Publications
2025
The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities
Dmitrijeva M*, Ruscheweyh HJ*, Feer L, Li K, Miravet-Verde S, Sintsova A, Mende DR, Zeller G, Sunagawa S✉
external page Nucleic Acids Res, 53(D1), D797–D805, 2025
2024
Plant microbiota feedbacks through dose-responsive expression of general non-self response genes
Keppler A Roulier M, Pfeilmeier S, Petti GC, Sintsova A, Maier BA, Bortfeld-Miller M, Sunagawa S, Zipfel C, Vorholt JA✉
external page Nature Plants, 2024
Metagenomic study of lake microbial mats reveals protease-inhibiting antiviral peptides from a core microbiome member
Padhi C, Field CM, Forneris CC, Olszewski D, Fraley AE, Sandu I, Scott TA, Farnung J, Ruscheweyh HJ, Narayan Panda A, Oxenius A, Greber UF, Bode JW, Sunagawa S, Raina V, Suar M, Piel J✉
external page PNAS, 121(49), 2024
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✉
external page Nature, 635(8038), 415-422, 2024
Metagenomic and -transcriptomic analyses of microbial nitrogen transformation potential, and gene expression in Swiss lake sediments
Baumann KBL*, Mazzoli A*, Salazar G, Ruscheweyh HJ, Muller B, Niederdorfer R, Sunagawa S, Lever MA, Lehmann MF, Burgmann H✉
external page ISME Commun, 4(1), ycae110, 2024
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✉
external page Cell Host Microbe, 32(10), 1758-1773, 2024
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✉
external page Microbiome, 12(1), 178, 2024
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, Gallia 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✉
external page Sci Data, 11(1), 989, 2024
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✉
external page Microbiome, 12(1), 65, 2024
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✉
external page Nat Commun, 15(1), 2557, 2024
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✉
external page Nat Microbiol, 9(4), 103-1116,2024
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✉
external page Cell, 187(5), 1206-1222.e16, 2024
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✉
external page Bioinformatics, 40(2), btae078, 2024
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
external page Chem Geol, 645, 121884, 2024
Functional and evolutionary significance of unknown genes from uncultivated taxa
Del Rio AR, 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✉
external page Nature, 626(7998), 377-384, 2024
2023
Animal-associated marine Acidobacteria with a rich natural-product repertoire
Leopold-Messer S*, Chepkirui C*, Mabesoone MFJ, Meyer J, Paoli L, Sunagawa S, Uria AR, Wakimoto T, Piel J✉
external page Chem, 9(12), 3696-3713,2023
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✉
external page Microbiome, 11(1), 265, 2023
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
external page Microbiol Mol Biol Rev, e0006323, 2023
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✉
external page Nucleic Acids Res, gkad943, 2023
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✉
external page PLoS Biol, 21(8), e3002253, 2023
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✉
external page Commun Earth Environ, 4(1), 311, 2023
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-Alió C, Agustí S, Gojobori T, Duarte CM, Gasol JM, Sánchez O✉, Acinas SG✉
external page ISME Commun, 3(1), 92, 2023
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✉
external page ISME Commun, 3(1), 83, 2023
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✉
external page Commun Earth Environ, 4, 281, 2023
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
external page Sci Rep, 13(1), 11589, 2023
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✉
external page npj biodivers, 2, 15, 2023
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✉
external page Genome Biol, 24(1), 123, 2023
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
external page Commun Biol, 6(1), 566, 2023
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
external page Nat Commun, 14(1), 3056, 2023
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
external page Nat Commun, 14(1), 3039, 2023
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✉
external page Nat Commun, 14(1), 3038, 2023
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✉
external page Nat Commun, 14(1), 3037, 2023
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
external page Sci Data, 10(1), 326, 2023
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
external page Sci Data, 10(1), 24, 2023
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✉
external page Nat Metab, 5(6), 1-13, 2023
Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota.
