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, gkae1004, 2024
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
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
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
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
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
Space, time and microdiversity: towards a resolution revolution in microbiomics
Paoli L, Sunagawa S✉
external page Environ Microbiol Rep: 13(1), 31-35, 2021
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
2019
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✉
external page Cell: 179(5), 1068-1083, 2019
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✉
external page Nat Commun: 10, 1014, 2019
2018
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✉
external page PLoS ONE: 3(10), e0206214, 2018
2017
Marine microbial diversity
Salazar G, Sunagawa S✉
external page Curr Biol: 27(11), R489-R494, 2017
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
2015
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✉ and Bork P✉
external page Science: 348(6237), 1261359, 2015
Computational eco-systems biology in Tara Oceans: translating data into knowledge
Sunagawa S, Karsenti E, Bowler C, Bork P
external page Mol Syst Biol: 11(5), 809, 2015
2013
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
external page Nat Methods: 10(12), 1196-1199, 2013
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✉
external page Nature: 493(7430), 45-50, 2013
2012
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
external page PLoS ONE: 7(10), e47656, 2012
2011
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
external page PLoS ONE: 6(5), e20392, 2011
2010
Threatened corals provide underexplored microbial habitats
Sunagawa S, Woodley CM, Medina M
external page PLoS ONE: 5(3), e9554, 2010
Coral host transcriptomic states are correlated with Symbiodinium genotypes.
DeSalvo MK*, Sunagawa S*, Fisher PL, Voolstra CR, Iglesias-Prieto R, Medina M
external page Mol Ecol: 19(6), 1174-1186, 2010
2009
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
external page BMC Genomics: 10, 258, 2009
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
external page PLoS ONE: 4(3), e4865, 2009
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
external page ISME J: 3(5), 512-521, 2009
2008
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
external page Comp Biochem Physiol B Biochem Mol Biol: 151(1), 133-138, 2008
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
external page Cienc Mar: 34(2), 113-123, 2008