Publications

• Guillem Salazar, Hans-Joachim Ruscheweyh, Falk Hildebrand, Silvia G Acinas, Shinichi Sunagawa. (2021) mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes. Bioinformatics
• Silvia G. Acinas, Pablo Sánchez, Guillem Salazar, Francisco M. Cornejo-Castillo, Marta Sebastián, Ramiro Logares, Marta Royo-Llonch, Lucas Paoli, Shinichi Sunagawa, Pascal Hingamp, Hiroyuki Ogata, Gipsi Lima-Mendez, Simon Roux, José M. González, Jesús M. Arrieta, Intikhab S. Alam, Allan Kamau, Chris Bowler, Jeroen Raes, Stéphane Pesant, Peer Bork, Susana Agustí, Takashi Gojobori, Dolors Vaqué, Matthew B. Sullivan, Carlos Pedrós-Alió, Ramon Massana, Carlos M. Duarte, Josep M. Gasol. (2021) Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Communications Biology 4 (1)
• Jakob Wirbel, Konrad Zych, Morgan Essex, Nicolai Karcher, Ece Kartal, Guillem Salazar, Peer Bork, Shinichi Sunagawa, Georg Zeller. (2021) Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox. Genome Biology 22 (1)
• Hisashi Endo, Romain Blanc-Mathieu, Yanze Li, Guillem Salazar, Nicolas Henry, Karine Labadie, Colomban de Vargas, Matthew B. Sullivan, Chris Bowler, Patrick Wincker, Lee Karp-Boss, Shinichi Sunagawa, Hiroyuki Ogata. (2020) Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions. Nature Ecology & Evolution 4 (12) 1639-1649
• Isabel Sanz-Sáez, Guillem Salazar, Pablo Sánchez, Elena Lara, Marta Royo-Llonch, Elisabet L. Sà, Teresa Lucena, María J. Pujalte, Dolors Vaqué, Carlos M. Duarte, Josep M. Gasol, Carlos Pedrós-Alió, Olga Sánchez, Silvia G. Acinas. (2020) Diversity and distribution of marine heterotrophic bacteria from a large culture collection. BMC Microbiology 20 (1)
• Clara Ruiz‐González, Mireia Mestre, Marta Estrada, Marta Sebastián, Guillem Salazar, Susana Agustí, Enrique Moreno‐Ostos, Isabel Reche, Xosé Antón Álvarez‐Salgado, Xosé Anxelu G. Morán, Carlos M. Duarte, M. Montserrat Sala, Josep M. Gasol. (2020) Major imprint of surface plankton on deep ocean prokaryotic structure and activity. Molecular Ecology 29 (10) 1820-1838
• Ramiro Logares, Ina M. Deutschmann, Pedro C. Junger, Caterina R. Giner, Anders K. Krabberød, Thomas S. B. Schmidt, Laura Rubinat-Ripoll, Mireia Mestre, Guillem Salazar, Clara Ruiz-González, Marta Sebastián, Colomban de Vargas, Silvia G. Acinas, Carlos M. Duarte, Josep M. Gasol, Ramon Massana. (2020) Disentangling the mechanisms shaping the surface ocean microbiota. Microbiome 8 (1)
• Victor M. Eguíluz, Guillem Salazar, Juan Fernández-Gracia, John K. Pearman, Josep M. Gasol, Silvia G. Acinas, Shinichi Sunagawa, Xabier Irigoien, Carlos M. Duarte. (2019) Scaling of species distribution explains the vast potential marine prokaryote diversity. Scientific Reports 9 (1)
• Guillem Salazar, Lucas Paoli, Adriana Alberti, Jaime Huerta-Cepas, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Christopher M. Field, Luis Pedro Coelho, Corinne Cruaud, Stefan Engelen, Ann C. Gregory, Karine Labadie, Claudie Marec, Eric Pelletier, Marta Royo-Llonch, Simon Roux, Pablo Sánchez, Hideya Uehara, Ahmed A. Zayed, Georg Zeller, Margaux Carmichael, Céline Dimier, Joannie Ferland, Stefanie Kandels, Marc Picheral, Sergey Pisarev, Julie Poulain, Silvia G. Acinas, Marcel Babin, Peer Bork, Chris