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Items: 1 to 50 of 529

1.

A pipeline for targeted metagenomics of environmental bacteria.

Grieb A, Bowers RM, Oggerin M, Goudeau D, Lee J, Malmstrom RR, Woyke T, Fuchs BM.

Microbiome. 2020 Feb 15;8(1):21. doi: 10.1186/s40168-020-0790-7.

PMID:
32061258
2.

Author Correction: Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes.

Roux S, Krupovic M, Daly RA, Borges AL, Nayfach S, Schulz F, Sharrar A, Matheus Carnevali PB, Cheng JF, Ivanova NN, Bondy-Denomy J, Wrighton KC, Woyke T, Visel A, Kyrpides NC, Eloe-Fadrosh EA.

Nat Microbiol. 2020 Feb 11. doi: 10.1038/s41564-020-0681-5. [Epub ahead of print]

PMID:
32047285
3.

Functional Signatures of the Epiphytic Prokaryotic Microbiome of Agaves and Cacti.

Flores-Núñez VM, Fonseca-García C, Desgarennes D, Eloe-Fadrosh E, Woyke T, Partida-Martínez LP.

Front Microbiol. 2020 Jan 17;10:3044. doi: 10.3389/fmicb.2019.03044. eCollection 2019.

4.

One Complete and Seven Draft Genome Sequences of Subdivision 1 and 3 Acidobacteria Isolated from Soil.

Eichorst SA, Trojan D, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Goodwin LA, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Woebken D.

Microbiol Resour Announc. 2020 Jan 30;9(5). pii: e01087-19. doi: 10.1128/MRA.01087-19.

5.

Giant virus diversity and host interactions through global metagenomics.

Schulz F, Roux S, Paez-Espino D, Jungbluth S, Walsh DA, Denef VJ, McMahon KD, Konstantinidis KT, Eloe-Fadrosh EA, Kyrpides NC, Woyke T.

Nature. 2020 Jan 22. doi: 10.1038/s41586-020-1957-x. [Epub ahead of print]

PMID:
31968354
6.

Niche differentiation is spatially and temporally regulated in the rhizosphere.

Nuccio EE, Starr E, Karaoz U, Brodie EL, Zhou J, Tringe SG, Malmstrom RR, Woyke T, Banfield JF, Firestone MK, Pett-Ridge J.

ISME J. 2020 Jan 17. doi: 10.1038/s41396-019-0582-x. [Epub ahead of print]

PMID:
31953507
7.

Genome analysis of the marine bacterium Kiloniella laminariae and first insights into comparative genomics with related Kiloniella species.

Wiese J, Imhoff JF, Horn H, Borchert E, Kyrpides NC, Göker M, Klenk HP, Woyke T, Hentschel U.

Arch Microbiol. 2019 Dec 16. doi: 10.1007/s00203-019-01791-0. [Epub ahead of print]

PMID:
31844948
8.

Diversity, evolution, and classification of virophages uncovered through global metagenomics.

Paez-Espino D, Zhou J, Roux S, Nayfach S, Pavlopoulos GA, Schulz F, McMahon KD, Walsh D, Woyke T, Ivanova NN, Eloe-Fadrosh EA, Tringe SG, Kyrpides NC.

Microbiome. 2019 Dec 10;7(1):157. doi: 10.1186/s40168-019-0768-5.

9.

Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria.

Rochman FF, Kwon M, Khadka R, Tamas I, Lopez-Jauregui AA, Sheremet A, V Smirnova A, Malmstrom RR, Yoon S, Woyke T, Dunfield PF, Verbeke TJ.

ISME J. 2019 Dec 3. doi: 10.1038/s41396-019-0561-2. [Epub ahead of print]

PMID:
31796935
10.

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.

Sevim V, Lee J, Egan R, Clum A, Hundley H, Lee J, Everroad RC, Detweiler AM, Bebout BM, Pett-Ridge J, Göker M, Murray AE, Lindemann SR, Klenk HP, O'Malley R, Zane M, Cheng JF, Copeland A, Daum C, Singer E, Woyke T.

Sci Data. 2019 Nov 26;6(1):285. doi: 10.1038/s41597-019-0287-z.

11.

Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere.

