Publications

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Soils research:

213. Freire-Zapata, V., Holland-Moritz, H., Cronin, D.R., Aroney, S., Smith, D.A., Wilson, R.M., Ernakovich, J.G., Woodcroft, B.J., Bagby, S.C., EMERGE 2012 Field Team, EMERGE Coordinators, Rich, V.I., Sullivan, M.B., Stegen, J.C., & Tfaily, M.M. 2024. Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient. Nature Microbiology. In Press.

209. McGivern, B.B., Cronin, D.R., Ellenbogen, J.B., Borton, M.A., Knutson, E.L., Freire-Zapata, V., Bouranis, J.A., Bernhardt, L., Hernandez, A.I., Flynn, R.M., Woyda, R., Cory, A.B., Wilson, R.M., Chanton, J.P., Woodcroft, B.J., Ernakovich, J.G., Tfaily, M.M., Sullivan, M.B., Tyson, G.W., Rich, V.I., Hagerman, A.E. & Wrighton, K.C. 2024. Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle. Nature Microbiology. 9: 1454–1466. LINK PDF

208. Sun†, C.L., Pratama†, A.A., Gazitúa, M.C., Cronin, D., McGivern, B.B., Wainaina, J.M., Vik, D.R., Zayed, A.A., Bolduc, B., IsoGenie Project Field Teams 2010-2017, IsoGenie and EMERGE Projects Coordinators, Wrighton, K.C., Rich, V.I., & Sullivan, M.B. 2024. Virus ecology and 7-year temporal dynamics across a permafrost thaw gradient. Environmental Microbiology. 26:e16665. LINK PDF († denotes co-first authors)

177. Greenlon, A., Sieradzki, E., Zablocki, O., Koch, B., Foley, M., Kimbrel, J., Hungate, B., Blazewicz, S., Nuccio, E., Sun, C., Chew, A., Mancilla, C.-J., Sullivan, M.B., Firestone, M., Pett-Ridge, J., & Banfield, J. 2022. Quantitative stable-isotope probing (qSIP) with metagenomics links microbial physiology and activity to soil moisture in Mediterranean-climate grassland ecosystems. mSystems. 7:e00417-22. LINK PDF

167. Sokol, N.W., Slessarev, E., Marschmann, G.L., Nicolas, A., Blazewicz, S.J., Brodie, E.L., Firestone, M.K., Foley, M.M., Hestrin, R., Hungate, B.A., Koch, B.J., Stone, B.W., Sullivan, M.B., Zablocki, O., LLNL Soil Microbiome Consortium & Pett-Ridge, J. 2022. Life and death in the soil microbiome: how ecological processes influence biogeochemistry. Nature Reviews Microbiology. 20:415–430. LINK PDF

137. Bolduc, B.†^, Hodgkins, S.B.†, Varner, R.K., Crill, P.M., McCalley, C.K., Chanton, J.P., Tyson, G.W., Riley, W.J., Palace, M., Duhaime, M.B., Hough, M.A., IsoGenie Project Coordinators, IsoGenie Project Team, A2A Project Team, Saleska, S.R., Sullivan, M.B., Rich, V.I.^ 2020.  The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research. PeerJ. 8:e9467. LINK PDF (^denotes co-corresponding authors) († denotes co-first authors)

122. Trubl, G., Roux, S., Solonenko, N., Li, Y., Bolduc, B., Rodriguez-Ramos, J., Eloe-Fadrosh, E.A., Rich, V., & Sullivan, M.B. 2019. Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils. PeerJ. 7:e7265.  LINK PDF

109. Martinez, M., Woodcroft, B., Ignacio Espinoza, J. C., Zayed, A., Singleton, C., Boyd, J., Li, Y-F., Purvine, S., Maughan, H., Hodgkins, S., Anderson, D., Sederholm, M.,Temperton, B., Bolduc, B., Isogenie Project Coordinators, Saleska, S., Tyson, G. & Rich V. 2019. Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov, Ca. Cryosericia class nov, Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov. Systematic and Applied Microbiology.  42:54-66.  LINK  PDF

104. Trubl, G., Jang, H. B., Roux, S., Emerson,  J., Solonenko, N., Vik, D., Solden, L., Ellenbogen, J., Runyon, A., Bolduc, B., Woodcroft, B., Saleska, S., Tyson, G., Wrighton, K., Sullivan, M.B. & Rich, V. 2018. Soil viruses are underexplored players in ecosystem carbon processing. mSystems.  3:e00076-18.  LINK  PDF

• Featured by the U.S. Dept. of Energy: LINK
• Top Cited article from the Editors of mSystems

101. Emerson, J.B., Roux, S., Brum, J.R., Bolduc, B., Woodcroft, B.J, Jang, H.B., Singleton, C.M., Solden, L.M., Naas, A.E., Boyd, J.A., Hodgkins, S.B., Wilson, R.M., Trubl, G., Li, C., Frolking, S., Pope, P.B., Wrighton, K.C., Crill, P.M., Chanton, J.P., Saleska, S.R., Tyson, G.W., Rich, V.I. & Sullivan, M.B. 2018. Host-linked soil viral ecology along a permafrost thaw gradient. Nature Microbiology. 3:870–880.   LINK   PDF

• Highlighted 24 July, 2018 in Nature Reviews Microbiology

69. Trubl, G, Solonenko, N., Chittick, L., Solonenko, S., Rich, V.I., & Sullivan, M.B. 2016.  Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient. PeerJ. 4:e1999.   LINK   PDF

 

Extremes research:

211. Zhong, Z.-P., Zablocki, O., Li, Y.-F., Van Etten, J., Mosley-Thompson, E., Rich, V., Thompson, L.^ & Sullivan, M.B.^ 2024. Glacier-preserved Tibetan Plateau viral community likely linked to warm-cold climate variations. Nature Geoscience. (^ denotes co-corresponding authors) LINK. PDF.

• Featured in The Conversation
• OSU press release
• Nature’s ‘Behind the Paper’ blogpost
• Featured in Popular Science
• Story at ABC News (Australia)

196. Zhong, Z.-P., Vik, D., Rapp, J.Z., Zablocki, O., Maughan, H., Temperton, B., Deming, J.W. & Sullivan, M.B. 2023. Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines. Microbiome. 11:174. LINK PDF

158. Rapp, J.Z., Sullivan, M.B., & Deming, J.W. 2021. Divergent genomic adaptations in the microbiomes of Arctic subzero sea-ice and cryopeg brines. Frontiers in Microbiology. In Press.

152.Zhong, Z., Tian, F., Roux, S., Gazitúa, M.C., Solonenko, N., Li, Y-F., Davis, M.E., Van Etten, J.L., Mosley-Thompson, E., Rich, V.I., Sullivan, M.B.^, & Thompson, L.G.^ 2021. Glacier ice archives potentially fifteen-thousand-year-old microbes and phages. Microbiome. 9:160. (^ denotes co-corresponding authors) LINK  PDF

• Featured in Science
• Article in Popular Mechanics
• Article in the New York Post
• Article in Newsweek
• Article in the Daily Mail

136. Vik, D., Gazitua, M.C., Sun, C.L., Zayed, A.A., Aldunate, M., Mulholland, M.R., Ulloa, O., Sullivan, M.B. 2020. Genome-resolved viral ecology in a marine oxygen minimum zone. Environmental Microbiology. In press. LINK PDF

133. Zhong, Z., Rapp, J.Z., Wainaina, J.M., Solonenko, N.E., Maughan, H., Carpenter, S.D., Cooper, Z.S., Jang, H.B., Bolduc, B., Deming, J.W., Sullivan, M.B. 2020. Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice. mSystems. 5:e00246-20. LINK PDF

106. Daly, R., Roux, S., Borton, M., Morgan, D., Johnston, M., Booker, A., Hoyt, D., Meulia, T., Wolfe, R., Hanson, A., Mouser, P., Moore, J., Wunch, K., Sullivan, M.B., Wrighton, K. & Wilkins, M. 2019. Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing. Nature Microbiology. 4: 352-361.  LINK  PDF

100. Zhong, Z., Solonenko, N.E., Gazitúa, M.C., Kenny, D.V., Mosley-Thompson, E., Rich, V.I., Van Etten, J.L., Thompson, L.G.^ & Sullivan, M.B.^ 2018. Clean low-biomass procedures and their application to ancient ice core microorganisms. Frontiers in Microbiology. 9:1094.  (^ denotes co-corresponding authors) LINK   PDF

 

Human research:

164. Danis-Wlodarczyk, K.M., Cai, A., Chen, A., Gittrich, M.R., Sullivan,M.B., Wozniak, D.J., & Abedon, S.T. 2021. Friends or Foes? Rapid Determination of Dissimilar Colistin and Ciprofloxacin Antagonism of Pseudomonas aeruginosa Phages. Pharmaceuticals. 14:1162. LINK PDF

146. Du, J.,  Zayed, A.A., Kigerl, K., Zane, K., Sullivan, M.B., & Popovich, P. 2021. Spinal cord injury changes the structure and functional potential of gut bacterial and viral communities. mSystems. 6:e01356-20. LINK PDF

• Interview by Technology Networks

145. Danis-Wlodarczyk, K.M., Cai, A., Chen, A., Gittrich, M., Sullivan, M.B., Wozniak, D.J., Abedon, S.T. 2020. In vitro analysis of colistin and ciprofloxacin antagonism of Pseudomonas aeruginosa phage PE2 infection activities.  bioRxiv preprint. LINK

139. Gregory, A.C.†, Zablocki, O.†, Zayed, A.A., Howell, A., Bolduc, B., Sullivan, M. B. 2020. The gut virome database reveals age-dependent patterns of virome diversity in the human gut. Cell Host & Microbe. 28:724-740 († denotes co-first authors) LINK PDF

127. Kigeri, K.A., Zane, K., Adams, K., Sullivan, M.B., & Popovich, P.G. 2019. The spinal cord-gut-immune axis as a master regulator of health and neurological function after spinal cord injury. Experimental Neurology. 323C:113085. LINK PDF

108. Howard-Varona, C., Vik, D., Solonenko, N., Gazitua, C., Hobbs, Z., Honaker, R., Kinkhabwala, A. & Sullivan, M.B. 2018. Whole-Genome Sequences of Phages p000v and p000y, Which Infect the Bacterial Pathogen Shiga-Toxigenic Escherichia coli. Microbiology Resource Announcements. e01400-18.  LINK  PDF

