Publications (*=equal contribution; #=corresponding author; total citations: 56455; h-factor: 87)
157. Inducing novel endosymbioses by implanting bacteria in fungi.
Giger GH, Ernst C, Richter I, Gassler T, Field CM, Sintsova A, Kiefer P, Gabelein CG, Guillaume–Gentil O, Scherlach K, Bortfeld-Miller M, Zambelli T, Sunagawa S, Kunzler M, Hertweck C, Vorholt JA
Nature:  2024.
156. Trait-based study predicts glycerol/diol dehydratases as a key function of the gut microbiota of hindgut-fermenting carnivores.
Li Q, Ruscheweyh HJ, Ostergaard LH, Libertella M, Simonsen KS, Sunagawa S, Scoma A, Schwab C, Ruscheweyh HJ, Ostergaard LH, Libertella M, Simonsen KS, Sunagawa S, Scoma A, Schwab C
Microbiome: 12(1), 178, 2024.
155. Salmonella Typhimurium screen identifies shifts in mixed-acid fermentation during gut colonization.
Nguyen BD, Sintsova A, Schubert C, Sichert A, Scheidegger C, Näf J, Huttman J, Lentsch V, Keys T, Rutschmann C, Christen P, Kiefer P, Keller P, Barthel M, Cuenca M, Christen B, Sauer U, Slack E, Vorholt JA, Sunagawa S, Hardt WD
Cell Host Microbe: S1931-3128(24)00322-6 2024.
154. The NEREA Augmented Observatory: an integrative approach to marine coastal ecology.
Campese L, Russo L, Abagnale M, Alberti A, Bachi G, Balestra C, Bellardini D, Buondonno A, Cardini U, Carotenuto Y, Checcucci G, Chiusano ML, D'Ambra I, D'Ippolito G, Di Capua I, Donnarumma V, Fontana A, Furia M, Galarza-Verkovitch D, Gallia1 R, Labadie K, Leone S, Licandro P, Longo A, Maselli M, Merquiol L, Murano C, Oliveira PH, Passarelli A, Percopo I, Perdereau A, Piredda R, Raffini F, Roncalli V, Ruscheweyh HJ, Russo E, Saggiomo M, Santinelli C, Sarno D, Sunagawa S, Tramontano F, Trano AC, Uttieri M, Wincker P, Zampicinini G, Casotti R, Conversano F, D'Alelio D, Iudicone D, Margiotta F, Montresor M, Russo L, Abagnale M, Alberti A, Bachi G, Balestra C, Bellardini D, Buondonno A, Cardini U, Carotenuto Y, Checcucci G, Chiusano ML, D'Ambra I, D'Ippolito G, Di Capua I, Donnarumma V, Fontana A, Furia M, Galarza-Verkovitch D, Gallia1 R, Labadie K, Leone S, Licandro P, Longo A, Maselli M, Merquiol L, Murano C, Oliveira PH, Passarelli A, Percopo I, Perdereau A, Piredda R, Raffini F, Roncalli V, Ruscheweyh HJ, Russo E, Saggiomo M, Santinelli C, Sarno D, Sunagawa S, Tramontano F, Trano AC, Uttieri M, Wincker P, Zampicinini G, Casotti R, Conversano F, D'Alelio D, Iudicone D, Margiotta F, Montresor M
Sci Data: 11, 989, 2024.
153. Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters.
Villena-Alemany C, Mujakic I, Fecskeova LK, Woodhouse J, Auladell A, Dean J, Hanusova M, Socha M, Gazulla CR, Ruscheweyh HJ, Sunagawa S, Silva Kavagutti V, Andrei AS, Grossart HP, Ghai R, Koblízek M, Piwosz K
Microbiome: 12(1), 65, 2024.
152. Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions.
Causevic S, Dubey M, Morales M, Salazar G, Sentchilo V, Carraro N, Ruscheweyh HJ, Sunagawa S, van der Meer JR
Nat Commun: 15(1), 2557, 2024.
151. Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags.
Daniel BBJ, Steiger Y, Sintsova A, Field CM, Nguyen BD, Schubert C, Cherrak Y, Sunagawa S, Hardt WD, Vorholt JA
Nat Microbiol: 9(1103–1116), 1103-1116, 2024.
150. A cryptic plasmid is among the most numerous genetic elements in the human gut.
Fogarty EC, Schechter MS, Lolans K, Sheahan ML, Veseli I, Moore RM, Kiefl E, Moody T, Rice PA, Yu MK, Mimee M, Chang EB, Ruscheweyh HJ, Sunagawa S, Mclellan SL, Willis AD, Comstock LE, Eren AM
Cell: 187(5), 1206-1222.e16, 2024.
149. mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants and isogenic strain populations.
Sintsova A, Ruscheweyh HJ, Field CM, Feer L, Nguyen BD, Daniel B, Hardt WD, Vorholt JA, Sunagawa S
Bioinformatics: 40(2), btae078, 2024.
148. Sea surface temperature reconstruction in the Pacific Ocean using multi-elemental proxy in Porites and Diploastrea corals: Application to Palau Archipelago.
Canesi M, Douville E, Montagna P, Bordier L, Caquineau S, Pons-Branchu E, Iwankow G, Stolarski J, Allemand D, Planes S, Moulin C, Lombard F, Bourdin G, Trouble R, Agostini S, Banaigs B, Boissin E, Boss E, Bowler C, de Vargas C, Flores JM, Forcioli D, Furla P, Gilson E, Galand PE, Pesant S, Sunagawa S, Thomas OP, Vega Thurber R, Voolstra CR, Wincker P, Zoccola D, Reynaud S
Chem Geol: 645, 121884, 2024.
147. Functional and evolutionary significance of unknown genes from uncultivated taxa.
Rodriguez Del Rio A, Giner-Lamia J, Cantalapiedra CP, Botas J, Deng Z, Hernandez-Plaza A, Munar-Palmer M, Santamaria-Hernando S, Rodriguez-Herva JJ, Ruscheweyh HJ, Paoli L, Schmidt TSB, Sunagawa S, Bork P, Lopez-Solanilla E, Coelho LP, Huerta-Cepas J
Nature: 626(7998), 377-384, 2024.
146. Animal-associated marine Acidobacteria with a rich natural-product repertoire.
Leopold-Messner S*, Chepkirui C*, Mabesoone MFJ, Meyer J, Paoli L, Sunagawa S, Uria AR, Wakimoto T, Piel J
Chem: 9(12), 3696-3713, 2023.
145. Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster.
Liu Y, Brinkhoff T, Berger M, Poehlein A, Voget S, Paoli L, Sunagawa S, Amann R, Simon M
Microbiome: 11(1), 265, 2023.
144. From microbiome composition to functional engineering, one step at a time.
Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt W-D, Hatzimanikatis V, Heiman CM, Herzog MK-M, Hockenberry A, Keel C, Keppler A, Lee S-J, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA
Microbiol Mol Biol Rev: 87(4), e0006323, 2023.
143. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.
Schmidt TSB*, Fullam A*, Ferretti P, Orakov A, Maistrenko OM, Ruscheweyh HJ, Letunic I, Duan Y, Van Rossum T, Sunagawa S, Mende DR, Finn RD, Kuhn M, Pedro Coelho L, Bork P
Nucl Acids Res: 52(D1), D777-D783, 2023.
142. The microbiota conditions a gut milieu that selects for wild-type Salmonella Typhimurium virulence.
Gul E, Bakkeren E, Salazar G, Steiger Y, Abi Younes A, Clerc M, Christen P, Fattinger SA, Nguyen BD, Kiefer P, Slack E, Ackermann M, Vorholt JA, Sunagawa S, Diard M, Hardt WD
PLoS Biol: 21(8):e3002253. doi: 10.1371/journal.pbio.3002253. PMID: 37651408; PMCID: PMC10499267.(8:e3002253. doi: 10.1371/journal.pbio.3002253. PMID: 37651408; PMCID: PMC10499267.), e3002253, 2023.
