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Items: 1 to 50 of 98

1.

Single Cell Genomics-Based Analysis of Gene Content and Expression of Prophages in a Diffuse-Flow Deep-Sea Hydrothermal System.

Labonté JM, Pachiadaki M, Fergusson E, McNichol J, Grosche A, Gulmann LK, Vetriani C, Sievert SM, Stepanauskas R.

Front Microbiol. 2019 Jun 12;10:1262. doi: 10.3389/fmicb.2019.01262. eCollection 2019.

2.

Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution.

Ren M, Feng X, Huang Y, Wang H, Hu Z, Clingenpeel S, Swan BK, Fonseca MM, Posada D, Stepanauskas R, Hollibaugh JT, Foster PG, Woyke T, Luo H.

ISME J. 2019 Apr 25. doi: 10.1038/s41396-019-0418-8. [Epub ahead of print]

PMID:
31024152
3.

Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems.

Sieracki ME, Poulton NJ, Jaillon O, Wincker P, de Vargas C, Rubinat-Ripoll L, Stepanauskas R, Logares R, Massana R.

Sci Rep. 2019 Apr 15;9(1):6025. doi: 10.1038/s41598-019-42487-1.

4.

Four Draft Single-Cell Genome Sequences of Novel, Nearly Identical Kiritimatiellaeota Strains Isolated from the Continental Deep Subsurface.

Sackett JD, Kruger BR, Becraft ED, Jarett JK, Stepanauskas R, Woyke T, Moser DP.

Microbiol Resour Announc. 2019 Mar 14;8(11). pii: e01249-18. doi: 10.1128/MRA.01249-18.

5.

Author Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria.

Matheus Carnevali PB, Schulz F, Castelle CJ, Kantor RS, Shih PM, Sharon I, Santini JM, Olm MR, Amano Y, Thomas BC, Anantharaman K, Burstein D, Becraft ED, Stepanauskas R, Woyke T, Banfield JF.

Nat Commun. 2019 Mar 26;10(1):1451. doi: 10.1038/s41467-019-09423-3.

6.

Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities.

Youssef NH, Farag IF, Hahn CR, Jarett J, Becraft E, Eloe-Fadrosh E, Lightfoot J, Bourgeois A, Cole T, Ferrante S, Truelock M, Marsh W, Jamaleddine M, Ricketts S, Simpson R, McFadden A, Hoff W, Ravin NV, Sievert S, Stepanauskas R, Woyke T, Elshahed M.

Appl Environ Microbiol. 2019 May 2;85(10). pii: e00110-19. doi: 10.1128/AEM.00110-19. Print 2019 May 15.

PMID:
30902854
7.

Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere.

Carr SA, Jungbluth SP, Eloe-Fadrosh EA, Stepanauskas R, Woyke T, Rappé MS, Orcutt BN.

ISME J. 2019 Jun;13(6):1457-1468. doi: 10.1038/s41396-019-0352-9. Epub 2019 Feb 7.

PMID:
30728468
8.

Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus.

Berube PM, Rasmussen A, Braakman R, Stepanauskas R, Chisholm SW.

Elife. 2019 Feb 1;8. pii: e41043. doi: 10.7554/eLife.41043.

9.

Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria.

Matheus Carnevali PB, Schulz F, Castelle CJ, Kantor RS, Shih PM, Sharon I, Santini JM, Olm MR, Amano Y, Thomas BC, Anantharaman K, Burstein D, Becraft ED, Stepanauskas R, Woyke T, Banfield JF.

Nat Commun. 2019 Jan 28;10(1):463. doi: 10.1038/s41467-018-08246-y. Erratum in: Nat Commun. 2019 Mar 26;10(1):1451.

10.

Genomics insights into ecotype formation of ammonia-oxidizing archaea in the deep ocean.

Wang Y, Huang JM, Cui GJ, Nunoura T, Takaki Y, Li WL, Li J, Gao ZM, Takai K, Zhang AQ, Stepanauskas R.

Environ Microbiol. 2019 Feb;21(2):716-729. doi: 10.1111/1462-2920.14518. Epub 2019 Jan 31.

PMID:
30592124
11.

Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis.