107. Howard-Varona, C., Vik, D., Solonenko, N., Li, Y., Gazitua, C., Chittick, L., Samiec, J., Jensen, A., Anderson, P., Howard-Varona, A., Kinkhabwala, A., Abedon, S. & Sullivan, M.B. 2018. Fighting Fire with Fire: Phage Potential for the Treatment of E. coli O157 Infection. Antibiotics.  7:e101.  LINK  PDF

105. Gregory, A.C., Sullivan, M.B., Segal, L.N. & Keller, B.C. 2018. Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome. Respiratory Research. 19:e174.  LINK  PDF

80. Kang, D.-W.†, Adams, J.B.†, Gregory, A.C.†, Borody, T., Chittick, L., Fasano, A., Khoruts, A., Geis, E., Maldonado, J., McDonough-Means, S., Pollard, E.L., Roux, S., Sadowsky, M.J., Schwarzberg Lipson, K., Sullivan, M.B.^, Caporaso, J.G.^ & Krajmalnik-Brown, R.^ 2017. Microbiota transfer alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome. 5:10.  († denotes co-first authors) (^ denotes co-corresponding authors)   LINK   PDF

• short 10-minute video for parents from James Adams M.D., available at http://autism.asu.edu

 

Tools development:

194. Vik, D., Bolduc, B., Roux, S., Sun, C.L., Pratama, A.A., Krupovic, M., & Sullivan, M.B. 2023. MArVD2: A machine learning-enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets. ISME Communications. In Press.

189. Ayala-Ortiz, C., Graf-Grachet, N., Freire-Zapata, V., Fudyma, J., Hildebrand, G., AminiTabrizi, R., Howard-Varona, C., Corilo, Y.E., Hess, N., Duhaime, M.B. & Sullivan, M.B., 2023. MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data. Microbiome. 11:1-14. LINK PDF [bioRxiv LINK]

187. Shaffer, M., Borton, M.A., Bolduc, B., Faria, J.P., Flynn, R.M., Ghadermazi, P., Edirisinghe, J.N., Wood-Charlson, E.M., Miller, C.S., Chan, S.H.J. and Sullivan, M.B. 2023. kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase. Bioinformatics. 39:p.btad110. LINK PDF

184. Ayala-Ortiz, C.O., Graf-Grachet, N., Freire-Zapata, V., Fudyma, J., Hildebrand, G., AminiTabrizi, R., Howard-Varona, C., Corilo, Y.E., Hess, N., Duhaime, M.B.O. & Sullivan, M.B. 2022. MetaboDirect: An Analytical Pipeline for the processing of FTICR-MS-based Metabolomics Data. Microbiome. In Press.  [bioRxiv LINK]

181. Gregory, A.C., Gerhardt, K., Zhong, Z., Bolduc, B., Temperton, B., Konstantinidis, K.T.C., & Sullivan, M.B. 2022. MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations. Microbiome. 10:49. LINK PDF

166. Jang, H.B., Chittick, L., Li, Y.-F., Zablocki, O., Sanderson, C.M., Carrillo, A., van den Engh, G., & Sullivan, M.B. 2022. Viral tag and grow: a scalable approach to capture and characterize infectious virus-host pairs. ISME Communications. 2:12.  LINK PDF

160. Garneau, J.R.^, Legrand, V., Marbouty, M., Press, M.O., Vik, D.R., Fortier, L.-C., Sullivan, M.B., Bikard, D., & Monot, M.^ 2021. High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome. Scientific Reports. 11:18319. (^ denotes co-corresponding authors) LINK PDF

153. Zayed, A.A.†, Lücking, D.†, Mohssen, M., Cronin, D., Bolduc, B., Gregory, A.C., Hargreaves, K.R., Piehowski, P.D., White III, R.A., Huang, E.L., Adkins, J.N., Roux, S., Moraru, C.^ & Sullivan, M.B.^.2021. efam: an expanded, metaproteome-supported HMM profile database of viral protein families. Bioinformatics. btab451. († denotes co-first authors)(^ denotes co-corresponding authors) LINK PDF

150.Pratama, A.A., Bolduc, B., Zayed, A.A., Zhong, Z., Guo, J., Vik, D., Gazitúa, M.C., Wainaina, J., Roux, S. & Sullivan, M.B. 2021. Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation. PeerJ. 9:e11447. LINK PDF

147. Zablocki, O., Michelsen, M., Burris, M., Solonenko, N., Warwick-Dugdale, J., Ghosh, R., Pett-Ridge, J., Sullivan, M.B. & Temperton, B. 2021. VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature. PeerJ. 9: e11088. PREPRINT LINK PDF

143. Guo, J., Bolduc, B., Zayed. A.A., Varsani, A., Dominguez-Huerta, G., Delmont, T.O., Pratama, A.A., Gazitua, M.C., Vik, D., Sullivan, M.B., Roux, S. 2021. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome. 9:37. LINK PDF

• A step by step workflow (on protocol.io) on how to use VirSorter2 with your own data can be found here
• You can access the testing data through this link: https://osf.io/vftg6/. Click “Download” in the upper right corner, which includes a “README” file briefly describing the files in it after you untar and decompress it.

142. Sakowski, E.G., Arora-Williams, K., Tian, F., Zayed, A.A., Zablocki, O., Sullivan, M.B., Preheim, S.P. 2021. Gene Fusion with epicPCR Captures in situ Interaction Dynamics and Virus-Host Range for Estuarine Actinophages. Nature Microbiology. 6:630-642. LINK PDF

[PP.G.2020]. Gregory, A.C., Gerhardt, K., Zhong, Z., Bolduc, B., Temperton, B., Konstantinidis, K.T.C., Sullivan, M.B. 2020. MetaPop: A pipeline for macro- and micro-diversity analyses and visualization of microbial and viral metagenome-derived populations. bioRxiv preprint. LINK

137. Bolduc, B.†^, Hodgkins, S.B.†, Varner, R.K., Crill, P.M., McCalley, C.K., Chanton, J.P., Tyson, G.W., Riley, W.J., Palace, M., Duhaime, M.B., Hough, M.A., IsoGenie Project Coordinators, IsoGenie Project Team, A2A Project Team, Saleska, S.R., Sullivan, M.B., Rich, V.I.^ 2020.  The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research. PeerJ. 8:e9467. LINK PDF (^denotes co-corresponding authors) († denotes co-first authors)

134. Shaffer M., Borton, M.A., McGivern, B.B., Zayed, A.A., La Rosa, S.L., Solden, L.M., Liu, P, Narrowe, A.B., Rodríguez-Ramos, J., Bolduc, B., Gazitua, M.C., Daly, R.A., Smith, G.J., Vik, D.R., Pope, P.B., Sullivan, M.B., Roux, S., Wrighton, K.C. 2020. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Research. 48(16):8883-8900. LINK PDF

117.  Jang, H.B.†, Bolduc, B.†, Zablocki, O., Kuhn, J., Roux, S., Adriaenssens, E.M., Brister, J.R., Kropinski, A.M., Krupovic, M., Lavigne, R., Turner, D., & Sullivan, M.B. 2019. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nature Biotechnology. 37:632–639. († denotes co-first authors)  LINK PDF

• Featured in Nature Microbiology
• DOE BER science highlight
• Behind the paper in Nature Research Bioengineering Community

110. Warwick-Dugdale, J., Solonenko, N., Moore, K., Chittick, L., Gregory, A.C., Allen, M.J., Sullivan, M.B., Temperton, B. 2018. Long-read viral metagenomics enables capture of abundant and microdiverse viral populations and their niche-defining genomic islands. PeerJ. 7:e6800. LINK  PDF

• Top-5 viewed article at PeerJ

93. Roux, S., Emerson, J.B., Eloe-Fadrosh, E.A. & Sullivan, M.B. 2017. Benchmarking viromics: An in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. PeerJ. 5:e3817.  LINK   PDF

86. Bolduc, B.†, Jang, H.B.†, Doulcier, G., You, Z.Q., Roux, S. & Sullivan, M.B., 2017. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PeerJ. 5: 3243. († denotes co-first authors)   LINK   PDF

81. Poulos, B.T., John, S.G., & Sullivan, M.B. 2017. Iron Chloride Flocculation of Bacteriophages from Seawater. Bacteriophages: Methods and Protocols. 1681.  LINK   PDF

• for updated protocol see protocols.io)

77. Bolduc, B., Youens-Clark, K., Roux, S., Hurwitz, B.L.^, & Sullivan, M.B.^ 2017. iVirus: facilitating new insights into viral ecology with software and community datasets imbedded in a cyberinfrastructure. ISMEJ. 11:7-14.   (^ denotes co-corresponding authors)  LINK   PDF

• iVirus highlighted in CyVerse
• CyVerse coverage of OSU’s Viromics Workshop

72. Roux, S. Solonenko, N. Dang, V.T. Poulos, B.T. Schwenck, S.M. Goldsmith, D.B. Coleman, M.L. Breitbart, M. Sullivan, M.B. 2016. Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. PeerJ. 4: e2777.   LINK   PDF

61. Roux, S., Hallam, S.J., Woyke, T., & Sullivan, M.B. 2015. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. eLife. 4:e08490.   LINK   PDF

• VirSorter Curated Dataset: Predicted viral sequences with automatic annotation, virus-host matrix, and Genome Clustering network.
• Highlighted 14 Aug 2015 in Nature Reviews Microbiology 13: 526-527.
• Article in Wired

54. Roux, S., Enault, F., Hurwitz, B.L., & Sullivan, M.B. 2015. VirSorter: mining viral signal from microbial genomic data. PeerJ. 3:e985.  LINK   PDF

• Selected in PeerJ Top Microbiology Papers – August 2015
  

52. Cunningham, B., Brum, J., Schwenck, S., Sullivan, M.B., & John, S. 2015. An inexpensive, accurate and precise wet-mount method for enumerating aquatic viruses. Applied Environmental Microbiology. 81:2995-3000.   LINK   PDF