141. Different environmental response strategies in sympatric corals from Pacific Islands.
Porro B*, Zamoum T*, Forcioli D, Gilson E, Poquet A, Di Franco E, Barnay-Verdier S, Lombard F, Voolstra CR, Hume BCC, Galand PE, Moulin C, Boissin E, Bourdin G, Iwankow G, Poulain J, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Trouble R, Thurber RV, Wincker P, Zoccola D, Planes S, Allemand D, Rottinger E, Furla P
Commun Earth Environ: 4(1), 311, 2023.
140. Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation.
Sanz-Saez I, Sanchez P, Salazar G, Sunagawa S, de Vargas C, Bowler C, Sullivan MB, Wincker P, Karsenti E, Pedrós-Alio C, Agustí S, Gojobori T, Duarte CM, Gasol JM, Sánchez O, Acinas SG
ISME Commun: 3(1), 92, 2023.
139. Ocean-wide comparisons of mesopelagic planktonic community structures.
Rigonato J*, Budinich M*, Murillo AA, Brandao MC, Pierella Karlusich JJ, Soviadan YD, Gregory AC, Endo H, Kokoszka F, Vik D, Henry N, Fremont P, Labadie K, Zayed AA, Dimier C, Picheral M, Searson S, Poulain J, Kandels S, Pesant S, Karsenti E; Tara Oceans coordinators; Bork P, Bowler C, de Vargas C, Eveillard D, Gehlen M, Iudicone D, Lombard F, Ogata H, Stemmann L, Sullivan MB, Sunagawa S, Wincker P, Chaffron S, Jaillon O
ISME Commun: 3(1), 83, 2023.
138. Multi-omics determination of metabolome diversity in natural coral populations in the Pacific Ocean.
Reddy MM*, Goossens C*, Zhou Y, Chaib S, Raviglione D, Nicole F, Hume BCC, Forcioli D, Agostini S, Boissin E, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Trouble R, Thurber RV, Wincker P, Zoccola D, Voolstra CR, Allemand D, Planes S, Thomas OP, Banaigs B
Commun Earth Environ: 4, 281, 2023.
137. Differences in carbonate chemistry up‐regulation of long‐lived reef‐building corals.
Canesi M, Douville E, Montagna P, TavianiM, Stolarski J, Bordier L, Dapoigny A, Coulabaly GEH, Simon AC, Agelou M, Fin J, Metzl N, Iwankow G, Allemand D, Planes S, Moulin C, Lombard F, Bourdin G, Troublé, Agostini S, Banaigs B, Boissin E, Boss E, Bowler C, de Vargas C, Flores M, Forcioli D, Furla P, Gilson E, Galand PE, Pesant S, Sunagawa S, Thomas OP, Thurber RV, Voolstra CR, Wincker P, Zoccola D, Reynaud S
Sci Rep: 13(1), 11589, 2023.
136. Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation trajectories.
Voolstra CR*, Hume BCC*, Armstrong E*, Mitushasi G, Porro B, Oury O, Agostini S, Boissin E, Poulain J, Carradec Q, Paz-García DA, Zoccola D, Magalon H, Moulin C, Bourdin G, Iwankow G, Romac S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville C, Flores M, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas O, Troublé R, Thurber RV, Wincker P, Serge Planes, Allemand D, Forcioli D
npj biodivers: 2, 15, 2023.
135. Pervasive tandem duplications and convergent evolution shape coral genomes.
Noel B*, Denoeud F*, Rouan A, Buitrago-López C, Capasso L, Poulain J, Boissin E, Pousse M, Da Silva C, Couloux A, Armstrong E, Carradec Q, Cruaud C, Labadie K, Le-Hoang J, Tambutté S, Barbe V, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Allemand D, Planes S, Gilson E, Zoccola D, Wincker P, Voolstra CR, Aury JM
Genome Biol: 24(1), 123, 2023.
134. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes.
Veglia AJ*, Bistolas KSI*, Voolstra CR, Hume BCC, Ruscheweyh HJ, Planes S, Allemand D, Boissin E, Wincker P, Poulain J, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Zoccola D, Correa AMS, Vega Thurber RL
Commun Biol: 6(1), 566, 2023.
133. Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean.
Armstrong E*, Le-Hoang J*, Carradec Q, Aury JM, Noel B, Hume BCC, Voolstra CR, Poulain J, Belser C, Paz-García DA, Cruaud C, Labadie K, Da Silva C, Moulin C, Boissin E, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Zoccola D, Planes S, Allemand D, Wincker P
Nat Commun: 14(1), 3056, 2023.
132. Diversity of the Pacific Ocean coral reef microbiome.
Galand PE, Ruscheweyh HJ, Salazar G, Hochart C, Henry N, Hume BCC, Oliveira PH, Perdereau A, Labadie K, Belser C, Boissin E, Romac S, Poulain J, Bourdin G, Iwankow G, Moulin C, Armstrong EJ, Paz-García DA, Ziegler M, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Thomas OP, Troublé R, Zoccola D, Voolstra CR, Thurber RV, Sunagawa S, Wincker P, Allemand D, Planes S
Nat Commun: 14(1), 3039, 2023.
131. Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals.
Rouan A*, Pousse M*, Djerbi N*, Porro B, Bourdin G, Carradec Q, Hume BC, Poulain J, Lê-Hoang J, Armstrong E, Agostini S, Salazar G, Ruscheweyh HJ, Aury JM, Paz-García DA, McMinds R, Giraud-Panis MJ, Deshuraud R, Ottaviani A, Morini LD, Leone C, Wurzer L, Tran J, Zoccola D, Pey A, Moulin C, Boissin E, Iwankow G, Romac S, de Vargas C, Banaigs B, Boss E, Bowler C, Douville E, Flores M, Reynaud S, Thomas OP, Troublé R, Thurber RV, Planes S, Allemand D, Pesant S, Galand PE, Wincker P, Sunagawa S, Röttinger E, Furla P, Voolstra CR, Forcioli D, Lombard F, Gilson E
Nat Commun: 14(1), 3038, 2023.
130. Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean.
Hochart C, Paoli L, Ruscheweyh HJ, Salazar G, Boissin E, Romac S, Poulain J, Bourdin G, Iwankow G, Moulin C, Ziegler M, Porro B, Armstrong EJ, Hume BCC, Aury JM, Pogoreutz C, Paz-García DA, Nugues MM, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Thomas OP, Troublé R, Wincker P, Zoccola D, Allemand D, Planes S, Thurber RV, Voolstra CR, Sunagawa S, Galand PE
Nat Commun: 14(1), 3037, 2023.
129. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition.
Belser C*, Poulain J*, Labadie K, Gavory F, Alberti A, Guy J, Carradec Q, Cruaud C, Da Silva C, Engelen S, Mielle P, Perdereau A, Samson G, Gas S; Genoscope Technical Team; Voolstra CR, Galand PE, Flores JM, Hume BCC, Perna G, Ziegler M, Ruscheweyh HJ, Boissin E, Romac S, Bourdin G, Iwankow G, Moulin C, Paz García DA, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Zoccola D, Scarpelli C, Jacoby EK, Oliveira PH, Aury JM, Allemand D, Planes S, Wincker P
Sci Data: 10(1), 326, 2023.
128. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems..
Lombard F, Bourdin G, Pesant S, Agostini S, Baudena A, Boissin E, Cassar N, Clampitt M, Conan P, Da Silva O, Dimier C, Douville E, Elineau A, Fin J, Flores JM, Ghiglione JF, Hume BCC, Jalabert L, John SG, Kelly RL, Koren I, Lin Y, Marie D, McMinds R, Mériguet Z, Metzl N, Paz-García DA, Pedrotti ML, Poulain J, Pujo-Pay M, Ras J, Reverdin G, Romac S, Rouan A, Röttinger E, Vardi A, Voolstra CR, Moulin C, Iwankow G, Banaigs B, Bowler C, de Vargas C, Forcioli D, Furla P, Galand PE, Gilson E, Reynaud S, Sunagawa S, Sullivan MB, Thomas OP, Troublé R, Thurber RV, Wincker P, Zoccola D, Allemand D, Planes S, Boss E, Gorsky G
Sci Data: 10(1), 324, 2023.
