa, Shinichi

Abstract

Database for the marker gene-based OTU (mOTU) profiler. The mOTUs profiler is a computational tool that estimates relative abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data. Github directory of the tool: link

Published
2023
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36. 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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37. Anaerobutyricum hallii promotes the functional depletion of a food carcinogen in diverse healthy fecal microbiota.

Author

Garcia, Alejandro Ramirez, Greppi, Anna, Constancias, Florentin, Ruscheweyh, Hans-Joachim, Gasser, Julie, Hurley, Katherine, Sturla, Shana J., Schwab, Clarissa, and Lacroix, Christophe

Subjects
ENTEROTYPES, HUMAN microbiota, SHORT-chain fatty acids, CARCINOGENS, FUNCTIONAL foods
Abstract

Introduction: Anaerobutyricum hallii is a human gut commensal that transforms the heterocyclic amine 2-amino-1-methyl-6-phenylimidazo [4,5-b] pyridine (PhIP), a carcinogen from cooked meat. The transformation mechanism involves the microbial production of acrolein from glycerol, and its conjugation with PhIP, thus blocking its mutagenic potential. A potential cancer prevention strategy could therefore involve supplementing complex human microbial communities with metabolically competent bacteria such as A. hallii that can deplete PhIP. However, it has not been established how the proportion of A. hallii in diverse healthy human gut microbial communities relates to functional capacity for PhIP transformation and, moreover, how supplementing microbiomes with A. hallii affects this function. Methods: In this study, shotgun metagenomics was used to study taxonomic profiling, the abundance of glycerol/diol dehydratase (gdh)-harboring taxa, the proportion of resident A. hallii, and the reconstruction of A. hallii population genomes in the fecal samples of 20 healthy young adult donors. Furthermore, the influence of supplementing 106 cells/mL of A. hallii DSM 3353 with diluted fecal microbiota was characterized. Results and discussion: Six microbiota were assigned to Bacteroides, nine to Prevotella, and five to Ruminococcus by enterotype-associated clustering. The total number of gdh copies in the 20 fecal microbiota expressed per 1010 bacterial cells ranged between 1.32 × 108 and 1.15 × 109. Eighteen out of the 20 donors were dominated by A. hallii, representing between 33% and 94% of the total gdh relative abundance of the samples. Themicrobiota with low A. hallii abundance (i.e., with a relative abundance < 1%) transformed less PhIP than the microbiota with high A. hallii abundance (i.e., with a relative abundance > 1%). Furthermore, supplementing the low-A. hallii-abundantmicrobiota with glycerol significantly increased the PhIP transformation capacity after 6 h while reducing total short-chain fatty acid (SCFA) levels, which is most likely due to acrolein production. Although acetate decreased in allmicrobiota with glycerol and with the combination of glycerol and A. hallii, for most of the microbiomes, butyrate production increased over time. Thus, for a significant number of diverse healthy human fecal microbiomes, and especially when they have little of the taxa to start with, supplementing A. hallii increases PhIP transformation. These findings suggest the need to test in vivo whether supplementing microbiomes with A. hallii reduces PhIP exposure. [ABSTRACT FROM AUTHOR]

Published
2023
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38. Diversity of the Pacific Ocean coral reef microbiome

Author

Galand, Pierre E., Ruscheweyh, Hans-Joachim, Salazar, Guillem, Hochart, Corentin, Henry, Nicolas, Hume, Benjamin C. C., Oliveira, Pedro H., Perdereau, Aude, Labadie, Karine, and Voolstra, Christian R.

Subjects
ddc:570
Abstract

Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems. published

Published
2023

39. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Author

Belser, Caroline, Poulain, Julie, Labadie, Karine, Gavory, Frederick, Alberti, Adriana, Guy, Julie, Carradec, Quentin, Cruaud, Corinne, Da Silva, Corinne, Engelen, Stefan, Mielle, Paul, Perdereau, Aude, Samson, Gaelle, Gas, Shahinaz, Voolstra, Christian R., Galand, Pierre E., Flores, J. Michel, Hume, Benjamin C.C., Perna, Gabriela, Ziegler, Maren, Ruscheweyh, Hans-Joachim, Sunagawa, Shinichi, and Genoscope Technical Team

Abstract

Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene., Scientific Data, 10 (1), ISSN:2052-4463

Published
2023
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40. mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes

Author

Swiss National Science Foundation, Agencia Estatal de Investigación (España), Biotechnology and Biological Sciences Research Council (UK), Salazar, Guillem, Ruscheweyh, Hans-Joachim, Hildebrand, Falk, Hildebrand, Falk , Silvia G., Sunagawa, Shinichi, Swiss National Science Foundation, Agencia Estatal de Investigación (España), Biotechnology and Biological Sciences Research Council (UK), Salazar, Guillem, Ruscheweyh, Hans-Joachim, Hildebrand, Falk, Hildebrand, Falk , Silvia G., and Sunagawa, Shinichi