47. Dang, V.T. & Sullivan, M.B. 2014. Emerging methods to study bacteriophage infection at the single-cell level. Frontiers in Microbiology. 5:724.   LINK   PDF

40. Solonenko, S.A. & Sullivan, M.B. 2013. Preparation of metagenomic libraries from naturally occurring marine viruses. Methods in Enzymology. Microbial Metagenomics, Metatranscriptomics, and Metaproteomics edition. 531:143–165.   LINK   PDF

37. Solonenko, S.A., Ignacio-Espinoza, J.C., Alberti, A., Cruaud, C., Hallam, S., Konstantinidis, K., Tyson, G., Wincker, P., & Sullivan, M.B. 2013. Sequencing platform and library preparation choices impact viral metagenomes. BMC Genomics. 14:320.   LINK   PDF

36. Brum, J.R., Schenck, R.O., & Sullivan, M.B. 2013. Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses. ISMEJ. 7:1738–1751.   LINK   PDF

33. Allers, E.†, Moraru, C.†, Duhaime, M.B., Beneze, E., Solonenko, N., Barrero-Canosa, J., Amann, R.^{^}, & Sullivan, M.B.^{^} 2013. Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses. Environmental Microbiology. 15:2306–2318.  († denotes co-first authors) (^ denotes co-corresponding authors)   LINK   PDF

29. Duhaime, M.B. & Sullivan, M.B. 2012. Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline. Virology. 434:181-186. LINK PDF

28. Deng, L., Gregory, A., Yilmaz, S., Poulos, B.T., Hugenholtz, P., & Sullivan, M.B. 2012. Contrasting life strategies of viruses that infect photo- and heterotrophic bacteria, as revealed by viral tagging. mBio. 3:e00373-12.   LINK   PDF

• Faculty of 1000 Prime recommended this article “of special significance” on 27 Aug 2013

26. Hurwitz, B.L., Deng, L., Poulos, B.T., & Sullivan, M.B. 2012. Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environmental Microbiology. 15:1428–1440.   LINK   PDF

25. Duhaime, M.B., Deng, L., Poulos, B.T., & Sullivan, M.B. 2012. Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: A rigorous assessment and optimization of the linker amplification method. Environmental Microbiolgy. 14:2526-2537. LINK   PDF

20. John, S.G., Mendez, C.B., Deng, L., Poulos, B., Kauffman, A.K.M., Kern, S., Brum, J., Polz, M.F., Boyle, E.A., & Sullivan, M.B. 2011. A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environmental Microbiology Reports. 3:195-202.   LINK   PDF

• Minor correction concerning buffer recipes:   PDF

Review articles:

182. Dominguez-Huerta, G., Wainaina, J.M., Zayed, A.A., Culley, A.I., Kuhn, J.H., & Sullivan, M.B. 2022. Crystal Ball: The RNA virosphere: how big and diverse is it? Environmental Microbiology. 25:209-215. LINK PDF

167. Sokol, N.W., Slessarev, E., Marschmann, G.L., Nicolas, A., Blazewicz, S.J., Brodie, E.L., Firestone, M.K., Foley, M.M., Hestrin, R., Hungate, B.A., Koch, B.J., Stone, B.W., Sullivan, M.B., Zablocki, O., LLNL Soil Microbiome Consortium & Pett-Ridge, J. 2022. Life and death in the soil microbiome: how ecological processes influence biogeochemistry. Nature Reviews Microbiology.  LINK PDF

163. Dutilh, B.E., Varsani, A., Tong, Y., Simmonds, P., Sabanadzovic, S., Rubino, L., Roux, S., Muñoz, A.R., Lood, C., Lefkowitz, E.J., Kuhn, J.H., Krupovic, M., Edwards, R.A., Brister, J.R., Adriaenssens, E., & Sullivan, M.B. 2021. Perspective on taxonomic classification of uncultivated viruses. Current Opinion in Virology. 51:207. LINK PDF

154. Abedon, S.T.^, Danis-Wlodarczyk, K.M., Wozniak, D.J. & Sullivan, M.B.^ 2021. Improving phage-biofilm in vitro experimentation. Viruses. 13(6):1175. (^ denotes corresponding author) LINK PDF

144. Correa, A.M.S., Howard-Varona, C., Coy, S.R., Buchan, A., Sullivan, M.B. & Weitz, J. 2021. Revisiting the rules of life for viruses of microorganisms. Nature Reviews Microbiology. 19:501-513. LINK PDF

131. Sunagawa, S.^, Acinas, S.G., Bork, P., Bowler, C., Tara Oceans Coordinators, Eveillard, D., Gorsky, G., Guidi, L., Iudicone, D., Karsenti, E., Lombard, F., Ogata, H., Pesant, S., Sullivan, M.B., Wincker, P., de Vargas, C.^ 2020. Tara Oceans: towards global ocean eco-systems biology. Nature Reviews Microbiology. 18:428–445. LINK PDF (^denotes co-corresponding authors)

121. Cavicchioli, R., Ripple, W.J., Timmis, K.N., Azam, F., Bakken, L.R., Baylis, M., Behrenfeld, M.J., Boetius, A., Boyd, P.W., Classen, A.T., Crowther, T.W., Danovaro, R., Foreman, C.M., Huisman, J., Hutchins, D.A., Jansson, J.K., Karl, D.M., Koskella, B., Mark Welch, D., Martiny, J.B.H., Moran, M., Orphan, V., Reay, D., Remais, J.V., Rich, V., Singh, B.K., Stein, L.Y., Stewart, F.J., Sullivan, M.B., van Oppen, M.J.H., Weaver, S.C., Webb, E.A., & Webster, N. 2019. Scientists’ Warning to Humanity: microorganisms and climate change. Nature Reviews Microbiology. 17:569-596. LINK PDF

82. Howard-Varona, C.†, Hargreaves, K.R.†, Abedon, S.T. & Sullivan, M.B. 2017. Lysogeny in nature – mechanisms, impact and ecology of temperate phages. ISMEJ. 16:1-10.  († denotes co-first authors)   LINK   PDF

79. Simmonds, P., Adams, M.J., Benko, M., Breitbart, M., Brister, J.R., Carstens, E.B., Davison, A.J., Delwart, E., Gorbalenya, A.E., Harrach, B., Hull, R., King, A.M.Q., Koonin, E.V., Krupovic, M., Kuhn, J.H., Lefkowitz, E.J., Nibert, M.L., Orton, R., Roosinck, M.J., Sabanadzovic, S., Sullivan, M.B., Suttle, C.A., Tesh, R.B., van der Vlugt, R.A., Varsani, A., & Zerbini, F.M. 2017. Virus taxonomy in the age of metagenomics. Nature Reviews in Microbiology. 15:161-168.   LINK   PDF

75. Sullivan, M.B., Weitz, J.S., & Wilhelm, S. 2016. Crystal Ball: Viral ecology comes of age. Environmental Microbiology Reports. 9: 33-35. LINK   PDF

51. Sullivan, M.B. 2015. Viromes, not gene markers for studying dsDNA viral communities. J Virology. 89:2459-2461. LINK   PDF

49. Brum, J.R., & Sullivan, M.B. 2015. Rising to the challenge: accelerated pace of discovery transforms marine virology. Nature Reviews Microbiology. 13:147–159. LINK   PDF

39. Ignacio-Espinoza, J.C., Solonenko, S.A., & Sullivan, M.B. 2013. The global virome: Not as big as we thought? Current Opinion in Virology. 3:566–571. LINK   PDF

 

All Sullivan lab publications, by year:

2024

213. Freire-Zapata, V., Holland-Moritz, H., Cronin, D.R., Aroney, S., Smith, D.A., Wilson, R.M., Ernakovich, J.G., Woodcroft, B.J., Bagby, S.C., EMERGE 2012 Field Team, EMERGE Coordinators, Rich, V.I., Sullivan, M.B., Stegen, J.C., & Tfaily, M.M. 2024. Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient. Nature Microbiology. In Press.

212. Crowther, T.W., Rappuoli, R., Corinaldesi, C., Danovaro, R., Donohue, T.J., Huisman, J., Stein, L.Y., Timmis, J.K., Timmis, K., Anderson, M.Z., Bakken, L.R., Baylis, M., Behrenfeld, M.J., Boyd, P.W., Brettell, I., Cavicchioli, R., Delavaux, C.S., Foreman, C.M., Jansson, J.K., Koskella, B., Milligan-McClellan, K., North, J.A., Peterson, D., Pizza, M., Ramos, J.L., Reay, D., Remais, J.V., Rich, V., Ripple, W.J., Singh, B.K., Smith, G.R., Stewart, F.J., Sullivan, M.B., van den Hoogen, J., van Oppen, M.J.H., Webster, N.S., Zohner, C.M., & van Galen, L.G. 2024. Scientists’ Call to Action: Microbes, Planetary Health, and the Sustainable Development Goals. Cell. In Press.

211. Zhong, Z.-P., Zablocki, O., Li, Y.-F., Van Etten, J., Mosley-Thompson, E., Rich, V., Thompson, L.^ & Sullivan, M.B.^ 2024. Glacier-preserved Tibetan Plateau viral community likely linked to warm-cold climate variations. Nature Geoscience. (^ denotes co-corresponding authors) LINK. PDF.

210. Tian*, F., Wainaina*, J.M., Howard-Varona, C., Domínguez-Huerta, G., Bolduc, B., Gazitúa, M.C., Smith, G., Gittrich, M.R., Zablocki, O., Cronin, D.R., Eveillard, D., Hallam, S.J. & Sullivan, M.B. 2024. Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans. Microbiome. 12:159. LINK PDF. (* denotes co-first authors)

209. McGivern, B.B., Cronin, D.R., Ellenbogen, J.B., Borton, M.A., Knutson, E.L., Freire-Zapata, V., Bouranis, J.A., Bernhardt, L., Hernandez, A.I., Flynn, R.M., Woyda, R., Cory, A.B., Wilson, R.M., Chanton, J.P., Woodcroft, B.J., Ernakovich, J.G., Tfaily, M.M., Sullivan, M.B., Tyson, G.W., Rich, V.I., Hagerman, A.E. & Wrighton, K.C. 2024. Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle. Nature Microbiology. 9: 1454–1466. LINK PDF

208. Sun†, C.L., Pratama†, A.A., Gazitúa, M.C., Cronin, D., McGivern, B.B., Wainaina, J.M., Vik, D.R., Zayed, A.A., Bolduc, B., IsoGenie Project Field Teams 2010-2017, IsoGenie and EMERGE Projects Coordinators, Wrighton, K.C., Rich, V.I., & Sullivan, M.B. 2024. Virus ecology and 7-year temporal dynamics across a permafrost thaw gradient. Environmental Microbiology. 26:e16665. LINK PDF († denotes co-first authors)

207. Joanna Warwick-Dugdale, J., Tian, F., Michelsen, M., Cronin, D., Moore, K., Farbos, A., Chittick, L., Bell, A., Buchholz, H., Parsons, R., Zayed, A., Allen, M., Sullivan, M.B., Temperton, B., & Bolaños, L. 2024. Long-read powered viral metagenomics in the oligotrophic Sargasso Sea. Nature Communications. In Press.