127. Metabolic landscape of the male mouse gut identifies different niches determined by microbial activities.
Meier KHU, Trouillon J, Li H, Lang M, Fuhrer T, Zamboni N, Sunagawa S, Macpherson AJ, Sauer U
Nat Metab: 5(6), 1-13, 2023.
126. Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota.
Hoces D, Greter G, Arnoldini M, Staubli ML, Moresi C, Sintsova A, Berent S, Kolinko I, Bansept F, Woller A, Häfliger J, Martens E, Hardt WD, Sunagawa S, Loverdo C, Slack E
eLife: 12, e81212, 2023.
125. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.
Fullam A, Letunic I, Schmidt TSB, Ducarmon QR, Karcher N, Khedkar S, Kuhn M, Larralde M, Maistrenko OM, Malfertheiner L, Milanese A, Rodrigues JFM, Sanchis-López C, Schudoma C, Szklarczyk D, Sunagawa S, Zeller G, Huerta-Cepas J, von Mering C, Bork P, Mende DR
Nucl Acids Res: 51(D1), D760-D766, 2023.
124. Cultivation-independent genomes greatly expand taxonomic profiling capabilities of mOTUs across various environments.
Ruscheweyh HJ*, Milanese A*, Paoli L, Karcher N, Clayssen Q, Keller MI, Wirbel J, Bork P, Mende DR, Zeller G#, Sunagawa S#
Microbiome: 10(1), 212, 2022.
123. The rearing environment persistently modulates mouse phenotypes from the molecular to the behavioural level.
Jaric I, Voelkl B, Clerc M, Schmid MW, Novak J, Rosso M, Rufener R, von Kortzfleisch VT, Richter SH, Buettner M, Bleich A, Amrein I, Wolfer DP, Touma C, Sunagawa S, Wurbel H
PLoS Biol: 20(10), e3001837, 2022.
122. Metabolic reconstitution of germ-free mice by a gnotobiotic microbiota varies over the circadian cycle.
Hoces D, Lan J, Sun W, Geiser T, Staubli ML, Cappio Barazzone E, Arnoldini M, Challa TD, Klug M, Kellenberger A, Nowok S, Faccin E, Macpherson AJ, Stecher B, Sunagawa S, Zenobi R, Hardt WD, Wolfrum C, Slack E
PLoS Biol: 20(9), e3001743, 2022.
121. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems.
Richter D*, Watteaux R*, Vannier T, Leconte J, Fremont P, Reygondeau G, Maillet N, Henry N, Benoit G, Da Silva O, Delmont TO, Fernandez-Guerra A, Suweis S, Narci R, Berney C, Eveillard D, Gavory F, Guidi L, Labadie K, Mahieu E, Poulain J, Romac S, Roux S, Dimier C, Kandels S, Picheral M, Searson S; Tara Oceans Coordinators, Pesant S, Aury JM, Brum JR, Lemaitre C, Pelletier E, Bork P, Sunagawa S, Lombard F, Karp-Boss L, Bowler C, Sullivan MB, Karsenti E, Mariadassou M, Probert I, Peterlongo P, Wincker P, de Vargas C, Ribera d'Alcala M, Iudicone D, Jaillon O
eLife: 11, e78129, 2022.
120. Priorities for ocean microbiome research.
Tara Ocean Foundation, Tara Oceans, European Molecular Biology Laboratory (EMBL), European Marine Biological Resource Centre - European Research Infrastructure Consortium (EMBRC-ERIC)
Nat Microbiol: 7, 937-947, 2022.
119. Biosynthetic potential of the global ocean microbiome.
Paoli L, Ruscheweyh HJ, Forneris CC, Hubrich F, Kautsar S, Bhushan A, Lotti A, Clayssen Q, Salazar G, Milanese A, Carlstrom CI, Papadopoulou C, Gehrig D, Karasikov M, Mustafa H, Larralde M, Carroll LM, Sanchez P, Zayed AA, Cronin DR, Acinas SG, Bork P, Bowler C, Delmont TO, Gasol JM, Gossert AD, Kahles A, Sullivan MB, Wincker P, Zeller G, Robinson SL#, Piel J#, Sunagawa S#
Nature: 607(7917), 111-118, 2022.
118. Diversity and ecological footprint of Global Ocean RNA viruses.
Dominguez-Huerta G*, Zayed AA*, Wainaina JM, Guo J, Tian F, Pratama AA, Bolduc B, Mohssen M, Zablocki O, Pelletier E, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Tara Oceans Coordinators, Bowler C, Eveillard D, Guidi L, Karsenti E, Kuhn JH, Ogata H, Wincker P, Culley A, Chaffron S, Sullivan MB
Science: 376(6598), 1202-1208, 2022.
117.  The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes.
Vernette C, Lecubin J, Sanchez P; Tara Oceans Coordinators, Sunagawa S, Delmont TO, Acinas SG, Pelletier E, Hingamp P, Lescot M
Nucl Acids Res: 50(W1), W516-26, 2022.
116. Terrestrial and marine influence on atmospheric bacterial diversity over the north Atlantic and Pacific Oceans.
Lang-Yona N, Flores JM, Haviv R, Alberti A, Poulain J, Belser C, Trainic M, Gat D, Ruscheweyh HJ, Wincker P, Sunagawa S, Rudich Y, Koren I, Vardi A
Commun Earth Environ: 3, 121, 2022.
115. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean.
Delmont T, Gaia M, Hinsinger DD, Fremont P, Vanni C, Fernandez-Guerra A, Eren MA, Kourlaiev A, d'Agata L, Clayssen Q, Villar E, Labadie K, Cruaud C, Poulain J, Da Silva C, Wessner M, Noel B, Aury JM, Sunagawa S, Acinas SG, Bork P, Sardet C, Stemmann L, Lescot M, Babin M, Gorsky G, Grimsley N, Guidi L, Hingamp P, Kandels S, Iudicone D, Ogata H, Pesant S, Sullivan MB, Not F, Karp-Boss L, Boss E, Cochrane G, Follows M, Poulton N, Raes J, Sieracki M, Speich S, de Vargas C, Bowler C, Karsenti E, Pelletier E, Wincker P, Jaillon O
Cell Genomics: 2, 100123, 2022.
114. Critical Assessment of Metagenome Interpretation - the second round of challenges.
Meyer F, Fritz A, Deng ZL, Koslicki D, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, Chen B, Chikhi R, Clausen PT, Cristian A, Dabrowski PW Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Urtiskiy G, Vecedomini R, Wang Zi, Wang Zhe, Wang Zho, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC
Nat Methods: 19(4), 429-440, 2022.
113. Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome.
Zayed AA*, Wainaina JM*, Dominguez-Huerta G*, Pelletier E, Guo J, Mohssen M, Tian F, Pratama AA, Bolduc B, Zablocki O, Cronin D, Solden L, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Ruscheweyh HJ, Salazar G, Shatoff E, Tara Oceans Coordinators, Bundschuh R, Fredrick K, Kubatko LS, Chaffron S, Culley AI, Sunagawa S, Kuhn JH, Wincker P, Sullivan MB
Science: 376(6589), 156-162, 2022.
112. Towards the biogeography of prokaryotic genes.
Coelho LP, Alves R, Del Rio AR, Myers PN, Cantalapiedra CP, Giner-Lamia J, Schmidt TS, Mende DR, Orakov A, Letunic I, Hildebrand F, Van Rossum T, Forslund SK, Khedkar S, Maistrenko OM, Pan S, Jia L, Ferretti P, Sunagawa S, Zhao XM, Nielsen HB, Huerta-Cepas J, Bork P
Nature: 601(7892), 252-256, 2022.
111. MetaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes.
Van Rossum T, Costea PI, Paoli L, Alves R, Thielemann R, Sunagawa S, Bork P
Bioinformatics: 38(4), 1162-1164, 2021.
110. Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean.
Royo-Llonch M, Sanchez P, Ruiz-Gonzalez C, Salazar G, Pedros-Alio C, Sebastian M, Labadie K, Paoli L, M Ibarbalz F, Zinger L, Churcheward B; Tara Oceans Coordinators, Chaffron S, Eveillard D, Karsenti E, Sunagawa S, Wincker P, Karp-Boss L, Bowler C, Acinas SG
Nat Microbiol: 6(12), 1561-1574, 2021.
109. The rumen microbiome inhibits methane formation through dietary choline supplementation.
Li Y, Kreuzer M, Clayssen Q, Ebert MO, Ruscheweyh HJ, Sunagawa S, Kunz C, Attwood G, Amelchanka S, Terranova M
Sci Rep: 11(1), 21761, 2021.
108. mOTUs: profiling taxonomic composition, transcriptional activity and strain populations of microbial communities.
Ruscheweyh HJ, Milanese A, Paoli L, Sintsova A, Mende DR, Zeller G, Sunagawa S#
Curr Protoc: 1(8), e218, 2021.
107. Macroscale patterns of oceanic zooplankton composition and size structure.
Brandao MC*, Benedetti F*, Martini S, Soviadan YD, Irisson JO, Romagnan JB, Elineau A, Desnos C, Jalabert L, Freire AS, Picheral M, Guidi L, Gorsky G, Bowler C, Karp-Boss L, Henry N, de Vargas C, Sullivan MB, Tara Oceans Consortium Coordinators, Stemmann L, Lombard F
Sci Rep: 11, 15714, 2021.
106. mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes.
Salazar G*, Ruscheweyh HJ*, Hildebrand F, Acinas SG, Sunagawa S#
Bioinformatics: 38(1), 270-272, 2021.
105. The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves.
Pfeilmeier S, Petti GC, Bortfeld-Miller M, Daniel B, Field CM, Sunagawa S, Vorholt JA
Nat Microbiol: 6(7), 852-864, 2021.
104. miR-802 regulates Paneth cell function and enterocyte differentiation in the mouse small intestine.
Goga A*, Yagabasan B*, Herrmanns K*, Godbersen S, Silva PN, Denzler R, Zund M, Furter M, Schwank G, Sunagawa S, Hardt WD, Stoffel M
Nat Commun: 12(1), 3339, 2021.
103. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities.
Acinas SG*, Sanchez P*, Salazar G*, Cornejo-Castillo FM*, Sebastian M, Logares R, Royo-Llonch M, Paoli L, Sunagawa S, Hingamp P, Ogata H, Lima-Mendez G, Roux S, Gonzalez JM, Arrieta JM, Alam IS, Kamau A, Bowler C, Raes J. Pesant S, Bork P, Agusti S, Gojobori T, Vaque D, Sullivan MB, Pedros-Alio C, Massana R. Duarte CM
Commun Biol: 4(1), 604, 2021.
102. A general non-self response as part of plant immunity.
Maier BA, Kiefer P, Field CM, Hemmerle L, Bortfeld-Miller M, Emmenegger B, Schafer M, Pfeilmeier S, Sunagawa S, Vogel CM, Vorholt JA
Nat Plants: 7, 696-705, 2021.
101. A roadmap for metagenomic enzyme discovery.
Robinson SL, Piel J, Sunagawa S
Nat Prod Rep: 38(11), 1994-2023, 2021.
100. Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.
Wirbel J, Zych K, Essex M, Karcher N, Kartal E, Salazar G, Bork P, Sunagawa S, Zeller G
Genome Biol: 22(1), 93, 2021.
99. High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains.
Zünd M, Ruscheweyh HJ, Field CM, Meyer N, Cuenca M, Hoces D, Hardt WD, Sunagawa S#
Microbiome: 9(1), 77, 2021.
98. A community perspective on the concept of marine holobionts: current status, challenges, and future directions.
Dittami SM, Arboleda E, Auguet JC, Bigalke A, Briand E, Cardenas P, Cardini U, Decelle J, Engelen AH, Eveillard D, Gachon CMM, Griffith SM, Harder T, Kayal E, Kazamia E, Lallier FH, Medina M, Marzinelli EM, Morganti TM, Nunez Pons L, Prado S, Pintado J, Saha M, Selosse MA, Skillings D, Stock W, Sunagawa S, Toulza E, Vorobev A, Leblanc C, Not F
PeerJ: 9, e10911, 2021.
97. Space, time and microdiversity: towards a resolution revolution in microbiomics.
Paoli L, Sunagawa S#
Environ Microbiol Rep: 13(1), 31-35, 2021.
96. Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions.
Endo H, Blanc-Mathieu R, Li Y, Salazar G, Henry N, Labadie K, deVargas C, Sullivan MB, Bowler C, Wincker P, Karp-Boss L, Sunagawa S, Ogata H
Nat Ecol Evol: 4(12), 1639-1649, 2020.
95. Tara Oceans: towards global ocean ecosystems biology.
Sunagawa S#, Acinas SG, Bork P, Bowler C, Tara Oceans Coordinators, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F, Ogata H, Pesant S, Sullivan MB, Wincker P, de Vargas C
Nat Rev Microbiol: 18(8), 428-445, 2020.
94. Import of aspartate and malate by DcuABC drives H2/fumarate respiration to promote initial Salmonella gut-lumen colonization.
Nguyen BD , Cuenca M, Hartl J, Gul E, Bauer R, Meile S, Ruthi J, Margot C, Heeb L, Besser F, Perez Escriva P, Fetz C, Furter M, Laganenka L, Keller P, Fuchs LM, Christen M, Porwollik S, McClelland M, Vorholt JA, Sauer U, Sunagawa S#, Christen B#, Hardt WD#
Cell Host Microbe: 27(6), 922-936, 2020.
93. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.
Maistrenko OM*, Mende D*, Luetge M, Hildebrand F, Schmidt TSB, Li SS, Matias Rodrigues JG, von Mering C, Coelho LP, Huerta-Cepas J, Sunagawa S, Bork P
ISME J: 14(5), 1247-1259, 2020.
92. Tara Pacific expedition’s atmospheric measurements. Marine aerosols across the Atlantic and Pacific Oceans. Overview and preliminary results.
Flores JM, Bourdin G, Altaratz O, Trainic M, Lang-Yona N, Dzimban E, Steinau S, Tettich F, Planes S, Allemand D, Agostini S, Banaigs B, Boissin E, Boss E, Douville E, Forcioli D, Furla P, Galand PE, Sullivan M, Gilson E, Lombard F, Moulin C, Pesant S, Poulain J, Reynaud S, Romac S, Sunagawa S, Thomas OP, Trouble R, de Vargas C, Vega Thurber R, Voolstra CR, Wincker P, Zoccola D, Bowler C, Gorsky G, Rudich Y, Vardi A, Koren I
Bull Am Meteorol Soc: 101(5), E536-E554, 2020.
91. A multi-producer microbiome generates chemical diversity in the marine sponge Mycale hentscheli .
Rust M, Helfrich EJN, Freeman MF, Nanudorn P, Field CM, Ruckert C, Kundig T, Page MJ, Webb VL, Kalinowski J, Sunagawa S, Piel J
PNAS: 117(17), 9508-9518, 2020.
90. Consistent host and organ-occupancy of phyllosphere bacteria in a community of wild herbaceous plant species.
Massoni J, Bortfeld-Miller M, Jardillier L, Salazar G, Sunagawa S, Vorholt JA
ISME J: 14(1), 245-258, 2020.
89. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
Mende DR, Letunic I, Maistrenko OM, Schmidt TSB, Milanese A, Paoli L, Hernández-Plaza A, Orakov AN, Forslund SK, Sunagawa S, Zeller G, Huerta-Cepas J, Coelho LP, Bork P
Nucl Acids Res: 48(D1), D621-D625, 2020.
88. Scaling of species distribution explains the vast potential marine prokaryote diversity.
Eguiluz VM, Salazar G, Fernandez-Gracia J, Pearman JK, Gasol JM, Acinas SG, Sunagawa S, Irigoien X, Duarte CM
Sci Rep: 9(1), 18710, 2019.
87. Expanding Tara Oceans protocols for underway ecosystemic sampling of the ocean-atmosphere interface during Tara Pacific expedition (2016-2018).
Gorsky G*, Bourdin G*, Lombard F*, Pedrotti ML*, Audrain S, Bin N, Boss E, Bowler C, Cassar N, Caudan L, Chabot G, Cohen NR, Cron D, De Vargas C, Dolan JR, Douville E, Elineau A, Flores JM, Ghiglione JF, Haentjens N, Hertau M, John SG, Kelly RL, Koren I, Lin Y, Marie D, Moulin C, Moucherie Y, Pesant S, Picheral M, Poulain J, Pujo-Pay M, Reverdin G, Romac S, Sullivan MB, Trainic M, Tressol M, Trouble R, Vardi A, Voolstra CR, Wincker P, Agostini S, Banaigs B, Boissin E, Forcioli D, Furla P, Galand PE, Gilson E, Reynaud S, Sunagawa S, Thomas OP, Vega Thurber RL, Zoccola D, Planes S, Allemand D, Karsenti E
Front Mar Sci: 6, 750, 2019.
86. Gene expression changes and community turnover differentially shape the global ocean metatranscriptome.
Salazar G*, Paoli L*, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sanchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Tara Oceans Coordinators, Acinas SG, Babin M, Bork P, Bowler C, de Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S#
Cell: 179(5), 1068-1083, 2019.
85. Global trends in marine plankton diversity across kingdoms of life.
Ibarbalz F, Henry N, Brandao MC, Martini S, Busseni G, Byrne H, Coelho LP, Endo H, Gasol JM, Gregory AC, Mahe F, Rigonato J, Royo-Llonch M, Salazar G, Sanz-Saez I, Scalco E, Soviadan D, Zayed AA, Zingone A, Labadie K, Ferland J, Marec C, Kandels S, Picheral M, Dimier C, Poulain J, Pisarev S, Carmichael M, Pesant S, Tara Oceans Coordinators, Babin M, Boss E, Iudicone D, Jaillon O, Acinas SG, Ogata H, Pelletier E, Stemmann L, Sullivan MB, Sunagawa S, Bopp L, de Vargas C, Karp-Boss L, Wincker P, Lombard F, Bowler C, Zinger L
Cell: 179(5), 1084-1097, 2019.
84. Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice.
Wotzka SY*, Kreuzer M*, Maier L, Arnoldini M, Nguyen BD, Brachmann AO, Berthold DL, Zünd M, Hausmann A, Bakkeren E, Hoces D, Gul E, Beutler M, Dolowschiak T, Zimmermann M, Fuhrer T, Moor K, Sauer U, Typas A, Piel J, Diard M, Macpherson AJ, Stecher B, Sunagawa S, Slack E, Hardt WD
Nat Microbiol: 4(12), 2164-2174, 2019.
83. Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere.
Carlstrom CI, Field CM, Bortfeld-Miller M, Muller B, Sunagawa S, Vorholt JA
Nat Ecol Evol: 3(10), 1445-1454, 2019.
82. The Tara Pacific expedition - A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean.
Planes S*, Allemand D*, Agostini S, Banaigs B, Boissin E, Boss E, Bourdin G, Bowler C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Ghiglione JF, Gilson E, Lombard F, Moulin C, Pesant S, Poulain J, Reynaud S, Romac S, Sullivan MB, Sunagawa S, Thomas OP, Trouble R, de Vargas C, Vega Thurber R, Voolstra CR, Wincker P, Zoccola D, Tara Pacific Consortium
PLoS Biol: 17(9), e3000483, 2019.
81. Marine DNA viral macro- and microdiversity from pole to pole.
Gregory AC*, Zayed AA*, Conceicao-Neto N, Temperton B, Bolduc B, Alberti A, Ardyna M, Arkhipova K, Carmichael M, Cruaud C, Dimier C, Dominguez-Huerta G, Ferland J, Kandels S, Liu Y, Marec C, Pesant S, Picheral M, Pisarev S, Poulain J, Tremblay JE, Vik D; Tara Oceans Coordinators, Babin M, Bowler C, Culley AI, de Vargas C, Dutilh BE, Iudicone D, Karp-Boss L, Roux S, Sunagawa S, Wincker P, Sullivan MB
Cell: 177(5), 1109-1123, 2019.
80. Gut microbial beta-glucuronidase and glycerol/diol dehydratase activity contribute to dietary heterocyclic amine biotransformation.
Zhang J, Lacroix C, Wortmann E, Ruscheweyh HJ, Sunagawa S, Sturla SJ, Schwab C
BMC Microbiol: 19(1), 99, 2019.
79. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.
Wirbel J*, Pyl PT*, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Nimeus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G
Nat Med: 25(4), 679-689, 2019.
78. Microbial abundance, activity, and population genomic profiling with mOTUs2.
Milanese A*, Mende DR*, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G#, Sunagawa S#
Nat Commun: 10, 1014, 2019.
77. Community-level responses to iron availability in open ocean planktonic ecosystems.
Caputi L*, Carradec Q*, Eveillard D*, Kirilovsky A*, Pelletier E*, Karlusich JJP, Vieira FRJ, Villar E, Chaffron S, Malviya S, Scalco E, Acinas SG, Alberti A, Aury JM, Benoiston AS, Bertrand A, Biard T, Bittner L, Boccara M, Brum JR, Brunet C, Busseni G, Carratala A, Claustre H, Coelho LP, Colin S, D'Aniello S, Da Silva C, Del Core M, Dore H, Gasparini S, Kokoszka F, Jamet JL, Lejeusne C, Lepoivre C, Lescot M, Lima-Mendez G, Lombard F, Lukes J, Maillet N, Madoui MA, Martinez E, Mazzocchi MG, Neou MB, Paz-Yepes J, Poulain J, Ramondenc S, Romagnan JB, Roux S, Manta DS, Sanges R, Speich S, Sprovieri M, Sunagawa S, Taillandier V, Tanaka A, Tirichine L, Trottier C, Uitz J, Veluchamy A, Vesela J, Vincent F, Yau S, Kandels-Lewis S, Searson S, Dimier C, Picheral M, Bork P, Boss E, De Vargas C, Follows MJ, Grimsley N, Guidi L, Hingamp P, Karsenti E, Sordino P, Stemmann L, Sullivan MB, Tagliabue A, Zingone A, Garczarek L, d'Ortenzio F, Testor P, Not F, d'Alcala MR, Wincker P, Bowler C, Iudicone D, Gorsky G, Jaillon O, Karp-Boss L, Krzic U, Ogata H, Pesant S, Raes J, Reynaud EG, Sardet C, Sieracki M, Velayoudon D, Weissenbach J and Tara Oceans Coordinators
Global Biogeochem Cycles: 33(3), 391-419, 2019.
76. Extensive transmission of microbes along the gastrointestinal tract.
Schmidt TSB*, Hayward MR*, Coelho LP, Li SS, Costea PI, Voigt AY, Wirbel J, Maistrenko OM, Alves RJ, Bergsten E, de Beaufort C, Sobhani I, Heintz-Buschart A, Sunagawa S, Zeller G, Wilmes P, Bork P
eLife: 8, e42693, 2019.
