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CRISPR Spacers Indicate Preferential Matching of Specific Virioplankton Genes.

Nasko DJ, Ferrell BD, Moore RM, Bhavsar JD, Polson SW, Wommack KE.

MBio. 2019 Mar 5;10(2). pii: e02651-18. doi: 10.1128/mBio.02651-18.


Reannotation of the Ribonucleotide Reductase in a Cyanophage Reveals Life History Strategies Within the Virioplankton.

Harrison AO, Moore RM, Polson SW, Wommack KE.

Front Microbiol. 2019 Feb 5;10:134. doi: 10.3389/fmicb.2019.00134. eCollection 2019.


Family A DNA Polymerase Phylogeny Uncovers Diversity and Replication Gene Organization in the Virioplankton.

Nasko DJ, Chopyk J, Sakowski EG, Ferrell BD, Polson SW, Wommack KE.

Front Microbiol. 2018 Dec 14;9:3053. doi: 10.3389/fmicb.2018.03053. eCollection 2018.


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. 2018 Dec 17. doi: 10.1038/nbt.4306. [Epub ahead of print]


Author Correction: Re-examination of the relationship between marine virus and microbial cell abundances.

Wigington CH, Sonderegger D, Brussaard CPD, Buchan A, Finke JF, Fuhrman JA, Lennon JT, Middelboe M, Suttle CA, Stock C, Wilson WH, Wommack KE, Wilhelm SW, Weitz JS.

Nat Microbiol. 2017 Nov;2(11):1571. doi: 10.1038/s41564-017-0042-1.


Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory.

Williamson KE, Fuhrmann JJ, Wommack KE, Radosevich M.

Annu Rev Virol. 2017 Sep 29;4(1):201-219. doi: 10.1146/annurev-virology-101416-041639. Review.


The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription in the Swine Gut Microbiome.

Johnson TA, Looft T, Severin AJ, Bayles DO, Nasko DJ, Wommack KE, Howe A, Allen HK.

MBio. 2017 Aug 8;8(4). pii: e00709-17. doi: 10.1128/mBio.00709-17.


Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology.

Marine RL, Nasko DJ, Wray J, Polson SW, Wommack KE.

ISME J. 2017 Nov;11(11):2479-2491. doi: 10.1038/ismej.2017.102. Epub 2017 Jul 21.


Re-examination of the relationship between marine virus and microbial cell abundances.

Wigington CH, Sonderegger D, Brussaard CP, Buchan A, Finke JF, Fuhrman JA, Lennon JT, Middelboe M, Suttle CA, Stock C, Wilson WH, Wommack KE, Wilhelm SW, Weitz JS.

Nat Microbiol. 2016 Jan 25;1:15024. doi: 10.1038/nmicrobiol.2015.24.


Presence of pathogenic Escherichia coli is correlated with bacterial community diversity and composition on pre-harvest cattle hides.

Chopyk J, Moore RM, DiSpirito Z, Stromberg ZR, Lewis GL, Renter DG, Cernicchiaro N, Moxley RA, Wommack KE.

Microbiome. 2016 Mar 22;4:9. doi: 10.1186/s40168-016-0155-4.


Dynamics of autochthonous soil viral communities parallels dynamics of host communities under nutrient stimulation.

Srinivasiah S, Lovett J, Ghosh D, Roy K, Fuhrmann JJ, Radosevich M, Wommack KE.

FEMS Microbiol Ecol. 2015 Jul;91(7). pii: fiv063. doi: 10.1093/femsec/fiv063. Epub 2015 Jul 6.


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.


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.


Counts and sequences, observations that continue to change our understanding of viruses in nature.

Wommack KE, Nasko DJ, Chopyk J, Sakowski EG.

J Microbiol. 2015 Mar;53(3):181-92. doi: 10.1007/s12275-015-5068-6. Epub 2015 Mar 3. Review.


Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses.

Sakowski EG, Munsell EV, Hyatt M, Kress W, Williamson SJ, Nasko DJ, Polson SW, Wommack KE.

Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):15786-91. doi: 10.1073/pnas.1401322111. Epub 2014 Oct 13.


Genome Sequence and Methylome of Soil Bacterium Gemmatirosa kalamazoonensis KBS708T, a Member of the Rarely Cultivated Gemmatimonadetes Phylum.

Debruyn JM, Radosevich M, Wommack KE, Polson SW, Hauser LJ, Fawaz MN, Korlach J, Tsai YC.

Genome Announc. 2014 Apr 3;2(2). pii: e00226-14. doi: 10.1128/genomeA.00226-14.


All hail reproducibility in microbiome research.

Ravel J, Wommack KE.

Microbiome. 2014 Mar 7;2(1):8. doi: 10.1186/2049-2618-2-8. No abstract available.


Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome.

Marine R, McCarren C, Vorrasane V, Nasko D, Crowgey E, Polson SW, Wommack KE.

Microbiome. 2014 Jan 30;2(1):3. doi: 10.1186/2049-2618-2-3.


Microbiome, demystifying the role of microbial communities in the biosphere.

Wommack KE, Ravel J.