206. Howard-Varona, C., Lindback, M.M., Fudyma, J.D., Krongauz, A., Solonenko, N.E., Zayed, A.A., Andreopoulos, W.B., Olson, H.M., Kim, Y.-M., Kyle, J.E., del Rio, T.G., Adkins, J.N., Tfaily, M.M., Paul, S., Sullivan*, M.B., & Duhaime*, M.B. 2024. Environment-specific virocell metabolic reprogramming. The ISME Journal. wrae055. LINK PDF (* denotes co-corresponding authors)

205. Charon, J., Olendraite, I., Forgia, M., Chong, L.C., Hillary, L.S., Roux, S., Kupczok, A., Debat, H.J., Sakaguchi, S., Tahzima, R., Nakagawa, S., Babaian, A., Abroi, A., Bejerman, N., Ben Mansour, K., Brown, K., Butkovic, A., Cervera, A., Charriat, F., Chen, G., Chiba, Y., De Coninck, L., Demina, T., Dominguez Huerta, G., Dubrulle, J., Gutiérrez, S., Harvey, E., Jayaraj Mallika, F.R., Karapliafis, D., Lim, S.J., Manjari, S.K., Mifsud, J.C., Nishimura, Y., Ortiz-Baez, A.S., Raco, M., Rivero, R., Sadiq, S., Saghaei, S., James, S.E., Shaikh, H.M., Sieradzki, E.T., Sullivan, M.B., Sun, Y., Wille, M., Wolf, Y., Zrelovs, N., & Neri, U. 2024. Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities. Frontiers in Virology. 4:1371958. LINK PDF

204. Zhong, Z.P., Du, J., Köstlbacher, S., Pjevac, P., Orlić, S. & Sullivan, M.B. 2024. Viral potential to modulate microbial methane metabolism varies by habitat. Nature Communications. 15:1857. LINK PDF

203. Baek, A., Lee, G.-E., Golconda, S., Rayhan, S., Manganaris, A.A., Chen, S., Tirumuru, N., Yu, H., Kim, S., Kimmel, C., Zablocki, O., Sullivan, M.B., Addepalli, B., Wu, L., & Kim, S. 2024. Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m6As. Nature Microbiology. 9:1340-1355. LINK PDF

2023

202. Pavlopoulos, G. A., Baltoumas, F. A., Liu, S., Selvitopi, O., Camargo, A. P., Nayfach, S., Azad, A., Roux, S., Call, L., Ivanova, N. N., Chen, I. M., Paez-Espino, D., Karatzas, E., Iliopoulos, I., Konstantinidis, K., Tiedje, J. M., Pett-Ridge, J., Baker, D., Visel, A., Ouzounis, C. A., Ovchinnikov, S., Buluç, A., [Novel Metagenome Protein Families Consortium, incl. Sullivan, M.B.] & Kyrpides, N. C. 2023. Unraveling the Functional Dark Matter through Global Metagenomics. Nature. 622:594–602. LINK PDF

201. Kaneko, H., Endo, H., Henry, N., Berney, C., Mahé, F., Poulain, J., Labadie, K., Beluche, O., El Hourany, R. Tara Oceans Coordinators [incl. Sullivan, M.B.], Chaffron, S., Wincker, P., Nakamura, R., Karp-Boss, L., Boss, E., Bowler, C., de Vargas, C., Tomii, K., & Ogata, H. 2023. Predicting global distributions of eukaryotic plankton communities from satellite data. ISME communications. 3:101. LINK PDF

200. Porro, B., Zamoum, T., Forcioli, D., Gilson, E., Poquet, A., Di Franco, E., Barnay-Verdier, S., Lombard, F., Voolstra, C.R., Hume, B.C.C., Galand, P.E., Moulin, C., Boissin, E., Bourdin, G., Iwankow, G., Poulain, J., Romac, S., Agostini, S., Banaigs, B., Boss, E., Bowler, C., de Vargas, C., Douville, E., Flores, M., Pesant, S., Reynaud, S., Sullivan, M.B., Sunagawa, S., Thomas, O.P., Troublé, R., Thurber, R.V., Wincker, P., Zoccola, D., Planes, S., Allemand, D., Röttinger, E., Furla, P. 2023. Different environmental response strategies in sympatric corals from Pacific Islands. Communications Earth & Environment. 4: 1–17. LINK PDF

199. Reddy, M.M., Goossens, C., Zhou, Y., Chaib, S., Raviglione, D., Nicolè, F., Hume, B.C.C., Forcioli, D., Agostini, S., Boissin, E., Boss, E., Bowler, C., de Vargas, C., Douville, E., Flores, M., Furla, P., Galand, P.E., Gilson, E., Lombard, F., Pesant, S., Reynaud, S., Sullivan, M.B., Sunagawa, S., Troublé, R., Thurber, R.V., Wincker, P., Zoccola, D., Voolstra, C.R., Allemand, D., Planes, S., Thomas, O.P., & Banaigs, B. 2023. Multi-omics determination of metabolome diversity in natural coral populations in the Pacific Ocean. Communications Earth & Environment. 4: 1–10. LINK PDF

198. Sanz-Sáez, I., Sánchez, P., Salazar, G., Sunagawa, S., de Vargas, C., Bowler, C., Sullivan, M.B., Wincker, P., Karsenti, E., Pedrós-Alió, C., Agustí, S., Gojobori, T., Duarte, C.M., Gasol, J.M., Sánchez, O., & Acinas, S.G. 2023. Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation. ISME Communications. 3: 1–13. LINK PDF

197. Yan, M., Pratama, A.A., Somasundaram, S., Li, Z., Jiang, Y., Sullivan, M.B., & Yu, Z. 2023. Interrogating the viral dark matter of the rumen ecosystem with a global virome database. Nature Communications. 14:5254. LINK PDF

196. Zhong, Z.-P., Vik, D., Rapp, J.Z., Zablocki, O., Maughan, H., Temperton, B., Deming, J.W. & Sullivan, M.B. 2023. Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines. Microbiome. 11:174. LINK PDF

195. Cui, L., Balalkundu, S., Liu, C., Ye, H., Hourihan, J., Rausch, A., Hauß, C., Nilsson, E., Hoetzinger, M., Holmfeldt, K., Zhang, W., Martinez-Alvarez, L., Peng, X., Tremblay, D., Moinau, S., Solonenko, N., Sullivan, M.B., Lee, Y.-J., Mulholland, A., Weigele, P., Crécy-Lagard, V. de, Dedon, P.C. & Hutinet, G. 2023. Four additional natural 7-deazaguanine derivatives in phages and how to make them. Nucleic Acid Research.  gkad657. LINK PDF

194. Vik, D., Bolduc, B., Roux, S., Sun, C.L., Pratama, A.A., Krupovic, M., & Sullivan, M.B. 2023. MArVD2: A machine learning-enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets. ISME Communications. 3:1–10. LINK PDF

193. Voolstra, C. R., Hume, B. C. C., Armstrong, E. J., Mitushasi, G., Porro, B., Oury, N., Agostini, S., Boissin, E., Poulain, J., Carradec, Q., Paz-García, D. A., Zoccola, D., Magalon, H., Moulin, C., Bourdin, G., Iwankow, G., Romac, S., Banaigs, B., Boss, E., Bowler, C., de Vargas, C., Douville, E., Flores, M., Furla, P., Galand, P. E., Gilson, E., Lombard, F., Pesant, S., Reynaud, S., Sullivan, M. B., Sunagawa, S., Thomas, O. P., Troublé, R., Thurber, R. V., Wincker, P., Planes, S., Allemand, D., & Forcioli, D. 2023. Disparate Genetic Divergence Patterns in Three Corals across a Pan-Pacific Environmental Gradient Highlight Species-Specific Adaptation. npj Biodiversity. 2:1–16. LINK PDF

192. Noel, B., Denoeud, F., Rouan, A., Buitrago-López, C., Capasso, L., Poulain, J., Boissin, E., Pousse, M., Da Silva, C., Couloux, A., Armstrong, E., Carradec, Q., Cruaud, C., Labadie, K., Lê-Hoang, J., Tambutté, S., Barbe, V., Moulin, C., Bourdin, G., Iwankow, G., Romac, S., Agostini, S., Banaigs, B., Boss, E., Bowler, C., de Vargas, C., Douville, E., Flores, J. M., Forcioli, D., Furla, P., Galand, P. E., Lombard, F., Pesant, S., Reynaud, S., Sullivan, M. B., Sunagawa, S., Thomas, O. P., Troublé, R., Thurber, R. V., Allemand, D., Planes, S., Gilson, E., Zoccola, D., Wincker, P., Voolstra, C. R., & Aury, J.-M. 2023. Pervasive Tandem Duplications and Convergent Evolution Shape Coral Genomes. Genome Biology. 24:123. LINK PDF

191. Rigonato, J., Budinich, M., Murillo, A. A., Brandão, M. C., Karlusich, J. J. P., Soviadan, Y. D., Gregory, A. C., Endo, H., Kokoszka, F., Vik, D., Henry, N., Frémont, P., Labadie, K., Zayed, A. A., Dimier, C., Picheral, M., Searson, S., Poulain, J., Kandels, S., Pesant, S., Karsenti, E., Coordinators, T. T. O., Bork, P., Bowler, C., Vargas, C. de, Eveillard, D., Gehlen, M., Iudicone, D., Lombard, F., Ogata, H., Stemmann, L., Sullivan, M. B., Sunagawa, S., Wincker, P., Chaffron, S., & Jaillon, O. 2023. Ocean-Wide Comparisons of Mesopelagic Planktonic Community Structures. ISME Communications. 3:83. LINK PDF