Bowler, Colomban de Vargas, Lionel Guidi, Pascal Hingamp, Daniele Iudicone, Lee Karp-Boss, Eric Karsenti, Hiroyuki Ogata, Stephane Pesant, Sabrina Speich, Matthew B. Sullivan, Patrick Wincker, Shinichi Sunagawa, Silvia G. Acinas, Marcel Babin, Peer Bork, Emmanuel Boss, Chris Bowler, Guy Cochrane, Colomban de Vargas, Michael Follows, Gabriel Gorsky, Nigel Grimsley, Lionel Guidi, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Stefanie Kandels-Lewis, Lee Karp-Boss, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Stephane Pesant, Nicole Poulton, Jeroen Raes, Christian Sardet, Sabrina Speich, Lars Stemmann, Matthew B. Sullivan, Shinichi Sunagawa, Patrick Wincker. (2019) Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. Cell 179 (5) 1068-1083.e21
• Federico M. Ibarbalz, Nicolas Henry, Manoela C. Brandão, Séverine Martini, Greta Busseni, Hannah Byrne, Luis Pedro Coelho, Hisashi Endo, Josep M. Gasol, Ann C. Gregory, Frédéric Mahé, Janaina Rigonato, Marta Royo-Llonch, Guillem Salazar, Isabel Sanz-Sáez, Eleonora Scalco, Dodji Soviadan, Ahmed A. Zayed, Adriana Zingone, Karine Labadie, Joannie Ferland, Claudie Marec, Stefanie Kandels, Marc Picheral, Céline Dimier, Julie Poulain, Sergey Pisarev, Margaux Carmichael, Stéphane Pesant, Marcel Babin, Emmanuel Boss, Daniele Iudicone, Olivier Jaillon, Silvia G. Acinas, Hiroyuki Ogata, Eric Pelletier, Lars Stemmann, Matthew B. Sullivan, Shinichi Sunagawa, Laurent Bopp, Colomban de Vargas, Lee Karp-Boss, Patrick Wincker, Fabien Lombard, Chris Bowler, Lucie Zinger, Silvia G. Acinas, Marcel Babin, Peer Bork, Emmanuel Boss, Chris Bowler, Guy Cochrane, Colomban de Vargas, Mick Follows, Gabriel Gorsky, Nigel Grimsley, Lionel Guidi, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Stefanie Kandels, Lee Karp-Boss, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Stéphane Pesant, Nicole Poulton, Jeroen Raes, Christian Sardet, Sabrina Speich, Lars Stemmann, Matthew B. Sullivan, Shinichi Sunagawa, Patrick Wincker. (2019) Global Trends in Marine Plankton Diversity across Kingdoms of Life. Cell 179 (5) 1084-1097.e21
• Julien Massoni, Miriam Bortfeld-Miller, Ludwig Jardillier, Guillem Salazar, Shinichi Sunagawa, Julia A. Vorholt. (2019) Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species. The ISME Journal 14 (1) 245-258
• Alessio Milanese, Daniel R Mende, Lucas Paoli, Guillem Salazar, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Pascal Hingamp, Renato Alves, Paul I Costea, Luis Pedro Coelho, Thomas S. B. Schmidt, Alexandre Almeida, Alex L Mitchell, Robert D. Finn, Jaime Huerta-Cepas, Peer Bork, Georg Zeller, Shinichi Sunagawa. (2019) Microbial abundance, activity and population genomic profiling with mOTUs2. Nature Communications 10 (1)
• Ernesto Villarino, James R. Watson, Bror Jönsson, Josep M. Gasol, Guillem Salazar, Silvia G. Acinas, Marta Estrada, Ramón Massana, Ramiro Logares, Caterina R. Giner, Massimo C. Pernice, M. Pilar Olivar, Leire Citores, Jon Corell, Naiara Rodríguez-Ezpeleta, José Luis Acuña, Axayacatl Molina-Ramírez, J. Ignacio González-Gordillo, Andrés Cózar, Elisa Martí, José A. Cuesta, Susana Agustí, Eugenio Fraile-Nuez, Carlos M. Duarte, Xabier Irigoien, Guillem Chust. (2018) Large-scale ocean connectivity and planktonic body size. Nature Communications 9 (1)