75. Antibiotics-induced monodominance of a novel gut bacterial order.
Hildebrand F, Moitinho-Silva L, Blasche S, Jahn MTT, Gossmann TI, Heuerta Cepas J, Hercog R, Luetge M, Bahram M, Pryszlak A, Alves RJ, Waszak SM, Zhu A, Ye L, Costea PI, Aalvink S, Belzer C, Forslund SK, Sunagawa S, Hentschel U, Merten C, Patil KR, Benes V, Bork P
Gut: 68(10), 1781-1790, 2019.
74. Minimum information about an uncultivated virus genome (MIUViG).
Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA
Nat Biotechnol: 37(1), 29-37, 2019.
73. Microbiota stability in healthy individuals after single-dose lactulose challenge - a randomized controlled study.
Wotzka SY*, Kreuzer M*, Maier L*, Zünd M*, Schlumberger M, Nguyen B, Fox M, Pohl D, Heinrich H, Rogler G, Biedermann L, Scharl M, Sunagawa S#, Hardt WD#, Misselwitz B#
PLoS ONE: 3(10), e0206214, 2018.
72. Structure and function of the global topsoil microbiome.
Bahram M*, Hildebrand F*, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, Pent M, Põlme S, Sunagawa S, Ryberg M, Tedersoo L, Bork P
Nature: 560(7717), 233-237, 2018.
71. Metagenomic analysis of gut microbial communities from a Central Asian population.
Kushugulova A*, Forslund SK*, Costea PI, Kozhakhmetov S, Khassenbekova Z, Urazova M, Nurgozhin T, Zhumadilov Z, Benberin V, Driessen M, Hercog R, Voigt AY, Benes V, Kandels-Lewis S, Sunagawa S, Letunic I, Bork P
BMJ Open: 8(7), e021682, 2018.
70. The Ocean Gene Atlas: exploring the biogeography of plankton genes online.
Villar E, Vannier T, Vernette C, Lescot M, Cuenca M, Alexandre A, Bachelerie P, Rosnet T, Pelletier E, Sunagawa S, Hingamp P
Nucl Acids Res: 46(W1), W289-W295, 2018.
69. Natural noncanonical protein splicing yields products with diverse β-amino acid residues.
Morinaka BI, Lakis E, Verest M, Helf MJ, Scalvenzi T, Vagstad AL, Sims J, Sunagawa S, Gugger M, Piel J
Science: 359(6377), 779-782, 2018.
68. A global ocean atlas of eukaryotic genes.
Carradec Q*, Pelletier E*, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, Lima-Mendez G, Rocha F, Tirichine L, Labadie K, Kirilovsky A, Bertrand A, Engelen S, Madoui MA, Meheust R, Poulain J, Romac S, Richter DJ, Yoshikawa G, Dimier C, Kandels-Lewis S, Picheral M, Searson S; Tara Oceans Coordinators, Jaillon O, Aury JM, Karsenti E, Sullivan MB, Sunagawa S, Bork P, Not F, Hingamp P, Raes J, Guidi L, Ogata H, de Vargas C, Iudicone D, Bowler C, Wincker P
Nat Commun: 9, 373, 2018.
67. Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans.
Seeleuthner Y*, Mondy S*, Lombard V, Carradec Q, Pelletier E, Wessner M, Leconte J, Mangot JF, Poulain J, Labadie K, Logares R, Sunagawa S, de Berardinis V, Salanoubat M, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Tara Oceans Coordinators, Pesant S, Poulton N, Stepanauskas R, Bork P, Bowler C, Hingamp P, Sullivan MB, Iudicone D, Massana R, Aury JM, Henrissat B, Karsenti E, Jaillon O, Sieracki M, de Vargas C, Wincker P
Nat Commun: 9, 310, 2018.
66. Enterotypes in the landscape of gut microbial community composition.
Costea PI, Hildebrand F, Manimozhiyan A, Backhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P
Nat Microbiol: 3(1), 8-16, 2018.
65. Subspecies in the global human gut microbiome.
Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P
Mol Syst Biol: 13(12), 960, 2017.
64. Salt-responsive gut commensal modulates TH17 axis and disease.
Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mahler A, Balogh A, Marko L, Vvedenskaya O, Kleiner FH, Tsvetkov D, Klug L, Costea PI, Sunagawa S, Maier L, Rakova N, Schatz V, Neubert P, Fratzer C, Krannich A, Gollasch M, Grohme DA, Corte-Real BF, Gerlach RG, Basic M, Typas A, Wu C, Titze JM, Jantsch J, Boschmann M, Dechend R, Kleinewietfeld M, Kempa S, Bork P, Linker RA, Alm EJ, Muller DN
Nature: 551(7682), 585-589, 2017.
63. Towards standards for human fecal sample processing in metagenomic studies.
Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P
Nat Biotechnol: 35(11), 1069-1076, 2017.
62. Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes.
Colin S, Coelho LP, Sunagawa S, Bowler C, Karsenti E, Bork P, Pepperkok R, de Vargas C
eLife: 6, e26066, 2017.
61. RNase H as gene modifier, driver of evolution and antiviral defense.
Moelling K*, Broecker F*, Russo G, Sunagawa S
Front Microbiol: 8, 1745, 2017.
60. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.
Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M; Genoscope Technical Team, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernandez-Gomez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL; Tara Oceans Consortium Coordinators, Pesant S, Karsenti E, Wincker P
Sci Data: 4, 170093, 2017.
59. metaSNV: A tool for metagenomic strain level analysis.
Costea PI*, Munch R*, Coelho LP, Paoli L, Sunagawa S, Bork P
PLoS ONE: 12(7), e0182392, 2017.
58. Marine microbial diversity.
Salazar G, Sunagawa S#
Curr Biol: 27(11), R489-R494, 2017.
57. Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naive Parkinson's disease patients.
Bedarf JR*, Hildebrand F*, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wullner U
Genome Med: 9(1), 3952-3971, 2017.
56. Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition - a metagenomic analysis.
Knoll RL, Forslund K, Kultima JR, Meyer CU, Kullmer U, Sunagawa S, Bork P, Gehring S
Am J Physiol Gastrointest Liver Physiol: 312(4), G327-G339, 2017.
55. proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
Mende DR, Letunic I, Huerta-Cepas J, Li SS, Forslund K, Sunagawa S, Bork P
Nucl Acids Res: 45(D1), D529-D534, 2016.
54. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.
Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaque D; Tara Oceans Coordinators, Bork P, Acinas SG, Wincker P, Sullivan MB
Nature: 537(7622), 689-693, 2016.
53. Human gut microbes impact host serum metabolome and insulin sensitivity.
Pedersen HK*, Gudmundsdottir V*, Nielsen HB*, Hyotylainen T*, Nielsen T*, Jensen BAH, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Dore J, Mattila I, Plichta DR, Poho P, Hellgren LI, Arumugam M, Sunagawa S, Vieira-Silva S, Jorgensen T, Holm JB, Trost K, MetaHit consortium, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD, Pedersen O
Nature: 535(7612), 376-381, 2016.
52. Colorectal cancer and the human gut microbiome: Reproducibility with whole-genome shotgun sequencing.
Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, Shi J, Bork P, Sinha R
PLoS ONE: 11(5), e0155362, 2016.
51. Global genetic capacity for mixotrophy in marine picocyanobacteria.
Yelton A, Acinas SG, Sunagawa S, Bork P, Pedros-Alio C, Chisholm S
ISME J: 10(12), 2946-2957, 2016.
50. Durable coexistence of donor and recipient strains after fecal microbiota transplantation.
Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Niewdorp M, Salojarvi J, Voigt AY, Zeller G, Sunagawa S#, de Vos WM#, Bork P#
Science: 352(6285), 586-589, 2016.
49. MOCAT2: a metagenomics assembly, annotation and profiling framework.
Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P
Bioinformatics: 32(16), 2520-2523, 2016.
48. Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.