Abstract

Profiling the taxonomic composition of microbial communities commonly involves the classification of ribosomal RNA gene fragments. As a trade-off to maintain high classification accuracy, existing tools are typically limited to the genus level. Here, we present mTAGs, a taxonomic profiling tool that implements the alignment of metagenomic sequencing reads to degenerate consensus reference sequences of small subunit ribosomal RNA genes. It uses DNA fragments, that is, paired-end sequencing reads, as count units and provides relative abundance profiles at multiple taxonomic ranks, including operational taxonomic units based on a 97% sequence identity cutoff. At the genus rank, mTAGs outperformed other tools across several metrics, such as the F1 score by >11% across data from different environments, and achieved competitive (F1 score) or better results (Bray–Curtis dissimilarity) at the sub-genus level

Published
2022

41. 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 T.L.C., 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, Strowig, Till, Bremges, Andreas, Sczyrba, Alexander, McHardy, Alice Carolyn, 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 T.L.C., 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, Strowig, Till, Bremges, Andreas, Sczyrba, Alexander, and McHardy, Alice Carolyn

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

42. Biosynthetic potential of the global ocean microbiome

Author

Helmut Horten Foundation, Swiss National Science Foundation, Gordon and Betty Moore Foundation, European Commission, Peter and Traudl Engelhorn Foundation, German Research Foundation, National Science Foundation (US), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), 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, Mikhaill, Mustafa, Harun, Larralde, Martin, Carroll, Laura M., Sánchez Fernández, 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, Sunagawa, Shinichi, Helmut Horten Foundation, Swiss National Science Foundation, Gordon and Betty Moore Foundation, European Commission, Peter and Traudl Engelhorn Foundation, German Research Foundation, National Science Foundation (US), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), 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, Mikhaill, Mustafa, Harun, Larralde, Martin, Carroll, Laura M., Sánchez Fernández, 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

Abstract

Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups1, this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds2,3. However, studying this diversity to identify genomic pathways for the synthesis of such compounds4 and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters (‘Candidatus Eudoremicrobiaceae’) that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments

Published
2022

43. NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis

Author

Singer, Jochen, Ruscheweyh, Hans-Joachim, Hofmann, Ariane L., Thurnherr, Thomas, Singer, Franziska, Toussaint, Nora C., Ng, Charlotte K Y., Piscuoglio, Salvatore, Beisel, Christian, Christofori, Gerhard, Dummer, Reinhard, Hall, Michael N., Krek, Wilhelm, Levesque, Mitchell P., Manz, Markus G., Moch, Holger, Papassotiropoulos, Andreas, Stekhoven, Daniel J., Wild, Peter, Wüst, Thomas, Rinn, Bernd, Beerenwinkel, Niko, and Berger, Bonnie

Abstract

Motivation Next-generation sequencing is now an established method in genomics, and massive amounts of sequencing data are being generated on a regular basis. Analysis of the sequencing data is typically performed by lab-specific in-house solutions, but the agreement of results from different facilities is often small. General standards for quality control, reproducibility and documentation are missing. Results We developed NGS-pipe, a flexible, transparent and easy-to-use framework for the design of pipelines to analyze whole-exome, whole-genome and transcriptome sequencing data. NGS-pipe facilitates the harmonization of genomic data analysis by supporting quality control, documentation, reproducibility, parallelization and easy adaptation to other NGS experiments. Availability and implementation https://github.com/cbg-ethz/NGS-pipe

Published
2021

47. A cross-biomes bacterial diversity shed light on ocean-atmosphere microbial transmission

Author

Lang-Yona, Naama, primary, Flores, J. Michel, additional, Haviv, Rotem, additional, Alberti, Adriana, additional, Poulain, Julie, additional, Belser, Caroline, additional, Trainic, Miri, additional, Gat, Daniella, additional, Ruscheweyh, Hans-Joachim, additional, Wincker, Patrick, additional, Sunagawa, Shinichi, additional, Rudich, Yinon, additional, Koren, Ilan, additional, and Vardi, Assaf, additional

Published
2021
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49. Additional file 2 of Multi-omics data integration reveals novel drug targets in hepatocellular carcinoma

Author

Dimitrakopoulos, Christos, Hindupur, Sravanth Kumar, Colombi, Marco, Liko, Dritan, Ng, Charlotte K. Y., Piscuoglio, Salvatore, Behr, Jonas, Moore, Ariane L., Singer, Jochen, Ruscheweyh, Hans-Joachim, Matter, Matthias S., Mossmann, Dirk, Terracciano, Luigi M., Hall, Michael N., and Beerenwinkel, Niko

Abstract

Additional file 2: Figure S2. A. Graph showing miRNA expression of miR-375 in L-dKO tumors (n=12) compared to control mice (n=6). B. mRNA expression analysis of indicated genes in 20-week-old L-dKO tumors compared to livers from age-matched control mice (n = 6). Expression for each gene is normalized to intensity of TBP gene expression (normalising control) in the corresponding mice. Two-sided unpaired t-test is used. Data is mean ± s.d.

Published
2021
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50. Reference genome-independent taxonomic profiling of microbiomes with mOTUs3

Author

Ruscheweyh, Hans-Joachim, primary, Milanese, Alessio, additional, Paoli, Lucas, additional, Karcher, Nicolai, additional, Clayssen, Quentin, additional, Metzger, Marisa Isabell, additional, Wirbel, Jakob, additional, Bork, Peer, additional, Mende, Daniel R., additional, Zeller, Georg, additional, and Sunagawa, Shinichi, additional

Published
2021
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