Microbiome. 2013 Jan 9;1(1):1. doi: 10.1186/2049-2618-1-1.


Draft Genome Sequence of Synechococcus sp. Strain CB0101, Isolated From the Chesapeake Bay Estuary.

Marsan D, Wommack KE, Ravel J, Chen F.

Genome Announc. 2014 Jan 9;2(1). pii: e01111-13. doi: 10.1128/genomeA.01111-13.


Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton.

Schmidt HF, Sakowski EG, Williamson SJ, Polson SW, Wommack KE.

ISME J. 2014 Jan;8(1):103-14. doi: 10.1038/ismej.2013.124. Epub 2013 Aug 29.


Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities.

Campbell BJ, Polson SW, Zeigler Allen L, Williamson SJ, Lee CK, Wommack KE, Cary SC.

Front Microbiol. 2013 Jul 24;4:182. doi: 10.3389/fmicb.2013.00182. eCollection 2013.


Direct assessment of viral diversity in soils by random PCR amplification of polymorphic DNA.

Srinivasiah S, Lovett J, Polson S, Bhavsar J, Ghosh D, Roy K, Fuhrmann JJ, Radosevich M, Wommack KE.

Appl Environ Microbiol. 2013 Sep;79(18):5450-7. doi: 10.1128/AEM.00268-13. Epub 2013 Jun 21.


Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes.

Santini S, Jeudy S, Bartoli J, Poirot O, Lescot M, Abergel C, Barbe V, Wommack KE, Noordeloos AA, Brussaard CP, Claverie JM.

Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):10800-5. doi: 10.1073/pnas.1303251110. Epub 2013 Jun 10.


VIROME: a standard operating procedure for analysis of viral metagenome sequences.

Wommack KE, Bhavsar J, Polson SW, Chen J, Dumas M, Srinivasiah S, Furman M, Jamindar S, Nasko DJ.

Stand Genomic Sci. 2012 Jul 30;6(3):427-39. doi: 10.4056/sigs.2945050. Epub 2012 Jul 27.


Evaluation of two approaches for assessing the genetic similarity of virioplankton populations as defined by genome size.

Jamindar S, Polson SW, Srinivasiah S, Waidner L, Wommack KE.

Appl Environ Microbiol. 2012 Dec;78(24):8773-83. doi: 10.1128/AEM.02432-12. Epub 2012 Oct 12.


Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing.

Lee CK, Herbold CW, Polson SW, Wommack KE, Williamson SJ, McDonald IR, Cary SC.

PLoS One. 2012;7(9):e44224. doi: 10.1371/journal.pone.0044224. Epub 2012 Sep 6.


High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage.

Ng TF, Marine R, Wang C, Simmonds P, Kapusinszky B, Bodhidatta L, Oderinde BS, Wommack KE, Delwart E.

J Virol. 2012 Nov;86(22):12161-75. doi: 10.1128/JVI.00869-12. Epub 2012 Aug 29.


A carbon free filter for collection of large volume samples of cellular biomass from oligotrophic waters.

Mailloux BJ, Dochenetz A, Bishop M, Dong H, Ziolkowski LA, Wommack KE, Sakowski EG, Onstott TC, Slater GF.

J Microbiol Methods. 2012 Sep;90(3):145-51. doi: 10.1016/j.mimet.2012.04.016. Epub 2012 May 3.


Interannual dynamics of viriobenthos abundance and morphological diversity in Chesapeake Bay sediments.

Helton RR, Wang K, Kan J, Powell DH, Wommack KE.

FEMS Microbiol Ecol. 2012 Feb;79(2):474-86. doi: 10.1111/j.1574-6941.2011.01238.x. Epub 2011 Nov 21.


Impacts of poultry house environment on poultry litter bacterial community composition.

Dumas MD, Polson SW, Ritter D, Ravel J, Gelb J Jr, Morgan R, Wommack KE.

PLoS One. 2011;6(9):e24785. doi: 10.1371/journal.pone.0024785. Epub 2011 Sep 16.


Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA.

Marine R, Polson SW, Ravel J, Hatfull G, Russell D, Sullivan M, Syed F, Dumas M, Wommack KE.

Appl Environ Microbiol. 2011 Nov;77(22):8071-9. doi: 10.1128/AEM.05610-11. Epub 2011 Sep 23.


Bias in bacteriophage morphological classification by transmission electron microscopy due to breakage or loss of tail structures.

Williamson KE, Helton RR, Wommack KE.

Microsc Res Tech. 2012 Apr;75(4):452-7. doi: 10.1002/jemt.21077. Epub 2011 Sep 14.


Abundance and distribution of Synechococcus spp. and cyanophages in the Chesapeake Bay.

Wang K, Wommack KE, Chen F.

Appl Environ Microbiol. 2011 Nov;77(21):7459-68. doi: 10.1128/AEM.00267-11. Epub 2011 Aug 5.


Repeating patterns of virioplankton production within an estuarine ecosystem.

Winget DM, Helton RR, Williamson KE, Bench SR, Williamson SJ, Wommack KE.

Proc Natl Acad Sci U S A. 2011 Jul 12;108(28):11506-11. doi: 10.1073/pnas.1101907108. Epub 2011 Jun 27.