190. Lombard, F., Bourdin, G., Pesant, S., Agostini, S., Baudena, A., Boissin, E., Cassar, N., Clampitt, M., Conan, P., Da Silva, O., Dimier, C., Douville, E., Elineau, A., Fin, J., Flores, J. M., Ghiglione, J.-F., Hume, B. C. C., Jalabert, L., John, S. G., Kelly, R. L., Koren, I., Lin, Y., Marie, D., McMinds, R., Mériguet, Z., Metzl, N., Paz-García, D. A., Pedrotti, M. L., Poulain, J., Pujo-Pay, M., Ras, J., Reverdin, G., Romac, S., Rouan, A., Röttinger, E., Vardi, A., Voolstra, C. R., Moulin, C., Iwankow, G., Banaigs, B., Bowler, C., de Vargas, C., Forcioli, D., Furla, P., Galand, P. E., Gilson, E., Reynaud, S., Sunagawa, S., Sullivan, M. B., Thomas, O. P., Troublé, R., Thurber, R. V., Wincker, P., Zoccola, D., Allemand, D., Planes, S., Boss, E., & Gorsky, G. 2023. Open Science Resources from the Tara Pacific Expedition across Coral Reef and Surface Ocean Ecosystems. Scientific Data. 10: 324. LINK PDF

189. Ayala-Ortiz, C., Graf-Grachet, N., Freire-Zapata, V., Fudyma, J., Hildebrand, G., AminiTabrizi, R., Howard-Varona, C., Corilo, Y.E., Hess, N., Duhaime, M.B. & Sullivan, M.B., 2023. MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data. Microbiome. 11:1-14. LINK PDF [bioRxiv LINK]

188. Armstrong, E., Lê-Hoang, J., Carradec, Q., Aury, J.M., Noel, B., Hume, B., Voolstra, C., Poulain, J., Belser, C., Paz-García, D., Cruaud, C., Labadie, K., Da Silva, C., Moulin, C., Boissin, E., Bourdin, G., Iwankow, G., Romac, S., Agostini, S., Banaigs, B., Boss, E., Bowler, C., De Vargas, C., Douville, E., Flores, J.M., Forcioli, D., Furla, P., Galand, P., Gilson, E., Lombard, F., Pesant, S., Reynaud, S., Sullivan, M.B., Sunagawa, S., Thomas, O., Troublé, R., Thurber, R.V., Zoccola, D., Planes, S., Allemand, D., & Wincker, P. 2023. Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean. Nature communications. In Press.

187. Shaffer, M., Borton, M.A., Bolduc, B., Faria, J.P., Flynn, R.M., Ghadermazi, P., Edirisinghe, J.N., Wood-Charlson, E.M., Miller, C.S., Chan, S.H.J. and Sullivan, M.B. 2023. kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase. Bioinformatics. 39:p.btad110. LINK PDF

186. Ibarbalz, F.M., Henry, N., Mahé, F., Ardyna, M., Zingone, A., Scalco, E., Lovejoy, C., Lombard, F., Jaillon, O., Iudicone, D., Malviya, S., Tara Oceans Coordinators, Sullivan, M.B., Chaffron, S., Karsenti, E., Babin, M., Boss, E., Wincker, P., Zinger, L., de Vargas, C., Bowler, C., & Karp-Boss, L. 2023. Pan-Arctic plankton community structure and its global connectivity. Elementa: Science of the Anthropocene. In Press.

185. Simmonds, P., Adriaenssens, E. M., Zerbini, F. M., Abrescia, N. G. A., Aiewsakun, P., Alfenas-Zerbini, P., Bao, Y., Barylski, J., Drosten, C., Duffy, S., Duprex, W. P., Dutilh, B. E., Elena, S. F., García, M. L., Junglen, S., Katzourakis, A., Koonin, E. V., Krupovic, M., Kuhn, J. H., Lambert, A. J., Lefkowitz, E. J., Łobocka, M., Lood, C., Mahony, J., Meier-Kolthoff, J. P., Mushegian, A. R., Oksanen, H. M., Poranen, M. M., Reyes-Muñoz, A., Robertson, D. L., Roux, S., Rubino, L., Sabanadzovic, S., Siddell, S., Skern, T., Smith, D. B., Sullivan, M. B., Suzuki, N., Turner, D., Doorslaer, K. V., Vandamme, A.-M., Varsani, A., & Vasilakis, N. 2023. Four Principles to Establish a Universal Virus Taxonomy. PLOS Biology. 21:e3001922. LINK PDF

2022

184. Nastasi, N., Anderson, M. Z., Balasubrahmaniam, N., Bope, A., Britt Jr., R. D., Cochran, S. J., Gill, Hegarty, B., Lee, J., Stamps, B. W., Stickney, A., Taylor, C. G., Tram, N. K., Van Dusen. J., Varaljay, V. A., Weir, M. H., Horack, J. M., Oglesbee, M., Sullivan, M. B., & Dannemiller, K. C. 2022. Application of emerging innovations in microbiome science to space development and settlement systems. 73^rdInternational Astronautical Congress, Paris, France.

183. Turner, D., Shkoporov, A.N., Lood, C., Millard, A.D., Dutilh, B.E., Alfenas-Zerbini, P., van Zyl, L.J., Aziz, R.K., Oksanen, H.M., Poranen, M.M., Kropinski, A.M., Barylski, J., Brister, J.R., Chanisvili, N., Edwards, R.A., Enault, F., Gillis, A., Knezevic, P., Krupovic, M., Kurtböke, I., Kushkina, A., Lavigne, R., Lehman, S., Lobocka, M., Moraru, C., Switt, A.M., Morozova, V., Nakavuma, J., Muñoz, A.R., Rūmnieks, J., Sarkar, B.L., Sullivan, M.B., Uchiyama, J., Wittmann, J., Yigang, T., Adriaenssens, E.M. 2022. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV Bacterial Viruses Subcommittee. Archives of Virology. 168:74. LINK PDF

182. Dominguez-Huerta, G., Wainaina, J.M., Zayed, A.A., Culley, A.I., Kuhn, J.H., & Sullivan, M.B. 2022. Crystal Ball: The RNA virosphere: how big and diverse is it? Environmental Microbiology. 25:209-215. LINK PDF

181. Gregory, A.C., Gerhardt, K., Zhong, Z., Bolduc, B., Temperton, B., Konstantinidis, K.T.C., & Sullivan, M.B. 2022. MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations. Microbiome. 10:49. LINK PDF

180. Howard-Varona, C., Roux, S., Bowen, B.P., Silva, L.P., Lau, R., Schwenck, S.M., Schwartz, S., Woyke, T., Northen, T., Sullivan, M.B., & Floge, S.A. 2022. Protist impacts on marine cyanovirocell metabolism. ISME Communications. 2(1):1-4. LINK PDF

179. Lombard, F., Bourdin, G., Pesant, S., Agostini, S., Baudena, A., Boissin, E., Cassar, N., Clampitt, M., Conan, P., Silva, O.D., Dimier, C., Douville, E., Elineau, A., Fin, J., Flores, J.M., Ghiglione, J.F., Hume, B.C., Jalabert, L., John, S.G., Kelly, R.L., Koren, I., Lin, Y., Marie, D., McMinds, R., Mériguet, Z., Metzl, N., Paz-García, D.A., Pedrotti, M.L, Poulain, J., Pujo-Pay, M., Ras, J., Reverdin, G., Romac, S., Rouan, A., Röttinger, E., Vardi, A., Voolstra, C.R., Moulin, C., Iwankow, G., Banaigs, B., Bowler, C., de Vargas, C., Forcioli, D., Furla, P., Galand, P.E., Gilson, E., Reynaud, S., Sunagawa, S., Sullivan, M.B., Thomas, O., Troublé, R., Thurber, R.V., Wincker, P., Zoccola, D., Allemand, D., Planes, S., Boss, E., & Gorsky, G. 2022. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems. Scientific Data. In Press.

178. Neri, U., Wolf, Y. I., Roux, S., Camargo, A. P., Lee, B., Kazlauskas, D., Chen, I. M., Ivanova, N., Zeigler Allen, L., Paez-Espino, D., Bryant, D. A., Bhaya, D., RNA virus Discovery Consortium, Krupovic, M., Dolja, V.V., Kyrpides, N.C., Koonin, E.V., & Gophna, U. 2022. Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell. In Press. LINK PDF

177. Greenlon, A., Sieradzki, E., Zablocki, O., Koch, B., Foley, M., Kimbrel, J., Hungate, B., Blazewicz, S., Nuccio, E., Sun, C., Chew, A., Mancilla, C.-J., Sullivan, M.B., Firestone, M., Pett-Ridge, J., & Banfield, J. 2022. Quantitative stable-isotope probing (qSIP) with metagenomics links microbial physiology and activity to soil moisture in Mediterranean-climate grassland ecosystems. mSystems. 7:e00417-22. LINK PDF

176. Zhou, Y.-L., Mara, P., Vik, D., Edgcomb, V.P., Sullivan, M.B., & Wang, Y. 2022. Ecogenomics reveals viromes in the deepest ocean trench of Earth. Communications Biology. 5:1055. LINK PDF

175. Paoli, L., Ruscheweyh, H.-J., Forneris, C.C., Hubrich, F., Kautsar, S., Bhushan, A., Lotti, A., Clayssen, Q., Salazar, G., Milanese, A., Carlström, C.I., Papadopoulou, C., Gehrig, D., Karasikov, M., Mustafa, H., Larralde, M., Carroll, L.M., Sánchez, P., Zayed, A.A., Cronin, D.R., Acinas, S.G., Bork, P., Bowler, C., Delmont, T.O., Gasol, J.M., Gossert, A.D., Kahles, A., Sullivan, M.B., Wincker, P., Zeller, G., Robinson, S.L., Piel, J., & Sunagawa, S. 2022. Biosynthetic potential of the global ocean microbiome. Nature. 607:111. LINK PDF