Jarett JK, Nayfach S, Podar M, Inskeep W, Ivanova NN, Munson-McGee J, Schulz F, Young M, Jay ZJ, Beam JP, Kyrpides NC, Malmstrom RR, Stepanauskas R, Woyke T.

Microbiome. 2018 Sep 17;6(1):161. doi: 10.1186/s40168-018-0539-8.

12.

Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments.

Berube PM, Biller SJ, Hackl T, Hogle SL, Satinsky BM, Becker JW, Braakman R, Collins SB, Kelly L, Berta-Thompson J, Coe A, Bergauer K, Bouman HA, Browning TJ, De Corte D, Hassler C, Hulata Y, Jacquot JE, Maas EW, Reinthaler T, Sintes E, Yokokawa T, Lindell D, Stepanauskas R, Chisholm SW.

Sci Data. 2018 Sep 4;5:180154. doi: 10.1038/sdata.2018.154.

13.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Jul 6;36(7):660. doi: 10.1038/nbt0718-660a. No abstract available.

PMID:
29979671
14.

A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments.

Munson-McGee JH, Peng S, Dewerff S, Stepanauskas R, Whitaker RJ, Weitz JS, Young MJ.

ISME J. 2018 Jun;12(7):1706-1714. doi: 10.1038/s41396-018-0071-7. Epub 2018 Feb 21.

15.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Feb 6;36(2):196. doi: 10.1038/nbt0218-196a. No abstract available.

16.

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. 2018 Jan 22;9(1):310. doi: 10.1038/s41467-017-02235-3.

17.

Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics.

Bergauer K, Fernandez-Guerra A, Garcia JAL, Sprenger RR, Stepanauskas R, Pachiadaki MG, Jensen ON, Herndl GJ.

Proc Natl Acad Sci U S A. 2018 Jan 16;115(3):E400-E408. doi: 10.1073/pnas.1708779115. Epub 2017 Dec 18.

18.

Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla.

Becraft ED, Woyke T, Jarett J, Ivanova N, Godoy-Vitorino F, Poulton N, Brown JM, Brown J, Lau MCY, Onstott T, Eisen JA, Moser D, Stepanauskas R.

Front Microbiol. 2017 Nov 28;8:2264. doi: 10.3389/fmicb.2017.02264. eCollection 2017.

19.

Author Correction: Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles.

Stepanauskas R, Fergusson EA, Brown J, Poulton NJ, Tupper B, Labonté JM, Becraft ED, Brown JM, Pachiadaki MG, Povilaitis T, Thompson BP, Mascena CJ, Bellows WK, Lubys A.

Nat Commun. 2017 Dec 12;8(1):2134. doi: 10.1038/s41467-017-02128-5.

20.

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations.

Garcia SL, Stevens SLR, Crary B, Martinez-Garcia M, Stepanauskas R, Woyke T, Tringe SG, Andersson SGE, Bertilsson S, Malmstrom RR, McMahon KD.

ISME J. 2018 Mar;12(3):742-755. doi: 10.1038/s41396-017-0001-0. Epub 2017 Dec 8.

21.

Characterization of Two Cryptic Plasmids Isolated in Haiti from Clinical Vibrio cholerae Non-O1/Non-O139.

Ceccarelli D, Garriss G, Choi SY, Hasan NA, Stepanauskas R, Pop M, Huq A, Colwell RR.

Front Microbiol. 2017 Nov 23;8:2283. doi: 10.3389/fmicb.2017.02283. eCollection 2017.

22.

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation.

Pachiadaki MG, Sintes E, Bergauer K, Brown JM, Record NR, Swan BK, Mathyer ME, Hallam SJ, Lopez-Garcia P, Takaki Y, Nunoura T, Woyke T, Herndl GJ, Stepanauskas R.

Science. 2017 Nov 24;358(6366):1046-1051. doi: 10.1126/science.aan8260.

PMID:
29170234
23.

Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs.

Becraft ED, Dodsworth JA, Murugapiran SK, Thomas SC, Ohlsson JI, Stepanauskas R, Hedlund BP, Swingley WD.

