Publications
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 pageBioinformatics: 40(2), btae078, 2024call_made
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 pageMicrobiome: 10(1): 212, 2022call_made
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 pageNature: 607(7917), 111-118, 2022call_made
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 pageCurr Protoc: 1(8), e218, 2021call_made
mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes
Salazar G*, Ruscheweyh HJ*, Hildebrand F, Acinas SG, Sunagawa S✉
external pageBioinformatics: 38(1), 270-272, 2021call_made
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 pageMicrobiome: 9, 77, 2021call_made
Space, time and microdiversity: towards a resolution revolution in microbiomics
Paoli L, Sunagawa S✉
external pageEnviron Microbiol Rep: 13(1), 31-35, 2021call_made
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 pageNat Rev Microbiol: 18(8), 428-445, 2020call_made
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 pageCell: 179(5), 1068-1083, 2019call_made
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 pageNat Commun: 10, 1014, 2019call_made
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 pagePLoS ONE: 3(10), e0206214, 2018call_made
2017
Marine microbial diversity
Salazar G, Sunagawa S✉
external pageCurr Biol: 27(11), R489-R494, 2017call_made
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 pageScience: 352(6285), 586-589, 2016call_made
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 pageScience: 348(6237), 1261359, 2015call_made
Computational eco-systems biology in Tara Oceans: translating data into knowledge
Sunagawa S, Karsenti E, Bowler C, Bork P
external pageMol Syst Biol: 11(5), 809, 2015call_made
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 pageNat Methods: 10(12), 1196-1199, 2013call_made
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 pageNature: 493(7430), 45-50, 2013call_made
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 pagePLoS ONE: 7(10), e47656, 2012call_made
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 pagePLoS ONE: 6(5), e20392, 2011call_made
2010
Threatened corals provide underexplored microbial habitats
Sunagawa S, Woodley CM, Medina M
external pagePLoS ONE: 5(3), e9554, 2010call_made
Coral host transcriptomic states are correlated with Symbiodinium genotypes.
DeSalvo MK*, Sunagawa S*, Fisher PL, Voolstra CR, Iglesias-Prieto R, Medina M
external pageMol Ecol: 19(6), 1174-1186, 2010call_made
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 pageBMC Genomics: 10, 258, 2009call_made
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 pagePLoS ONE: 4(3), e4865, 2009call_made
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 pageISME J: 3(5), 512-521, 2009call_made
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 pageComp Biochem Physiol B Biochem Mol Biol: 151(1), 133-138, 2008call_made
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 pageCienc Mar: 34(2), 113-123, 2008call_made