Hoces D, Greter G, Arnoldini M, Stäubli 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✉
external page eLife, e81212, 2023
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✉
external page Nucleic Acids Res, 51(D1), D760-D766, 2023
2022
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✉
external page Microbiome, 10(1), 212, 2022
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, Würbel H✉
external page PLoS Biol, 20(10), e3001837, 2022
Metabolic reconstitution of germ-free mice by a gnotobiotic microbiota varies over the circadian cycle
Hoces D, Lan J, Sun W, Geiser T, Stäubli 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✉
external page PLoS Biol, 20(9), e3001743, 2022
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✉
external page eLife, 1, e78129, 2022
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✉
external page Nature, 607(7917), 111-118, 2022
external page Link to Ocean Microbiomics Database
external page Video on YouTube (1), external page Video on YouTube (2), ETH News article
Priorities for ocean microbiome research
Tara Ocean Foundation, Tara Oceans, European Molecular Biology Laboratory (EMBL) and European Marine Biological Resource Centre - European Research Infrastructure Consortium (EMBRC-ERIC)*
*Abreu A, Bourgois E, Gristwood A, Troublé R, Acinas SG, Bork P, Boss E, Bowler C, Budinich M, Chaffron S, de Vargas C, Delmont TO, Eveillard D, Guidi L, Iudicone D, Kandels S, Morlon H, Lombard F, Pepperkok R, Pierella Karlusich JJ, Piganeau G, Régimbeau A, Sommeria-Klein G, Stemmann L, Sullivan MB, Sunagawa S, Wincker P, Zablocki O, Arendt D, Bilic J, Bork P, Finn R, Heard E, Kandels S, Pepperkok R, Rouse B, Vamathevan J, Casotti R, Cancio I, Cunliffe M, Kervella AE, Kooistra WHCF, Obst M, Pade N, Power DM, Santi I, Tsagaraki TM, Vanaverbeke J
external page Nat Microbiol, 7, 937-947, 2022
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✉
external page Science, 376(6598), 1202-1208, 2022
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✉
external page Nucl Acids Res, 50(W1), W516–26,2022
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✉
external page Commun Earth Environ, 3, 121, 2022
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
external page Cell Genomics, 2, 100123, 2022
Critical Assessment of Metagenome Interpretation: the second round of challenges
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external page Science, 376(6589), 156-162, 2022
Towards the biogeography of prokaryotic genes
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2021
MetaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes
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Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean
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external page Nat Microbiol, 6(12), 1561–1574, 2021
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
external page Sci Rep, 11(1), 21761, 2021
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✉
external page Curr Protoc, 1(8), e218, 2021
mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes
Salazar G*, Ruscheweyh HJ*, Hildebrand F, Acinas SG, Sunagawa S✉
external page Bioinformatics, 38(1), 270-272,2021
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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✉
external page Nat Microbiol, 6(7), 852-864, 2021
miR-802 regulates Paneth cell function and enterocyte differentiation in the mouse small intestine
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external page Nat Commun, 12, 3339, 2021
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities
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external page Commun Biol, 4, 604, 2021
A general non-self response as part of plant immunity
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external page Nat Plants, 7, 696-705, 2021
A roadmap for metagenomic enzyme discovery
Robinson SL✉, Piel J, Sunagawa S
external page Nat Prod Rep, 38(11),1994-2023, 2021
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✉
external page Genome Biol, 22, 93, 2021
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✉
external page Microbiome, 9, 77, 2021
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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
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Space, time and microdiversity: towards a resolution revolution in microbiomics
Paoli L, Sunagawa S✉
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2020
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, de Vargas C, Sullivan MB, Bowler C, Wincker P, Karp-Boss L, Sunagawa S, Ogata H✉
external page Nat Ecol Evol, 4(12), 1639-1649, 2020
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✉
external page Nat Rev Microbiol, 18(8), 428-445, 2020
Import of aspartate and malate by DcuABC drives H2/fumarate respiration to promote initial Salmonella gut-lumen colonization in mice
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✉
external page Cell Host Microbe, 27(6), 922-936, 2020
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✉
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A multiproducer microbiome generates chemical diversity in the marine sponge Mycale hentscheli
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external page PNAS, 117(17), 9508–9518, 2020