Cornejo-Castillo FM, Cabello AM, Salazar G, Sanchez-Baracaldo P, Lima-Mendez G, Hingamp P, Alberti A, Sunagawa S, Bork P, de Vargas C, Raes J, Bowler C, Wincker P, Zehr JP, Gasol JM, Massana R, Acinas SG
Nat Commun: 7, 11071, 2016.
47. Plankton networks driving carbon export in the oligotrophic ocean.
Guidi L*, Chaffron S*, Bittner L*, Eveillard D*, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, Coelho LP, Ignacio Espinoza JC, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Tara Oceans coordinators, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G
Nature: 532(7600), 465-470, 2016.
46. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.
Forslund K*, Hildebrand F*, Nielsen T*, Falony G*, Le Chatelier E*, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen L, Voigt AY, Vestergaard H, Hercog R, Costea PI, Kultima JR, Li J, Jorgensen T, Levenez F, Dore J, MetaHIT consort., Nielsen HB, Brunak A, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O
Nature: 528(7581), 262-266, 2015.
45. eggNOG 4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
Huerta-Cepas, J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen L, von Mering C, Bork P
Nucl Acids Res: 44(D1), D286-D293, 2015.
44. Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes).
Heras J, McClintock K, Sunagawa S, Aguilar A
BMC Genomics: 16, 656, 2015.
43. Open science resources for the discovery and analysis of Tara Oceans data.
Pesant S, Not F, Picheral M, Kandels-Lewis S, Le Bescot N, Gorsky G, Iudicone D, Karsenti E, Speich S, Trouble R, Dimier C, Searson S, Tara Oceans Consortium Coordinators
Sci Data: 2, 150023, 2015.
42. Computational eco-systems biology in Tara Oceans: translating data into knowledge.
Sunagawa S, Karsenti E, Bowler C, Bork P
Mol Syst Biol: 11(5), 809, 2015.
41. Structure and function of the global ocean microbiome.
Sunagawa S*#, Coelho LP*, Chaffron S*, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Coordinators , Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P
Science: 348(6237), 1261359, 2015.
40. Eukaryotic plankton diversity in the sunlit ocean.
de Vargas C*, Audic S*, Henry N*, Decelle J*, Mahe F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horak A, Jaillon O, Lima-Mendez G, Lukes J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Coordinators , Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki M, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E
Science: 348(6237), 1261605, 2015.
39. Patterns and ecological drivers of ocean viral communities.
Brum JR*, Ignacio-Espinoza C*, Roux S*, Doulcier G, Acinas S, Alberti A, Chaffron S, Cruaud C, de Vargas C, Gasol JM, Gorsky G, Gregory AC, Guidi L, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Poulos BT, Schwenck SM, Speich S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Coordinators , Karsenti E, Bork P, Bowler C, Sunagawa S, Wincker P, Sullivan MB
Science: 348(6237), 1261498, 2015.
38. Environmental characteristics of Agulhas rings affect interocean plankton transport.
Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d'Ortenzio F, Gattuso JP, Grima N, Guidi L, Hill CN, Jahn O, Jamet JL, Le Goff H, Lepoivre C, Malviya S, Pelletier E, Romagnan JB, Roux S, Santini S, Scalco E, Schwenck SM, Tanaka A, Testor P, Vannier T, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans coordinators, Acinas SG, Bork P, Boss E, de Vargas C, Gorsky G, Ogata H, Pesant S, Sullivan MB, Sunagawa S, Wincker P, Karsenti E, Bowler C, Not F, Hingamp P, Iudicone D
Science: 348(6237), 1261447, 2015.
37. Determinants of community structure in the global plankton interactome.
Lima-Mendes G*, Faust K*, Henry N*, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Cabello AM, Coppola L, Cornejo-Castillo FM, d'Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Lonch M, Salazar G, Sanchez P, Sebastian M, Souffreau C, Dimier C, Picheral P, Searson S, Kandels-Lewis S, Tara Oceans Coordinators, Gorsky G, Not F, Ogata H, Speich S, Weissenbach J, Wincker P, Bontempi G, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Bowler C, Karsenti E, de Vargas C, Raes J
Science: 348(6237), 1262073, 2015.
36. Inter-individual differences in the gene content of human gut bacterial species.
Zhu A, Sunagawa S, Mende DR, Bork P
Genome Biol: 16(1), 82, 2015.
35. Temporal and technical variability of human gut metagenomes.
Voigt AY, Costea PI, Kultima JR, Li SS, Zeller G, Sunagawa S, Bork P
Genome Biol: 16(1), 73, 2015.
34. Potential of fecal microbiota for early stage detection of colorectal cancer.
Zeller G*, Tap J*, Voigt AY*, Sunagawa S, Kultima JR, Costea PI, Amiot A, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Bohm J, Tournigand C, Van Nhieu JT, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P
Mol Syst Biol: 10, 766, 2014.
33. Metagenomic 16S rDNA Illumina Tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.
Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, Sarmento H, Ogata H, Hingamp P, de Vargas C, Raes J, Lima-Mendez G, Poulain J, Jaillon O, Wincker P, Kandels-Lewis S, Karsenti E, Bork P, Acinas SG
Environ Microbiol: 16(9), 2659-2671, 2014.
32. An integrated catalog of reference genes in the human gut microbiome.
Li J*, Jia H*, Cai X*, Zhong H*, Feng Q*, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S, Zhang D, Zhang Z, Chen W, Zhao H, Al-Aama JY, Edris E, Yang H, Wang J, Hansen T, Nielsen HB, Brunak S, Kristiansen K, Guarner F, Pedersen O, Dore J, Ehrlich SD, MetaHIT Consortium, Bork P, Wang J
Nat Biotechnol: 32(8), 834-841, 2014.
31. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
Nielsen HB*, Almeida M*, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Dore J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Leonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sorensen S, Tap J, Tims S, Ussery DW, Yamada T, MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD
Nat Biotechnol: 32(8), 822-828, 2014.
30. Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata.
Closek CJ, Sunagawa S, DeSalvo MD, Piceno YM, DeSantis TZ, Brodie EL, Weber MX, Voolstra CR, Andersen GL, Medina M
ISME J: 8(12), 2411-2422, 2014.
29. Classification and quantification of bacteriophage taxa in human gut metagenomes.
Waller A, Yamada T, Kristensen DM, Kultima JR, Sunagawa S, Koonin EV, Bork P
ISME J: 8(7), 1391-1402, 2014.
28. A fair comparison.
Costea PI, Zeller G, Sunagawa S, Bork P
Nat Methods: 11, 359, 2014.
27. Metagenomic insights into the human gut resistome and the forces that shape it.
Forslund K, Sunagawa S, Coelho LP, Bork P
Bioessays: 36, 316-329, 2014.
26. Metagenomic species profiling using universal phylogenetic marker genes.
Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen OP, Guarner F, de Vos WM, Wang J, Li J, Dore J, Ehrlich SD, Stamatakis A, Bork P
Nat Methods: 10(12), 1196-1199, 2013.
25. Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.
Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, Ferrera I, Sarmento H, Villar E, Lima-Mendez G, Faust K, Sunagawa S, Claverie JM, Moreau H, Desdevises Y, Bork P, Raes J, DeVargas C, Karsenti E, Kandels-Lewis S, Jaillon O, Not F, Pesant S, Wincker P, Ogata H
ISME J: 7(9), 1678-1695, 2013.
24. Richness of human gut microbiome correlates with metabolic markers.
Le Chatelier E*, Nielsen T*, Qin J*, Prifti E*, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jorgensen T, Brandslund I, Nielsen B, Juncker A, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Cleement K, Dore J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T, MetaHIT consortium, Bork P, Jun W, Ehrlich SD, Pedersen O
Nature: 500(7464), 541-546, 2013.
23. Accurate and universal delineation of prokaryotic species.
Mende DR, Sunagawa S, Zeller G, Bork P
Nat Methods: 10(9), 881-884, 2013.