Doud DFR, Bowers RM, Schulz F, De Raad M, Deng K, Tarver A, Glasgow E, Vander Meulen K, Fox B, Deutsch S, Yoshikuni Y, Northen T, Hedlund BP, Singer SW, Ivanova N, Woyke T.

ISME J. 2019 Nov 21. doi: 10.1038/s41396-019-0557-y. [Epub ahead of print]

PMID:
31754206
12.

Improved Draft Genome Sequence of Microbacterium sp. Strain LKL04, a Bacterial Endophyte Associated with Switchgrass Plants.

Sahib MR, Yang P, Bokros N, Shapiro N, Woyke T, Kyrpides NC, Xia Y, DeBolt S.

Microbiol Resour Announc. 2019 Nov 7;8(45). pii: e00927-19. doi: 10.1128/MRA.00927-19.

13.

Draft Genome Sequence of Mn(II)-Oxidizing Bacterium Oxalobacteraceae sp. Strain AB_14.

Bushman TJ, Akob DM, Bohu T, Beyer A, Woyke T, Shapiro N, Lapidus A, Klenk HP, Küsel K.

Microbiol Resour Announc. 2019 Oct 24;8(43). pii: e01024-19. doi: 10.1128/MRA.01024-19.

14.

Conservation of Endophyte Bacterial Community Structure Across Two Panicum Grass Species.

Singer E, Bonnette J, Woyke T, Juenger TE.

Front Microbiol. 2019 Sep 27;10:2181. doi: 10.3389/fmicb.2019.02181. eCollection 2019.

15.

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes.

García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M.

Front Microbiol. 2019 Sep 23;10:2083. doi: 10.3389/fmicb.2019.02083. eCollection 2019.

16.

A single-cell genome perspective on studying intracellular associations in unicellular eukaryotes.

Tyml T, Date SV, Woyke T.

Philos Trans R Soc Lond B Biol Sci. 2019 Nov 25;374(1786):20190082. doi: 10.1098/rstb.2019.0082. Epub 2019 Oct 7.

17.

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes.

Roux S, Krupovic M, Daly RA, Borges AL, Nayfach S, Schulz F, Sharrar A, Matheus Carnevali PB, Cheng JF, Ivanova NN, Bondy-Denomy J, Wrighton KC, Woyke T, Visel A, Kyrpides NC, Eloe-Fadrosh EA.

Nat Microbiol. 2019 Nov;4(11):1895-1906. doi: 10.1038/s41564-019-0510-x. Epub 2019 Jul 22. Erratum in: Nat Microbiol. 2020 Feb 11;:.

18.

Beyond the census of human gut dwellers.

Woyke T.

Nat Rev Microbiol. 2019 Jul;17(7):401. doi: 10.1038/s41579-019-0220-7. No abstract available.

PMID:
31127248
19.

Sulfate-Reducing Bacteria That Produce Exopolymers Thrive in the Calcifying Zone of a Hypersaline Cyanobacterial Mat.

Spring S, Sorokin DY, Verbarg S, Rohde M, Woyke T, Kyrpides NC.

Front Microbiol. 2019 Apr 24;10:862. doi: 10.3389/fmicb.2019.00862. eCollection 2019.

20.

Complete Genome Sequence of Serratia quinivorans Strain 124R, a Facultative Anaerobe Isolated on Organosolv Lignin as a Sole Carbon Source.

Chaput G, Ford J, DeDiego L, Narayanan A, Tam WY, Whalen M, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Glavina Del Rio T, DeAngelis K.

Microbiol Resour Announc. 2019 May 2;8(18). pii: e00409-19. doi: 10.1128/MRA.00409-19.

21.

Genome-informed Bradyrhizobium taxonomy: where to from here?

Avontuur JR, Palmer M, Beukes CW, Chan WY, Coetzee MPA, Blom J, Stępkowski T, Kyrpides NC, Woyke T, Shapiro N, Whitman WB, Venter SN, Steenkamp ET.

Syst Appl Microbiol. 2019 Jul;42(4):427-439. doi: 10.1016/j.syapm.2019.03.006. Epub 2019 Apr 4.

PMID:
31031014
22.

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 Sep;13(9):2150-2161. doi: 10.1038/s41396-019-0418-8. Epub 2019 Apr 25.