The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010.

Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, Tiedje J, Ley R, Fierer N, Field D, Kyrpides N, Glöckner FO, Klenk HP, Wommack KE, Glass E, Docherty K, Gallery R, Stevens R, Knight R.

Stand Genomic Sci. 2010 Dec 25;3(3):249-53. doi: 10.4056/aigs.1443528.


Unraveling the viral tapestry (from inside the capsid out).

Polson SW, Wilhelm SW, Wommack KE.

ISME J. 2011 Feb;5(2):165-8. doi: 10.1038/ismej.2010.81. Epub 2010 Jun 17. No abstract available. Erratum in: ISME J. 2011 Feb;5(2):366.


Census of the viral metagenome within an activated sludge microbial assemblage.

Parsley LC, Consuegra EJ, Thomas SJ, Bhavsar J, Land AM, Bhuiyan NN, Mazher MA, Waters RJ, Wommack KE, Harper WF Jr, Liles MR.

Appl Environ Microbiol. 2010 Apr;76(8):2673-7. doi: 10.1128/AEM.02520-09. Epub 2010 Feb 12.


Functional viral metagenomics and the next generation of molecular tools.

Schoenfeld T, Liles M, Wommack KE, Polson SW, Godiska R, Mead D.

Trends Microbiol. 2010 Jan;18(1):20-9. doi: 10.1016/j.tim.2009.10.001. Epub 2009 Nov 5. Review.


Acyl-homoserine lactones can induce virus production in lysogenic bacteria: an alternative paradigm for prophage induction.

Ghosh D, Roy K, Williamson KE, Srinivasiah S, Wommack KE, Radosevich M.

Appl Environ Microbiol. 2009 Nov;75(22):7142-52. doi: 10.1128/AEM.00950-09. Epub 2009 Sep 25.


Diverse and dynamic populations of cyanobacterial podoviruses in the Chesapeake Bay unveiled through DNA polymerase gene sequences.

Chen F, Wang K, Huang S, Cai H, Zhao M, Jiao N, Wommack KE.

Environ Microbiol. 2009 Nov;11(11):2884-92. doi: 10.1111/j.1462-2920.2009.02033.x. Epub 2009 Aug 24.


Diel and daily fluctuations in virioplankton production in coastal ecosystems.

Winget DM, Wommack KE.

Environ Microbiol. 2009 Nov;11(11):2904-14. doi: 10.1111/j.1462-2920.2009.02038.x. Epub 2009 Aug 24.


Seasonal dynamics and metagenomic characterization of estuarine viriobenthos assemblages by randomly amplified polymorphic DNA PCR.

Helton RR, Wommack KE.

Appl Environ Microbiol. 2009 Apr;75(8):2259-65. doi: 10.1128/AEM.02551-08. Epub 2009 Feb 13.


Isolation independent methods of characterizing phage communities 2: characterizing a metagenome.

Wommack KE, Bench SR, Bhavsar J, Mead D, Hanson T.

Methods Mol Biol. 2009;502:279-89. doi: 10.1007/978-1-60327-565-1_16.


Methods for the isolation of viruses from environmental samples.

Wommack KE, Williamson KE, Helton RR, Bench SR, Winget DM.

Methods Mol Biol. 2009;501:3-14. doi: 10.1007/978-1-60327-164-6_1.


Lysogenic virus-host interactions predominate at deep-sea diffuse-flow hydrothermal vents.

Williamson SJ, Cary SC, Williamson KE, Helton RR, Bench SR, Winget D, Wommack KE.

ISME J. 2008 Nov;2(11):1112-21. doi: 10.1038/ismej.2008.73. Epub 2008 Aug 21.


Phages across the biosphere: contrasts of viruses in soil and aquatic environments.

Srinivasiah S, Bhavsar J, Thapar K, Liles M, Schoenfeld T, Wommack KE.

Res Microbiol. 2008 Jun;159(5):349-57. doi: 10.1016/j.resmic.2008.04.010. Epub 2008 May 8. Review.


Assembly of viral metagenomes from yellowstone hot springs.

Schoenfeld T, Patterson M, Richardson PM, Wommack KE, Young M, Mead D.

Appl Environ Microbiol. 2008 Jul;74(13):4164-74. doi: 10.1128/AEM.02598-07. Epub 2008 Apr 25.


Global-scale processes with a nanoscale drive: the role of marine viruses.

Brussaard CP, Wilhelm SW, Thingstad F, Weinbauer MG, Bratbak G, Heldal M, Kimmance SA, Middelboe M, Nagasaki K, Paul JH, Schroeder DC, Suttle CA, Vaqué D, Wommack KE.

ISME J. 2008 Jun;2(6):575-8. doi: 10.1038/ismej.2008.31. Epub 2008 Apr 3. No abstract available.


Randomly amplified polymorphic DNA PCR as a tool for assessment of marine viral richness.

Winget DM, Wommack KE.

Appl Environ Microbiol. 2008 May;74(9):2612-8. doi: 10.1128/AEM.02829-07. Epub 2008 Mar 14.

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