• Elena Lara, Dolors Vaqué, Elisabet Laia Sà, Julia A. Boras, Ana Gomes, Encarna Borrull, Cristina Díez-Vives, Eva Teira, Massimo C. Pernice, Francisca C. Garcia, Irene Forn, Yaiza M. Castillo, Aida Peiró, Guillem Salazar, Xosé Anxelu G. Morán, Ramon Massana, Teresa S. Catalá, Gian Marco Luna, Susana Agustí, Marta Estrada, Josep M. Gasol, Carlos M. Duarte. (2017) Unveiling the role and life strategies of viruses from the surface to the dark ocean. Science Advances 3 (9) e1602565
• Marta Royo-Llonch, Isabel Ferrera, Francisco M. Cornejo-Castillo, Pablo Sánchez, Guillem Salazar, Ramunas Stepanauskas, José M. González, Michael E. Sieracki, Sabrina Speich, Lars Stemmann, Carlos Pedrós-Alió, Silvia G. Acinas. (2017) Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes. Frontiers in Microbiology 8
• Guillem Salazar, Shinichi Sunagawa. (2017) Marine microbial diversity. Current Biology 27 (11) R489-R494
• Francisco M. Cornejo-Castillo, Ana M. Cabello, Guillem Salazar, Patricia Sánchez-Baracaldo, Gipsi Lima-Mendez, Pascal Hingamp, Adriana Alberti, Shinichi Sunagawa, Peer Bork, Colomban de Vargas, Jeroen Raes, Chris Bowler, Patrick Wincker, Jonathan P. Zehr, Josep M. Gasol, Ramon Massana, Silvia G. Acinas. (2016) Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton. Nature Communications 7 (1)
• Clara Ruiz-González, Guillem Salazar, Ramiro Logares, Lorenzo Proia, Josep M. Gasol, Sergi Sabater. (2015) Weak Coherence in Abundance Patterns Between Bacterial Classes and Their Constituent OTUs Along a Regulated River. Frontiers in Microbiology 6
• Guillem Salazar, Francisco M. Cornejo-Castillo, Encarna Borrull, Cristina Díez-Vives, Elena Lara, Dolors Vaqué, Jesús M. Arrieta, Carlos M. Duarte, Josep M. Gasol, Silvia G. Acinas. (2015) Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes. Molecular Ecology 24 (22) 5692-5706
• Guillem Salazar, Francisco M Cornejo-Castillo, Verónica Benítez-Barrios, Eugenio Fraile-Nuez, X Antón Álvarez-Salgado, Carlos M Duarte, Josep M Gasol, Silvia G Acinas. (2015) Global diversity and biogeography of deep-sea pelagic prokaryotes. The ISME Journal 10 (3) 596-608
• S. Agusti, J. I. González-Gordillo, D. Vaqué, M. Estrada, M. I. Cerezo, G. Salazar, J. M. Gasol, C. M. Duarte. (2015) Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump. Nature Communications 6 (1)
• Federico Baltar, Joakim Palovaara, Maria Vila-Costa, Guillem Salazar, Eva Calvo, Carles Pelejero, Cèlia Marrasé, Josep M. Gasol, Jarone Pinhassi. (2015) Response of rare, common and abundant bacterioplankton to anthropogenic perturbations in a Mediterranean coastal site. FEMS Microbiology Ecology 91 (6)
• G. Lima-Mendez, K. Faust, N. Henry, J. Decelle, S. Colin, F. Carcillo, S. Chaffron, J. C. Ignacio-Espinosa, S. Roux, F. Vincent, L. Bittner, Y. Darzi, J. Wang, S. Audic, L. Berline, G. Bontempi, A. M. Cabello, L. Coppola, F. M. Cornejo-Castillo, F. d’Ovidio, L. De Meester, I. Ferrera, M.-J. Garet-Delmas, L. Guidi, E. Lara, S. Pesant, M. Royo-Llonch, G. Salazar, P. Sanchez, M. Sebastian, C. Souffreau, C. Dimier, M. Picheral, S. Searson, S. Kandels-Lewis, G. Gorsky, F. Not, H. Ogata, S. Speich, L. Stemmann, J. Weissenbach, P. Wincker, S. G. Acinas, S. Sunagawa, P. Bork, M. B. Sullivan, E. Karsenti, C. Bowler, C. de Vargas, J. Raes, NA NA. (2015) Determinants of community structure in the global plankton interactome. Science 348 (6237) 1262073-1262073