22. Country-specific antibiotic use practices impact the human gut resistome.
Forslund K, Sunagawa S, Kultima JR, Mende D, Arumugam M, Typas A, Bork P
Genome Res: 23(7), 1163-1169, 2013.
21. Genomic variation landscape of the human gut microbiome.
Schloissnig S*, Arumugam M*, Sunagawa S*, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P
Nature: 493(7430), 45-50, 2013.
20. MOCAT: a metagenomics assembly and gene prediction toolkit.
Kultima JR*, Sunagawa S*, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, Wang J, Bork P
PLoS ONE: 7(10), e47656, 2012.
19. Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.
Bayer T*, Aranda M*, Sunagawa S, Yum LK, DeSalvo MK, Lindquist E, Coffroth MA, Voolstra CR, Medina M
PLoS ONE: 7(4), e35269, 2012.
18. Transcriptomic responses to darkness stress point to common coral bleaching mechanisms.
DeSalvo MK, Estrada E, Sunagawa S, Medina M
Coral Reefs: 31(1), 215-228, 2012.
17. Assessment of metagenomic assembly using simulated next generation sequencing data.
Mende DR*, Waller AS*, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J, Bork P
PLoS ONE: 7(2), e31386, 2012.
16. A holistic approach to marine eco-systems biology.
Karsenti E, Acinas SG, Bork P, Bowler C, De Vargas C, Raes J, Sullivan M, Arendt D, Benzoni F, Claverie JM, Follows M, Gorsky G, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Krzic U, Not F, Ogata H, Pesant S, Reynaud EG, Sardet C, Sieracki ME, Speich S, Velayoudon D, Weissenbach J, Wincker P, Abergel C, Arslan D, Audic S, Aury JM, Babic N, Beaufort L, Bittner L, Boss E, Boutte C, Brum J, Carmichael M, Casotti R, Chambouvet A, Chang P, Chica C, Clerissi C, Colin S, Cornejo-Castillo FM, Da Silva C, De Monte S, Decelle J, Desdevises Y, Dimier C, Dolan J, Duhaime M, Durrieu de Madron X, d'Ortenzio F, d'Ovidio F, Ferrera I, Garczarek L, Garet-Delmas MJ, Gasmi S, Gasol JM, Grimsley N, Heilig R, Ignacio-Espinoza J, Jamet JL, Karp-Boss L, Katinka M, Khalili H, Kolber Z, Le Bescot N, Le Gofff H, Lima-Mendez G, Mahe F, Mazzocchi MG, Montresor M, Morin P, Noel B, Pedros-Alio C, Pelletier E, Perez Y, Picheral M, Piganeau G, Poirot O, Poulain J, Poulton N, Prejger F, Prihoda J, Probert I, Rampal J, Reverdin G, Romac S, Romagnan JB, Roullier F, Rouviere C, Samson G, Santini S, Sarmento H, Sciandra A, Solonenko S, Stemmann L, Subirana L, Sunagawa S, Tanaka A, Testor P, Thompson A, Tichanne-Seltzer V, Tirichine L, Toulza E, Tozzi S, Veluchamy A, Zingone A
PLoS Biol: 9(10), e1001177, 2011.
15. Rapid evolution of coral proteins responsible for interaction with the environment.
Voolstra CR*, Sunagawa S*, Matz MV, Bayer T, Aranda M, Buschiazzo E, DeSalvo MK, Lindquist E, Szmant AM, Coffroth MA, Medina M
PLoS ONE: 6(5), e20392, 2011.
14. Enterotypes of the human gut microbiome.
Arumugam M*, Raes J*, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Dore J; MetaHIT Consortium, Antolin M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Merieux A, Melo Minardi R, M'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P
Nature: 473(7346), 174-180, 2011.
13. Transcriptomic responses to heat stress and bleaching in the Elkhorn coral Acropora palmata.
DeSalvo MK, Sunagawa S, Voolstra CR, Medina M
Mar Ecol Prog Ser: 402, 97-113, 2010.
12. Threatened corals provide underexplored microbial habitats.
Sunagawa S, Woodley CM, Medina M
PLoS ONE: 5(3), e9554, 2010.
11. The porcelain crab transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database.
Abderrahmane T, Wang M, Lindquist E, Tanaka Y, Teranishi KS, Sunagawa S, Wong M, Stillman JH
PLoS ONE: 5(2), e9327, 2010.
10. Coral host transcriptomic states are correlated with Symbiodinium genotypes.
DeSalvo MK*, Sunagawa S*, Fisher PL, Voolstra CR, Iglesias-Prieto R, Medina M
Mol Ecol: 19(6), 1174-1186, 2010.
9. Gene expression microarray analysis encompassing metamorphosis and the onset of calcification in the scleractinian coral Montastraea faveolata.
Reyes-Bermudez A, DeSalvo MK, Voolstra CR, Sunagawa S, Szmant AM, Iglesias-Prieto R, Medina M
Mar Genom: 2(3-4), 149-159, 2009.
8. Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont.
Sunagawa S, Wilson EC, Thaler M, Smith ML, Caruso C, Pringle JR, Weis VM, Medina M, Schwarz JA
BMC Genom: 10, 258, 2009.
7. Evolutionary analysis of orthologous cDNA sequences from cultured and symbiotic dinoflagellate symbionts of reef-building corals (Dinophyceae: Symbiodinium).
Voolstra CR, Sunagawa S, Schwarz JA, Coffroth MA, Yellowlees D, Leggat W, Medina M
Comp Biochem Physiol D Genomics Proteomics: 4(2), 67-74, 2009.
6. The host transcriptome remains unaltered during the establishment of coral-algal symbioses.
Voolstra CR, Schwarz JA, Schnetzer J, Sunagawa S, Desalvo MK, Szmant AM, Coffroth MA, Medina M
Mol Ecol: 18(9), 1823-1833, 2009.
5. Identification and gene expression analysis of a taxonomically restricted cysteine-rich protein family in reef-building corals.
Sunagawa S, DeSalvo MK, Voolstra CR, Reyes-Bermudez A, Medina M
PLoS ONE: 4(3), e4865, 2009.
4. Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata.
Sunagawa S, DeSantis TZ, Piceno YM, Brodie EL, DeSalvo MK, Voolstra CR, Weil E, Andersen GL, Medina M
ISME J: 3(5), 512-521, 2009.
3. Differential gene expression during thermal stress and bleaching in the Caribbean coral Montastraea faveolata.
DeSalvo MK, Voolstra CR, Sunagawa S, Schwarz JA, Stillman JH, Coffroth MA, Szmant AM, Medina M
Mol Ecol: 17(17), 3952-3971, 2008.
2. Hyperthermic stress-induced increase in the expression of glutamate-cysteine ligase and glutathione levels in the symbiotic sea anemone Aiptasia pallida.
Sunagawa S, Choi J, Forman HJ, Medina M
Comp Biochem Physiol B Biochem Mol Biol: 151(1), 133-138, 2008.
1. Variation in cell densities and pigment concentrations of symbiotic dinoflagellates in the coral Pavona clavus in the eastern Pacific (Costa Rica).
Sunagawa S, Cortés J, Jiménez C, Lara R
Cienc Mar: 34(2), 113-123, 2008.
. .
,

[top]
 Book Chapters
Metagenomics of the coral holobiont.
Medina M and Sunagawa S.
In Nelson K., (Ed.) Encyclopedia of Metagenomics: SpringerReference (www.springerreference.com). Springer-Verlag Berlin Heidelberg, 2013.
[top]
Theses
Ph.D.: Microbial Diversity and Transcriptome Profiling in Coral Holobionts [pdf]

M.Sc.: Seasonal Variations in Symbiont Densities and Skeletal Phosphorus Concentrations in the Eastern Pacific (Costa Rica) Coral Pavona clavus [pdf]

Diploma: Analysis of Small Fusion Partners to Increase the Stability of Poorly-Soluble Proteins: a Perspective for the Structural Analysis by NMR Spectroscopy? [pdf]
[top]