Front Microbiol. 2017 Oct 31;8:2082. doi: 10.3389/fmicb.2017.02082. eCollection 2017.

24.

Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients.

Hawley AK, Nobu MK, Wright JJ, Durno WE, Morgan-Lang C, Sage B, Schwientek P, Swan BK, Rinke C, Torres-Beltrán M, Mewis K, Liu WT, Stepanauskas R, Woyke T, Hallam SJ.

Nat Commun. 2017 Nov 15;8(1):1507. doi: 10.1038/s41467-017-01376-9.

25.

Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes.

Royo-Llonch M, Ferrera I, Cornejo-Castillo FM, Sánchez P, Salazar G, Stepanauskas R, González JM, Sieracki ME, Speich S, Stemmann L, Pedrós-Alió C, Acinas SG.

Front Microbiol. 2017 Jul 25;8:1317. doi: 10.3389/fmicb.2017.01317. eCollection 2017.

26.

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893. Erratum in: Nat Biotechnol. 2018 Feb 6;36(2):196. Nat Biotechnol. 2018 Jul 6;36(7):660.

27.

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, Fernández-Gómez 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. 2017 Aug 1;4:170093. doi: 10.1038/sdata.2017.93.

28.

Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles.

Stepanauskas R, Fergusson EA, Brown J, Poulton NJ, Tupper B, Labonté JM, Becraft ED, Brown JM, Pachiadaki MG, Povilaitis T, Thompson BP, Mascena CJ, Bellows WK, Lubys A.

Nat Commun. 2017 Jul 20;8(1):84. doi: 10.1038/s41467-017-00128-z. Erratum in: Nat Commun. 2017 Dec 12;8(1):2134.

29.

Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae.

Collingro A, Köstlbacher S, Mussmann M, Stepanauskas R, Hallam SJ, Horn M.

ISME J. 2017 Oct;11(10):2334-2344. doi: 10.1038/ismej.2017.95. Epub 2017 Jun 23.

30.

Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes.

Luo H, Huang Y, Stepanauskas R, Tang J.

Nat Microbiol. 2017 Jun 12;2:17091. doi: 10.1038/nmicrobiol.2017.91.

PMID:
28604700
31.

Fundamental differences in diversity and genomic population structure between Atlantic and Pacific Prochlorococcus.

Kashtan N, Roggensack SE, Berta-Thompson JW, Grinberg M, Stepanauskas R, Chisholm SW.

ISME J. 2017 Sep;11(9):1997-2011. doi: 10.1038/ismej.2017.64. Epub 2017 May 19.

32.

Genomic exploration of individual giant ocean viruses.

Wilson WH, Gilg IC, Moniruzzaman M, Field EK, Koren S, LeCleir GR, Martínez Martínez J, Poulton NJ, Swan BK, Stepanauskas R, Wilhelm SW.

ISME J. 2017 Aug;11(8):1736-1745. doi: 10.1038/ismej.2017.61. Epub 2017 May 12.

33.

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter.

Landry Z, Swan BK, Herndl GJ, Stepanauskas R, Giovannoni SJ.

MBio. 2017 Apr 18;8(2). pii: e00413-17. doi: 10.1128/mBio.00413-17.

34.

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems.

Jungbluth SP, Glavina Del Rio T, Tringe SG, Stepanauskas R, Rappé MS.

PeerJ. 2017 Apr 6;5:e3134. doi: 10.7717/peerj.3134. eCollection 2017.

35.

Strategies to improve reference databases for soil microbiomes.

Choi J, Yang F, Stepanauskas R, Cardenas E, Garoutte A, Williams R, Flater J, Tiedje JM, Hofmockel KS, Gelder B, Howe A.

ISME J. 2017 Apr;11(4):829-834. doi: 10.1038/ismej.2016.168. Epub 2016 Dec 9. No abstract available.

36.

De novo synthesis and functional analysis of the phosphatase-encoding gene acI-B of uncultured Actinobacteria from Lake Stechlin (NE Germany).

Srivastava A, McMahon KD, Stepanauskas R, Grossart HP.

Int Microbiol. 2015 Dec;18(4):39-47. doi: 10.2436/20.1501.01.262.

37.

Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling.