PMID:
31024152
23.

Improved Draft Genome Sequence of Pseudomonas poae A2-S9, a Strain with Plant Growth-Promoting Activity.

Xia Y, DeBolt S, Ma Q, McDermaid A, Wang C, Shapiro N, Woyke T, Kyrpides NC.

Microbiol Resour Announc. 2019 Apr 11;8(15). pii: e00275-19. doi: 10.1128/MRA.00275-19.

24.

Improved Draft Genome Sequence of Bacillus sp. Strain YF23, Which Has Plant Growth-Promoting Activity.

Xia Y, DeBolt S, Ma Q, McDermaid A, Wang C, Shapiro N, Woyke T, Kyrpides NC.

Microbiol Resour Announc. 2019 Apr 11;8(15). pii: e00099-19. doi: 10.1128/MRA.00099-19.

25.

High-quality draft genome sequence of Pseudomonas aeruginosa san ai, an environmental isolate resistant to heavy metals.

Izrael-Živković L, Beškoski V, Rikalović M, Kazazić S, Shapiro N, Woyke T, Gojgić-Cvijović G, Vrvić MM, Maksimović N, Karadžić I.

Extremophiles. 2019 Jul;23(4):399-405. doi: 10.1007/s00792-019-01092-w. Epub 2019 Apr 5.

PMID:
30949775
26.

Complete Genome Sequence for Asinibacterium sp. Strain OR53 and Draft Genome Sequence for Asinibacterium sp. Strain OR43, Two Bacteria Tolerant to Uranium.

Brzoska RM, Huntemann M, Clum A, Chen A, Kyrpides N, Palaniappan K, Ivanova N, Mikhailova N, Ovchinnikova G, Varghese N, Mukherjee S, Reddy TBK, Daum C, Shapiro N, Woyke T, Bollmann A.

Microbiol Resour Announc. 2019 Apr 4;8(14). pii: e01701-18. doi: 10.1128/MRA.01701-18.

27.

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.

28.

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.

29.

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.

30.

Draft Genome of Burkholderia cenocepacia TAtl-371, a Strain from the Burkholderia cepacia Complex Retains Antagonism in Different Carbon and Nitrogen Sources.

Rojas-Rojas FU, Sánchez-López D, Tapia-García EY, Arroyo-Herrera I, Maymon M, Humm E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Ivanova N, Kyrpides N, Woyke T, Shapiro N, Hirsch AM, Ibarra JA, Estrada-de Los Santos P.

Curr Microbiol. 2019 May;76(5):566-574. doi: 10.1007/s00284-019-01657-0. Epub 2019 Feb 28.

31.

Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens.

Berghuis BA, Yu FB, Schulz F, Blainey PC, Woyke T, Quake SR.

Proc Natl Acad Sci U S A. 2019 Mar 12;116(11):5037-5044. doi: 10.1073/pnas.1815631116. Epub 2019 Feb 27.

32.

Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California.

Ul-Hasan S, Bowers RM, Figueroa-Montiel A, Licea-Navarro AF, Beman JM, Woyke T, Nobile CJ.

PLoS One. 2019 Feb 14;14(2):e0212355. doi: 10.1371/journal.pone.0212355. eCollection 2019.

33.

Direct pathway cloning of the sodorifen biosynthetic gene cluster and recombinant generation of its product in E. coli.

Duell ER, D'Agostino PM, Shapiro N, Woyke T, Fuchs TM, Gulder TAM.

Microb Cell Fact. 2019 Feb 7;18(1):32. doi: 10.1186/s12934-019-1080-6.

34.

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.

35.

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.

36.

Entities inside one another - a matryoshka doll in biology?

Woyke T, Schulz F.

Environ Microbiol Rep. 2019 Feb;11(1):26-28. doi: 10.1111/1758-2229.12716. Epub 2018 Dec 26. No abstract available.

PMID:
30588764
37.

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. 2019 Jan;37(1):29-37. doi: 10.1038/nbt.4306. Epub 2018 Dec 17.

38.

Plant compartment and genetic variation drive microbiome composition in switchgrass roots.

Singer E, Bonnette J, Kenaley SC, Woyke T, Juenger TE.