174. Tara Ocean Foundation, the Tara Oceans Consortium, European Molecular Biology Laboratory (EMBL) & European Marine Biological Resource Centre – European Research Infrastructure Consortium (EMBRC-ERIC). 2022. Priorities for ocean microbiome research. Nature Microbiology. 7:937. LINK PDF

173. Vernette, C., Lecubin, J., Sanchez, P., Tara Oceans Coordinators, Sunagawa, S., Delmont, T.O., Acinas, S.G., Pelletier, E., Hingamp, P., & Lescot, M. 2022. The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. Nucleic Acids Research. 50:516. LINK PDF

172. Richter, D.J.†, Watteaux,R.†, Vannier, T.†, Leconte, J., Frémont, P., Reygondeau, G., Maillet, N., Henry, N., Benoit, G., Da Silva, O., Delmont, T.O., Fernàndez-Guerra, A., Suweis, S., Narci, R., Berney, C., Eveillard, D., Gavory, F., Guidi, L., Labadie, K., Mahieu,E., Poulain, J., Romac, S., Roux, S., Dimier, C., Kandels, S., Picheral, M., Searson, S., Tara Oceans Coordinators, Pesant, S., Aury, J.-M., Brum, J.R., Lemaitre, C., Pelletier, E., Bork, P., Sunagawa, S., Lombard, F., Karp-Boss, L., Bowler, C., Sullivan, M.B., Karsenti, E., Mariadassou, M., Probert, I., Peterlongo, P.,Wincker, P., de Vargas, C.*, d’Alcalà, M.R.*, Iudicone, D.*, & Jaillon, O.* 2022. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. eLife. 11: e78129. († denotes co-first authors, * denotes co-corresponding authors) LINK PDF

171. Dominguez-Huerta, G.†, Zayed, A.A.†, Wainaina, J.M., Guo, J., Tian, F., Pratama, A.A., Bolduc, B., Mohssen, M., Zablocki, O., Pelletier, E., Delage, E., Alberti, A., Aury, J.-M., Carradec, Q., da Silva, C., Labadie, K., Poulain, J., Tara Oceans Coordinators, Bowler, C., Eveillard, D., Guidi, L., Karsenti, E., Kuhn, J.H., Ogata, H., Wincker, P., Culley, A., Chaffron, S., & Sullivan, M.B. 2022. Diversity and ecological footprint of Global Ocean RNA viruses. Science. 376: 1202-1208. († denotes co-first authors). LINK PDF

• NewScientist coverage here
• Axios coverage here
• OSU press release here

170. Zayed, A.A.†, Wainaina, J.M.†, Dominguez-Huerta, G.†, Pelletier, E., Guo, J., Mohssen, M., Tian, F., Pratama, A.A., Bolduc, B., Zablocki, O., Cronin, D., Solden, L., Delage, E., Alberti, A., Aury, J.-M., Carradec, Q., da Silva, C., Labadie, K., Poulain, J., Ruscheweyh, H.-J., Salazar, G., Shatoff, E., Tara Oceans Coordinators, Bundschuh, R., Fredrick, K., Kubatko, L.S., Chaffron, S., Culley, A.I., Sunagawa, S., Kuhn, J.H., Wincker, P., & Sullivan, M.B. 2022. Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome. Science. 376: 156-162. († denotes co-first authors). LINK PDF

• OSU press release
• “The Scientist” interview of Matt Sullivan here
• Coverage from the Smithsonian Magazine: here

169. Fremin B.j., Global Phage Small Open Reading Frame (GP-SmORF) Consortium, Bhatt, A.S., & Kyrpides, N.C. 2022. Revealing Thousands of Small, Novel Genes in Global Phage Genomes. Cell Reports. 39:110984. LINK PDF

168. Moran, M.A.^, Kujawinksi, E.B.^, Schroer, W.F., Amin, S.A., Bates, N.R., Bertrand, E.M., Braakman, R., Brown, C.T., Covert, M.W., Doney, S.C., Dyhrman, S.T., Edison, A.S., Eren, A.M., Levine, N.M., Li, L., Ross, A.C., Saito, M.A., Santoro, A.E., Segré, D., Shade, A., Sullivan, M.B., & Vardi, A. 2022. Microbial metabolites in the marine carbon cycle. Nature Microbiology. 7:508. (^ denotes co-corresponding authors) LINK PDF

167. Sokol, N.W., Slessarev, E., Marschmann, G.L., Nicolas, A., Blazewicz, S.J., Brodie, E.L., Firestone, M.K., Foley, M.M., Hestrin, R., Hungate, B.A., Koch, B.J., Stone, B.W., Sullivan, M.B., Zablocki, O., LLNL Soil Microbiome Consortium & Pett-Ridge, J. 2022. Life and death in the soil microbiome: how ecological processes influence biogeochemistry. Nature Reviews Microbiology. 20:415–430. LINK PDF
166. Jang, H.B., Chittick, L., Li, Y.-F., Zablocki, O., Sanderson, C.M., Carrillo, A., van den Engh, G., & Sullivan, M.B. 2022. Viral tag and grow: a scalable approach to capture and characterize infectious virus-host pairs. ISME Communications. 2:12.  LINK PDF

2021

165. Bolduc, B., Zablocki, O., Guo, J., Zayed, A.A., Vik, D., Dehal, P., Wood-Charlson, E.M., Arkin, A., Merchant, N., Pett-Ridge, J., Roux, S., Vaughn, M., & Sullivan, M.B. 2021. iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology. ISME Communications. 1:77. LINK PDF

164. Danis-Wlodarczyk, K.M., Cai, A., Chen, A., Gittrich, M.R., Sullivan,M.B., Wozniak, D.J., & Abedon, S.T. 2021. Friends or Foes? Rapid Determination of Dissimilar Colistin and Ciprofloxacin Antagonism of Pseudomonas aeruginosa Phages. Pharmaceuticals. 14:1162. LINK PDF

163. Dutilh, B.E., Varsani, A., Tong, Y., Simmonds, P., Sabanadzovic, S., Rubino, L., Roux, S., Muñoz, A.R., Lood, C., Lefkowitz, E.J., Kuhn, J.H., Krupovic, M., Edwards, R.A., Brister, J.R., Adriaenssens, E., & Sullivan, M.B. 2021. Perspective on taxonomic classification of uncultivated viruses. Current Opinion in Virology. 51:207. LINK PDF

162. Varner, R.K., Crill, P.M., Frolking, S., McCalley, C.K., Burke, S.A., Chanton, J.P., Holmes, M.E., Isogenie Project Coordinators, Saleska, S., & Palace, M.W. 2021. Permafrost thaw driven changes in hydrology and vegetation cover increase trace gas emissions and climate forcing in Stordalen Mire from 1970 to 2014. Philosophical Transactions A. 380: 20210022. LINK PDF

161. Brum, J.R., Jurgensen, S., Roux, S., Schwenck, S., Stewart, F., & Sullivan, M.B. 2021. Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state. ISMEJ. LINK PDF

160. Garneau, J.R.^, Legrand, V., Marbouty, M., Press, M.O., Vik, D.R., Fortier, L.-C., Sullivan, M.B., Bikard, D., & Monot, M.^ 2021. High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome. Scientific Reports. 11:18319. (^ denotes co-corresponding authors) LINK PDF

159. Brandão, M.C.†^, Benedetti, F.†^, Martini, S., Soviadan, Y.D., Irisson, J.-O., Romagnan, J.-B., Elineau, A., Desnos, C., Jalabert, L., Freire, A.S., Picheral, M., Guidi, L., Gorsky, G., Bowler, C., Karp-Boss, L., Henry, N., de Vargas, C., Sullivan, M.B., Tara Oceans Consortium Coordinators, Stemmann, L., & Lombard, F. 2021. Macroscale patterns of oceanic zooplankton composition and size structure. Scientific Reports. 11:15714. († denotes co-first authors)(^ denotes co-corresponding authors) LINK PDF

158. Rapp, J.Z., Sullivan, M.B., & Deming, J.W. 2021. Divergent genomic adaptations in the microbiomes of Arctic subzero sea-ice and cryopeg brines. Frontiers in Microbiology. 12:701186. LINK  PDF

157. Krupovic, M., Turner, D., Morozova, V., Dyall-Smith, M., Oksanen, H.M., Edwards, R., Dutilh, B.E., Lehman, S.M., Reyes, A., Baquero, D.P., Sullivan, M.B., Uchiyama, J., Nakavuma, J., Barylski, J., Young, M.J., Du, S., Alfenas-Zerbini, P., Kushkina, A., Kropinski, A.M., Kurtböke, I., Brister, J.R., Lood, C., Sarkar, B.L., Yigang, T., Liu, Y., Huang, L., Wittmann, J., Chanishvili, N., van Zyl, L.J., Rumnieks, J., Mochizuki, T., Jalasvuori, M., Aziz, R.K., Lobocka, M., Stedman, K.M., Shkoporov, A., Gillis, A., Peng, X., Enault, F., Knezevic, P., Lavigne, R., Rhee, S-K., Cvirkaite-Krupovic, V., Moraru, C., Moreno-Switt, A.I., Poranen, M.M., Millard, A., Prangishvili, D., & Adriaenssens, E.M. 2021. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: Update of taxonomy changes in 2021. Archives of Virology. LINK PDF

156. Flores, J.M.^, Bourdin, G., Kostinski, A.B., Altaratz, O., Dagan, G., Lombard, F., Haëntjens, N., Boss, E., Sullivan, M.B., Gorsky, G., Lang-Yona, N., Trainic, M., Romac, S., Voolstra, C.R., Rudich, Y., Vardi, A., & Koren, I^. 2021. Diel cycle of sea spray aerosol concentration. Nature Communications. 12:5476. LINK PDF (^ denotes co-corresponding authors)

155. Chaffron, S.†, Delage, E.†, Budinich, M., Vintache, D., Henry, N., Nef, C., Ardyna, M., Zayed, A.A., Junger, P.C., Galand, P.E., Lovejoy, C., Murray, A., Sarmento, H., Tara Oceans coordinators, Acinas, S., Babin, B., Iudicone, D., Jaillon, O., Sullivan, M.B., Karsenti, E., Wincker, P., Karp-Boss, L., Bowler, C., de Vargas, C. & D. Eveillard. 2021. Environmental vulnerability of the global ocean epipelagic plankton community interactome. Science Advances. 7:eabg1921. († denotes co-first authors) LINK PDF