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✉
external page Bull Am Meteorol Soc, E536–E554, 2020
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✉
external page ISME J, 14(1), 245-258, 2020
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✉
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2019
Scaling of species distribution explains the vast potential marine prokaryote diversity
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external page Sci Rep, 9(1), 18710, 2019
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
external page Front Mar Sci, 6, 750, 2019
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external page Cell, 179(5), 1068-1083, 2019
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Global trends in marine plankton diversity across kingdoms of life
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external page Nat Microbiol, 4(12), 2164-2174,2019
Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere
Carlström CI, Field CM, Bortfeld-Miller M, Müller B, Sunagawa S, Vorholt JA✉
external page Nat Ecol Evol, 3(10), 1445-1454, 2019
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
external page PLoS Biol, 17(9), e3000483, 2019
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✉
external page Cell, 177(5), 1109-1123, 2019
Gut microbial beta-glucuronidase and glycerol/diol dehydratase activity contribute to dietary heterocyclic amine biotransformation
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external page BMC Microbiol, 19(1), 99, 2019
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✉
external page Nat Med, 25, 679–689, 2019
Microbial abundance, activity and population genomic profiling with mOTUs2
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external page Nat Commun, 10, 1014, 2019
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✉
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Community-level responses to iron availability in open ocean planktonic ecosystems
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2018
Microbiota stability in healthy individuals after single-dose lactulose challenge - a randomized controlled study
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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✉
external page Nature, 560(7717), 233-237, 2018
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
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The Ocean Gene Atlas: exploring the biogeography of plankton genes online
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Natural noncanonical protein splicing yields products with diverse β-amino acid residues
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external page Science, 359(6377), 779-782, 2018
A global ocean atlas of eukaryotic genes
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Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans
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2017
Subspecies in the global human gut microbiome
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external page Nature, 551(7682), 585-589, 2017
Towards standards for human fecal sample processing in metagenomic studies
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Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes
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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 Coordinators, Pesant S, Karsenti E, Wincker P✉
external page Sci Data, 4, 170093, 2017
metaSNV: A tool for metagenomic strain level analysis
Costea PI*, Munch R*, Coelho LP, Paoli L, Sunagawa S, Bork P✉
external page PLoS ONE, 12(7), e0182392, 2017
Marine microbial diversity
Salazar G, Sunagawa S✉
external page Curr Biol, 27(11), R489-R494, 2017
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✉
external page Genome Med, 9(1), 3952-3971, 2017
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✉
external page Am J Physiol Gastrointest Liver Physiol, 312(4), G327-G339, 2017
2016
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✉
external page Nucl Acids Res, 45(D1), D529-D534, 2016
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✉
external page Nature, 537(7622), 689-693, 2016
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✉
external page Nature, 535(7612), 376-381, 2016
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
external page PLoS ONE, 11(5), e0155362, 2016
Global genetic capacity for mixotrophy in marine picocyanobacteria
Yelton A, Acinas SG, Sunagawa S, Bork P, Pedros-Alio C, Chisholm S✉
external page ISME J, 10(12), 2946-2957, 2016
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✉
external page Science, 352(6285), 586-589, 2016
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✉
external page Bioinformatics, 32(16), 2520-2523, 2016
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✉
external page Nat Commun, 7, 11071, 2016
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✉
external page Nature, 532(7600), 465-470, 2016
Disentangling disease- and drug signatures of the human gut microbiome: the case of type 2 diabetes mellitus
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 consortium, Nielsen HB, Brunak A, Raes J, Hansen T, Wang J, Ehrlich SD✉, Bork P✉, Pedersen O✉
external page Nature, 528(7581), 262-266, 2015