Environ Microbiol Rep. 2019 Apr;11(2):185-195. doi: 10.1111/1758-2229.12727. Epub 2019 Jan 31.

39.

Genome Sequences of Actinobacteria from Extreme Environments in Colombia.

Cantillo A, Shapiro N, Woyke T, Kyrpides NC, Baena S, Zambrano MM.

Microbiol Resour Announc. 2018 Dec 6;7(22). pii: e01384-18. doi: 10.1128/MRA.01384-18. eCollection 2018 Dec.

40.

High-Quality Draft Genome Sequences of Eight Bacteria Isolated from Fungus Gardens Grown by Trachymyrmex septentrionalis Ants.

Kopac S, Beatty H, Gialopsos P, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Ng V, Ivanova N, Kyrpides N, Woyke T, Klassen JL.

Microbiol Resour Announc. 2018 Jul 19;7(2). pii: e00871-18. doi: 10.1128/MRA.00871-18. eCollection 2018 Jul.

41.

Draft Genome Sequences of New Isolates and the Known Species of the Family Microbacteriaceae Associated with Plants.

Vasilenko OV, Starodumova IP, Dorofeeva LV, Tarlachkov SV, Prisyazhnaya NV, Chizhov VN, Subbotin SA, Huntemann M, Clum A, Duffy K, Pillay M, Palaniappan K, Varghese N, Chen IA, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Whitman WB, Evtushenko LI.

Microbiol Resour Announc. 2018 Sep 20;7(11). pii: e01051-18. doi: 10.1128/MRA.01051-18. eCollection 2018 Sep.

42.

Hidden diversity of soil giant viruses.

Schulz F, Alteio L, Goudeau D, Ryan EM, Yu FB, Malmstrom RR, Blanchard J, Woyke T.

Nat Commun. 2018 Nov 19;9(1):4881. doi: 10.1038/s41467-018-07335-2.

43.

Elucidating Bacterial Gene Functions in the Plant Microbiome.

Levy A, Conway JM, Dangl JL, Woyke T.

Cell Host Microbe. 2018 Oct 10;24(4):475-485. doi: 10.1016/j.chom.2018.09.005. Review.

44.

Leveraging single-cell genomics to expand the fungal tree of life.

Ahrendt SR, Quandt CA, Ciobanu D, Clum A, Salamov A, Andreopoulos B, Cheng JF, Woyke T, Pelin A, Henrissat B, Reynolds NK, Benny GL, Smith ME, James TY, Grigoriev IV.

Nat Microbiol. 2018 Dec;3(12):1417-1428. doi: 10.1038/s41564-018-0261-0. Epub 2018 Oct 8.

45.

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes.

Chen IA, Chu K, Palaniappan K, Pillay M, Ratner A, Huang J, Huntemann M, Varghese N, White JR, Seshadri R, Smirnova T, Kirton E, Jungbluth SP, Woyke T, Eloe-Fadrosh EA, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2019 Jan 8;47(D1):D666-D677. doi: 10.1093/nar/gky901.

46.

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.

47.

Thermus sediminis sp. nov., a thiosulfate-oxidizing and arsenate-reducing organism isolated from Little Hot Creek in the Long Valley Caldera, California.

Zhou EM, Xian WD, Mefferd CC, Thomas SC, Adegboruwa AL, Williams N, Murugapiran SK, Dodsworth JA, Ganji R, Li MM, Ding YP, Liu L, Woyke T, Li WJ, Hedlund BP.

Extremophiles. 2018 Nov;22(6):983-991. doi: 10.1007/s00792-018-1055-2. Epub 2018 Sep 15.

PMID:
30219948
48.

Genome-Based Taxonomic Classification of the Phylum Actinobacteria.

Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M.

Front Microbiol. 2018 Aug 22;9:2007. doi: 10.3389/fmicb.2018.02007. eCollection 2018.

49.

Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria.

Ganesh S, Bertagnolli AD, Bristow LA, Padilla CC, Blackwood N, Aldunate M, Bourbonnais A, Altabet MA, Malmstrom RR, Woyke T, Ulloa O, Konstantinidis KT, Thamdrup B, Stewart FJ.

ISME J. 2018 Nov;12(11):2706-2722. doi: 10.1038/s41396-018-0223-9. Epub 2018 Jul 10.

50.

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

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