154. Abedon, S.T.^, Danis-Wlodarczyk, K.M., Wozniak, D.J. & Sullivan, M.B.^ 2021. Improving phage-biofilm in vitro experimentation. Viruses. 13(6):1175. (^ denotes corresponding author) LINK PDF

153. Zayed, A.A.†, Lücking, D.†, Mohssen, M., Cronin, D., Bolduc, B., Gregory, A.C., Hargreaves, K.R., Piehowski, P.D., White III, R.A., Huang, E.L., Adkins, J.N., Roux, S., Moraru, C.^ & Sullivan, M.B.^.2021. efam: an expanded, metaproteome-supported HMM profile database of viral protein families. Bioinformatics. In Press. († denotes co-first authors)(^ denotes co-corresponding authors) LINK PDF

152. Zhong, Z., Tian, F., Roux, S., Gazitúa, M.C., Solonenko, N., Li, Y-F., Davis, M.E., Van Etten, J.L., Mosley-Thompson, E., Rich, V.I., Sullivan, M.B.^ & Thompson, L.G.^ 2021. Glacier ice archives potentially fifteen-thousand-year-old microbes and phages. Microbiome. 9:160. (^ denotes corresponding author) LINK PDF

• The preprint was featured in Science, with articles in Popular Mechanics, New York Post, Newsweek, Daily Mail, etc
• BBC interview of Matt Sullivan here

151. Kieft, K., Zhou, Z., Anderson, R.E., Buchan, A., Campbell, B.J., Hallam, S.J., Hess, M., Sullivan, M.B., Walsh, D.A., Roux, S., & Anantharaman, K. 2021. Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages. Nature Communications. 12:3503. LINK PDF

150. Bachy, C., Yung, C.C.M., Needham, D.M.,Gazitúa, M.C.,  Roux, S., Limardo, A.J., Choi, C.J., Jorgens, D.M., Sullivan, M.B. & Worden, A.Z. 2021. Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts. ISMEJ. In Press. LINK PDF

149. Pratama, A.A., Bolduc, B., Zayed, A.A., Zhong, Z., Guo, J., Vik, D., Gazitúa, M.C., Wainaina, J., Roux, S. & Sullivan, M.B. 2021. Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation. PeerJ (9):e11447. LINK PDF

148. Acinas, S.G., Sánchez, P., Salazar, G., Cornejo-Castillo, F.M., Sebastián, M., Logares, R., Royo-Llonch, M., Paoli, L., Sunagawa, S., Hingamp, P., Ogata, H., Lima-Mendez, G., Roux, S., González, J.M., Arrieta, J.M., Alam, I.S., Kamau, A., Bowler, C., Raes, J., Pesant, S., Bork, P., Agustí, S., Gojobori, T., Vaqué, D., Sullivan, M.B., Pedrós-Alió, C., Massana, R., Duarte, C.M. & Gasol, J.M. 2021. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Communications Biology. In Press. LINK PDF

147. Zablocki, O., Michelsen, M., Burris, M., Solonenko, N., Warwick-Dugdale, J., Ghosh, R., Pett-Ridge, J., Sullivan, M.B. & Temperton, B. 2021. VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature. PeerJ. 9: e11088. PREPRINT LINK PDF

146. Du, J.,  Zayed, A.A., Kigerl, K., Zane, K., Sullivan, M.B. & Popovich, P. 2021. Spinal cord injury changes the structure and functional potential of gut bacterial and viral communities. mSystems. 6(3):e01356-20. LINK PDF

• Interview by Technology Networks

145. Gazitua, M.C.†, Vik, D.†, Roux, S., Gregory, A.C., Bolduc, B., Widner, B., Mulholland, M.R., Hallam, S.J., Ulloa, O. & Sullivan, M.B. 2021. Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters. ISMEJ. 15:981-998. († denotes co-first authors) LINK PDF

144. Correa, A.M.S., Howard-Varona, C., Coy, S.R., Buchan, A., Sullivan, M.B. & Weitz, J. 2021. Revisiting the rules of life for viruses of microorganisms. Nature Reviews Microbiology. 19:501-513. LINK PDF

143. Guo, J., Bolduc, B., Zayed, A.A., Varsani, A., Dominguez-Huerta, G., Delmont, T.O., Pratama, A.A., Gazitua, M.C., Vik, D., Sullivan, M.B., & Roux, S. 2021. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome. 9:37. LINK PDF

• A step by step workflow (on protocol.io) on how to use VirSorter2 with your own data can be found here
• You can access the testing data through this link: https://osf.io/vftg6/. Click “Download” in the upper right corner, which includes a “README” file briefly describing the files in it after you untar and decompress it.

142. Sakowski, E.G., Arora-Williams, K., Tian, F., Zayed, A.A., Zablocki, O., Sullivan, M.B., & Preheim, S.P. 2021. Gene Fusion with epicPCR Captures in situ Interaction Dynamics and Virus-Host Range for Estuarine Actinophages. Nature Microbiology. 6:630-642. LINK PDF

141. Kaneko, H., Blanc-Mathieu, R., Endo, H., Chaffron, S., Delmont, T.O., Gaia, M., Henry, N., Hernández-Velázquez, R., Nguyen, C.H., Mamitsuka, H., Forterre, P., Jaillon, O., de Vargas, C., Sullivan, M.B., Suttle, C.A., Guidi, L. & Ogata, H. 2021. Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean. Iscience. 24:102002. PREPRINT LINK PDF

2020

140. Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Schulz, F., Wu, D., Paez-Espino, D., Chen, I-M., Huntemann, M., Palaniappan, K., Ladau, J., Mukherjee, S., Reddy, T.B.K., Nielsen, T., Kirton, E., Faria, J.P., Edirisinghe, J.N., Henry, C.S., Jungbluth, S.P., Chivian, D., Dehal, P., Wood-Charlson, E.M., Arkin, A.P., Tringe, S.G., Visel, A., IMG/M Data Consortium (including Sullivan, M.B.), Woyke, T., Mouncey, N.J., Ivanova, N.N., Kyrpides, N.C. & Eloe-Fadrosh, E.A. 2020. A genomic catalog of Earth’s microbiome. Nature Biotechnology. 39:499-509. LINK PDF

[PP.H.2020]. Hackl, T., Laurenceau, R., Ankenbrand, M.J., Bliem, C., Cariani, Z., Thomas, E., Dooley, K.D., Arellano, A.A., Hogle, S.L., Berube, P., Leventhal, G.E., Luo, E., Eppley, J., Zayed, A.A., Beaulaurier, J., Stepanauskas, R., Sullivan, M.B., DeLong, E.F., Biller, S.J., Chisholm, S.W. 2020. Novel integrative elements and genomic plasticity in ocean ecosystems. bioRxiv preprint. LINK

[PP.DW.2020]. Danis-Wlodarczyk, K.M., Cai, A., Chen, A., Gittrich, M., Sullivan, M.B., Wozniak, D.J., Abedon, S.T. 2020. In vitro analysis of colistin and ciprofloxacin antagonism of Pseudomonas aeruginosa phage PEV2 infection activities.  bioRxiv preprint. LINK

[PP.G.2020]. Gregory, A.C., Gerhardt, K., Zhong, Z., Bolduc, B., Temperton, B., Konstantinidis, K.T.C., Sullivan, M.B. 2020. MetaPop: A pipeline for macro- and micro-diversity analyses and visualization of microbial and viral metagenome-derived populations. bioRxiv preprint. LINK

139. Gregory, A.C.†, Zablocki, O.†, Zayed, A.A., Howell, A., Bolduc, B., Sullivan, M.B. 2020. The gut virome database reveals age-dependent patterns of virome diversity in the human gut. Cell Host & Microbe. 28:724-740. († denotes co-first authors) LINK PDF

138. Mara, P., Vik, D., Pachiadaki, M.G., Suter, E.A., Poulos,, B., Taylor, G.T., Sullivan, M.B, Edgcomb, V.P. 2020. Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco basin redoxcline. ISMEJ. 14:3079-3092. LINK PDF

[PP.G.2020]. Gittrich, M., Liu, Y.,Tian, F., Crouch, A., Jang, H.B., Du, J., Sullivan, M.B. 2020. The ecology of phage resistance: the key to successful phage therapy? Preprints. LINK PDF

137. Bolduc, B.†^, Hodgkins, S.B.†, Varner, R.K., Crill, P.M., McCalley, C.K., Chanton, J.P., Tyson, G.W., Riley, W.J., Palace, M., Duhaime, M.B., Hough, M.A., IsoGenie Project Coordinators, IsoGenie Project Team, A2A Project Team, Saleska, S.R., Sullivan, M.B., Rich, V.I.^ 2020.  The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research. PeerJ. 8:e9467. (^denotes co-corresponding authors) († denotes co-first authors) LINK PDF

136. Vik, D., Gazitua, M.C., Sun, C.L., Zayed, A.A., Aldunate, M., Mulholland, M.R., Ulloa, O., Sullivan, M.B. 2020. Genome-resolved viral ecology in a marine oxygen minimum zone. Environmental Microbiology. In press. LINK PDF

135. Endo, H., Blanc-Mathieu, R., Li, Y., Salazar, G., Henry, N., Labadie, K., de Vargas, C., Sullivan, M.B., Bowler, C., Wincker, P., Karp-Boss, L., Sunagawa, S., Ogata, H. 2020. Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions. Nature Ecology & Evolution. 4:1639–1649. LINK PDF

134. Shaffer M., Borton, M.A., McGivern, B.B., Zayed, A.A., La Rosa, S.L., Solden, L.M., Liu, P, Narrowe, A.B., Rodríguez-Ramos, J., Bolduc, B., Gazitua, M.C., Daly, R.A., Smith, G.J., Vik, D.R., Pope, P.B., Sullivan, M.B., Roux, S., Wrighton, K.C. 2020. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Research. 48:8883-8900. LINK PDF