Wasmund K, Cooper M, Schreiber L, Lloyd KG, Baker BJ, Petersen DG, Jørgensen BB, Stepanauskas R, Reinhardt R, Schramm A, Loy A, Adrian L.

MBio. 2016 May 3;7(3). pii: e00266-16. doi: 10.1128/mBio.00266-16.

38.

Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments.

Dyksma S, Bischof K, Fuchs BM, Hoffmann K, Meier D, Meyerdierks A, Pjevac P, Probandt D, Richter M, Stepanauskas R, Mußmann M.

ISME J. 2016 Aug;10(8):1939-53. doi: 10.1038/ismej.2015.257. Epub 2016 Feb 12.

39.

Ecological Genomics of the Uncultivated Marine Roseobacter Lineage CHAB-I-5.

Zhang Y, Sun Y, Jiao N, Stepanauskas R, Luo H.

Appl Environ Microbiol. 2016 Jan 29;82(7):2100-2111. doi: 10.1128/AEM.03678-15.

40.

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria.

Eiler A, Mondav R, Sinclair L, Fernandez-Vidal L, Scofield DG, Schwientek P, Martinez-Garcia M, Torrents D, McMahon KD, Andersson SG, Stepanauskas R, Woyke T, Bertilsson S.

ISME J. 2016 Aug;10(8):1902-14. doi: 10.1038/ismej.2015.260. Epub 2016 Jan 19.

41.

Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines.

Ngugi DK, Blom J, Stepanauskas R, Stingl U.

ISME J. 2016 Jun;10(6):1383-99. doi: 10.1038/ismej.2015.214. Epub 2015 Dec 11.

42.

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs.

Munson-McGee JH, Field EK, Bateson M, Rooney C, Stepanauskas R, Young MJ.

Appl Environ Microbiol. 2015 Nov;81(22):7860-8. doi: 10.1128/AEM.01539-15. Epub 2015 Sep 4.

43.

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population.

Labonté JM, Field EK, Lau M, Chivian D, Van Heerden E, Wommack KE, Kieft TL, Onstott TC, Stepanauskas R.

Front Microbiol. 2015 Apr 22;6:349. doi: 10.3389/fmicb.2015.00349. eCollection 2015.

44.

Wiretapping into microbial interactions by single cell genomics.

Stepanauskas R.

Front Microbiol. 2015 Apr 8;6:258. doi: 10.3389/fmicb.2015.00258. eCollection 2015. No abstract available.

45.

Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution.

Martijn J, Schulz F, Zaremba-Niedzwiedzka K, Viklund J, Stepanauskas R, Andersson SG, Horn M, Guy L, Ettema TJ.

ISME J. 2015 Nov;9(11):2373-85. doi: 10.1038/ismej.2015.46. Epub 2015 Apr 7.

46.

Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton.

Labonté JM, Swan BK, Poulos B, Luo H, Koren S, Hallam SJ, Sullivan MB, Woyke T, Wommack KE, Stepanauskas R.

ISME J. 2015 Nov;9(11):2386-99. doi: 10.1038/ismej.2015.48. Epub 2015 Apr 7.

47.

Re-defining microbial diversity from its single-celled building blocks.

Stepanauskas R.

Environ Microbiol Rep. 2015 Feb;7(1):36-7. doi: 10.1111/1758-2229.12226. No abstract available.

48.

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount.

Field EK, Sczyrba A, Lyman AE, Harris CC, Woyke T, Stepanauskas R, Emerson D.

ISME J. 2015 Mar 17;9(4):857-70. doi: 10.1038/ismej.2014.183.

49.

Hidden diversity in honey bee gut symbionts detected by single-cell genomics.

Engel P, Stepanauskas R, Moran NA.

PLoS Genet. 2014 Sep 11;10(9):e1004596. doi: 10.1371/journal.pgen.1004596. eCollection 2014 Sep.

50.

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics.

Roux S, Hawley AK, Torres Beltran M, Scofield M, Schwientek P, Stepanauskas R, Woyke T, Hallam SJ, Sullivan MB.

Elife. 2014 Aug 29;3:e03125. doi: 10.7554/eLife.03125.

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