• S. Sunagawa, L. P. Coelho, S. Chaffron, J. R. Kultima, K. Labadie, G. Salazar, B. Djahanschiri, G. Zeller, D. R. Mende, A. Alberti, F. M. Cornejo-Castillo, P. I. Costea, C. Cruaud, F. d’Ovidio, S. Engelen, I. Ferrera, J. M. Gasol, L. Guidi, F. Hildebrand, F. Kokoszka, C. Lepoivre, G. Lima-Mendez, J. Poulain, B. T. Poulos, M. Royo-Llonch, H. Sarmento, S. Vieira-Silva, C. Dimier, M. Picheral, S. Searson, S. Kandels-Lewis, C. Bowler, C. de Vargas, G. Gorsky, N. Grimsley, P. Hingamp, D. Iudicone, O. Jaillon, F. Not, H. Ogata, S. Pesant, S. Speich, L. Stemmann, M. B. Sullivan, J. Weissenbach, P. Wincker, E. Karsenti, J. Raes, S. G. Acinas, P. Bork, E. Boss, C. Bowler, M. Follows, L. Karp-Boss, U. Krzic, E. G. Reynaud, C. Sardet, M. Sieracki, D. Velayoudon, NA NA. (2015) Structure and function of the global ocean microbiome. Science 348 (6237) 1261359-1261359
• Silvia G. Acinas, Isabel Ferrera, Hugo Sarmento, Cristina Díez-Vives, Irene Forn, Clara Ruiz-González, Francisco M. Cornejo-Castillo, Guillem Salazar, Josep M. Gasol. (2014) Validation of a new catalysed reporter deposition-fluorescencein situhybridization probe for the accurate quantification of marineBacteroidetespopulations. Environmental Microbiology 17 (10) 3557-3569
• Isabel Ferrera, Carles M. Borrego, Guillem Salazar, Josep M. Gasol. (2013) Marked seasonality of aerobic anoxygenic phototrophic bacteria in the coastal NW Mediterranean Sea as revealed by cell abundance, pigment concentration and pyrosequencing ofpufMgene. Environmental Microbiology 16 (9) 2953-2965
• Ramiro Logares, Shinichi Sunagawa, Guillem Salazar, Francisco M. Cornejo-Castillo, Isabel Ferrera, Hugo Sarmento, Pascal Hingamp, Hiroyuki Ogata, Colomban de Vargas, Gipsi Lima-Mendez, Jeroen Raes, Julie Poulain, Olivier Jaillon, Patrick Wincker, Stefanie Kandels-Lewis, Eric Karsenti, Peer Bork, Silvia G. Acinas. (2013) Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environmental Microbiology 16 (9) 2659-2671
• Raquel Rodríguez-Martínez, Gabrielle Rocap, Guillem Salazar, Ramon Massana. (2013) Biogeography of the uncultured marine picoeukaryote MAST-4: temperature-driven distribution patterns. The ISME Journal 7 (8) 1531-1543
• Z. Salvadó, F. N. Arroyo-López, J. M. Guillamón, G. Salazar, A. Querol, E. Barrio. (2011) Temperature Adaptation Markedly Determines Evolution within the GenusSaccharomyces. Applied and Environmental Microbiology 77 (7) 2292-2302
• Carmen Rojo, Guillem Salazar. (2010) Why are there so many kinds of planktonic consumers? The answer lies in the allometric diet breadth. Hydrobiologia 653 (1) 91-102
• Carmen Rojo, Matilde Segura, María A. Rodrigo, Guillem Salazar. (2008) Factors controlling the colonial structure of Pediastrum tetras (Chlorophyceae). Hydrobiologia 617 (1) 143-155
• Carmen Rojo, María A. Rodrigo, Guillem Salazar, Miguel Álvarez-Cobelas. (2008) Nitrate uptake rates in freshwater plankton: the effect of food web structure. Marine and Freshwater Research 59 (8) 717