133. Zhong, Z., Rapp, J.Z., Wainaina, J.M., Solonenko, N.E., Maughan, H., Carpenter, S.D., Cooper, Z.S., Jang, H.B., Bolduc, B., Deming, J.W.^, Sullivan, M.B.^ 2020. Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice. mSystems. 5:e00246-20. LINK PDF (^denotes co-corresponding authors)

132. Flores, J.M.^, Bourdin, G., Altaratz, O., Trianic, M., Lang-Yona, N., Dzimban, E., Steinau, S., Tettich, F., Planes, S., Allemand, D., Agostini, S., Banaigs, B., Boissin, E., Boss, E., Douville, E., Forcioli, D., Furla, P., Galand, P.E., Sullivan, M., Gilson, E., Lombard, F., Moulin, C., Pesant, S., Poulain, J., Reynaud, S., Romac, S., Sunagawa, S., Thomas, O.P., Troublé, R., de Vargas, C., Vega Thurber, R., Voolstra, C.R., Wincker, P., Zoccola, D., Bowler, C., Gorsky, G., Rudich, Y., Vardi, A.^, Koren, I.^ 2020. Tara Pacific Expedition’s Atmospheric Measurements of Marine Aerosols across the Atlantic and Pacific Oceans. Bulletin of the American Meteorological Society. 101:E536–E554. LINK PDF (^denotes co-corresponding authors)

131. Sunagawa, S.^, Acinas, S.G., Bork, P., Bowler, C., Tara Oceans Coordinators, Eveillard, D., Gorsky, G., Guidi, L., Iudicone, D., Karsenti, E., Lombard, F., Ogata, H., Pesant, S., Sullivan, M.B., Wincker, P., de Vargas, C.^ 2020. Tara Oceans: towards global ocean eco-systems biology. Nature Reviews Microbiology. 18:428–445. LINK PDF (^denotes co-corresponding authors)

130. Tisza, M.J., Pastrana, D.V., Welch, N.L., Stewart, B., Peretti, A., Starrett, G.J., Pang, Y.S., Krishnamurthy, S.R., Pesavento, P.A., McDermott, D.H., Murphy, P.M., Whited, J.L., Miller, B., Brenchley, J.M., Rosshart, S.P., Rehermann, B., Doorbar, J., Ta’ala, B.A., Pletnikova, O., Troncoso, J., Resnick, S.M., Bolduc, B., Sullivan, M.B., Varsani, A., Segall, A.M., & Buck, C.B. 2020. Discovery of several thousand highly diverse circular DNA viruses. eLife. 9:e51971. LINK PDF

129. Howard-Varona, C., Lindback, M., Bastien, G., Solonenko, N., Zayed, A., Jang, H.B., Andreopoulos, B., Brewer, H., Glavina del Rio, T., Adkins, J., Paul, S., Sullivan, M.B.^, & Duhaime, M.^ 2020. Phage-specific metabolic reprogramming of virocells. ISMEJ. 14:881-895. LINK PDF  (^denotes co-corresponding authors)

• JGI Science Highlights

 

2019

128. Gorsky, G., Bourdin, G., Lombard, F., Pedrotti, M.L., Audrain, S., Bin, N., Boss, E., Bowler, C., Cassar, N., Caudan, L., Chabot, G., Cohen, N., Cron, D., de Vargas, C., Dolan, J., Douville, E., Elineau, A., Flores, M., Ghiglione, J.F., Haëntjens, N., Hertau, M., John, S., Kelly, R., Koren, I., Lin, Y., Marie, D., Moulin, C., Moucherie, J., Pesant, S., Picheral, M., Poulain, J., Pujo-Pay, M., Reverdin, G., Romac, S., Sullivan, M.B., Trainic, M., Tressol, M., Troublé, R., Vardi, A., Voolstra, C., Wincker, P., Agostini, S., Banaigs, B., Boissin, E., Forcioli, D., Furla, P., Galand, P.E., Gilson, E., Reynaud, S., Sunagawa, S., Thomas, O.P., Thurber, R.V., Zoccola, D., Planes, S., Allemand, D., & Karsenti, E. 2019. Expanding Tara Oceans protocols for underway, ecosystemic sampling of the ocean-atmosphere interface during Tara Pacific expedition. Frontiers in Marine Science. 6:750. LINK PDF

127. Kigeri, K.A., Zane, K., Adams, K., Sullivan, M.B., & Popovich, P.G. 2019. The spinal cord-gut-immune axis as a master regulator of health and neurological function after spinal cord injury. Experimental Neurology. 323C:113085. LINK PDF

126. Schmidt, J.O., Bograd, S. J., Arrizabalaga, H., Barbeaux, S.J., Barth, J.A., Boyer, T., Brodie, S., Cross, S., Druon, J.N., Fransson, A., Hartog, J., Hazen, E., Karstensen, J., Hobday, A.J., Jacox, M., Kupschus, S., Lopez, J., Madureira, L.A., Filho, J.E.M., Miloslavich, P., Santos, C.P., Scales, K.L., Speich, S., Sullivan, M.B., Szoboszlai, A., Tommasi, D., Wallace, D., & Zador, S. 2019. Future ocean observations to connect climate, fisheries and marine ecosystems. Frontiers in Marine Science. 6:550. LINK PDF

125. Planes, S., Allemand, D., Agostini, S., Banaigs, B., Boissin, E., Boss, E., Bourdin, G., Bowler, C., Douville, E., Flores, J.M., Forcioli, D., Furla, P., Galand, P.E., Ghiglione, J.F., Gilson, E., Lombard, F., Moulin, C., Pesant, S., Poulain, J., Reynaud, S., Romac, S., Sullivan, M.B., Sunagawa, S., Thomas, O.P., Troublé, R., de Vargas, C., Thurber, R.V., Voolstra, C.R., Wincker, P., Zoccola, D., & the Tara Pacific Consortium. 2019. The Tara Pacific expedition—A pan-ecosystemic approach of the “-omics” complexity of coral reef holobionts across the Pacific Ocean. PLoS Biology. 17:e3000483. LINK PDF

124. Zimmerman, A., Howard-Varona, C., Needham, D.M., John, S., Worden, A.Z., Sullivan, M.B., Waldbauer, J.R., & Coleman, M.L. 2019. Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nature Reviews Microbiology. 18:21-34. LINK PDF

123. Ruiz-Perez, C.A., Tsementzi, D., Hatt, J.K., Sullivan, M.B., & Konstantinidis, K.T. 2019. Prevalence of viral photosynthesis genes along a freshwater to saltwater transect in Southeast USA. Environmental Microbiology Reports. 11:672–689. LINK PDF

122. Trubl, G., Roux, S., Solonenko, N., Li, Y., Bolduc, B., Rodriguez-Ramos, J., Eloe-Fadrosh, E.A., Rich, V., & Sullivan, M.B. 2019. Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils. PeerJ. 7:e7265.  LINK PDF

121. Cavicchioli, R., Ripple, W.J., Timmis, K.N., Azam, F., Bakken, L.R., Baylis, M., Behrenfeld, M.J., Boetius, A., Boyd, P.W., Classen, A.T., Crowther, T.W., Danovaro, R., Foreman, C.M., Huisman, J., Hutchins, D.A., Jansson, J.K., Karl, D.M., Koskella, B., Mark Welch, D., Martiny, J.B.H., Moran, M., Orphan, V., Reay, D., Remais, J.V., Rich, V., Singh, B.K., Stein, L.Y., Stewart, F.J., Sullivan, M.B., van Oppen, M.J.H., Weaver, S.C., Webb, E.A., & Webster, N. 2019. Scientists’ Warning to Humanity: microorganisms and climate change. Nature Reviews Microbiology. 17:569-596. LINK PDF

120. Wilpiszeski, R., Aufrecht, J., Retterer, S., Sullivan, M.B., Graham, D., Pierce, E., Zablocki, O., Palumbo, A., & Elias, D. 2019. Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales. Applied and Environmental Microbiology. 85:e00324. LINK PDF

119. Barylski, J., Enault, F., Dutilh, B.E., Schuller, M.B.P., Edwards, R.A., Gillis, A., Klumpp, J., Knezevic, P., Krupovic, M., Kuhn, J.H., Lavigne, R., Oksanen, H.M., Sullivan, M.B., Jang, H.B., Wittmann, J., Tolstoy, I., Brister, J.R., Kropinski, A.M., & Adriaenssens, E.M. 2019. Analysis of Spounaviruses as a case study for the overdue reclassification of tailed bacteriophages. Systematic Biology. 69:110–123. LINK PDF

118.  Zimmerman, A.E., Bachy, C., Ma, X., Roux, S., Jang, H.B., Sullivan, M.B., Waldbauer, J.R., & Worden, A.Z. 2019. Closely related viruses of the marine picoeukaryotic alga Ostreococcus lucimarinus exhibit different ecological strategies. Environmental Microbiology. 21:2148–2170. LINK PDF

117.  Jang, H.B.†, Bolduc, B.†, Zablocki, O., Kuhn, J., Roux, S., Adriaenssens, E.M., Brister, J.R., Kropinski, A.M., Krupovic, M., Lavigne, R., Turner, D., & Sullivan, M.B. 2019. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nature Biotechnology. 37:632–639. († denotes co-first authors)  LINK PDF

• Featured in Nature Microbiology
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116. Ibarbalz, F.M., Henry, N., Brandao, M.C., Martini, S., Busseni, G., Byrne, H., Coelho, L.P., Endo, H., Gasol, J.M., Gregory, A.C., Mahe, F., Rigonato, J., Royo-Llonch, M., Salazar, G., Sanz-Saez, I., Scalco, E., Soviadan, D., Zayed, A.A., Zingone, A., Labadie, K., Ferland, J., Marec, C., Kandels, S., Picheral, M., Dimier, C., Poulain, J., Pisarev, S., Carmichael, M., Pesant, S., Tara Oceans Coordinators, Babin, M., Boss, E., Iudicone, D., Jaillon, O., Acinas, S.G., Ogata, H., Pelletier, E., Stemmann, L., Sullivan, M.B., Sunagawa, S., Bopp, L., de Vargas, C., Karp-Boss, L., Wincker, P., Lombard, F., Bowler, C., & Zinger, L. 2019. Global Trends in Marine Plankton Diversity across Kingdoms of Life. Cell. 179:1084-1097. LINK PDF

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115. Salazar, G., Paoli, L., Alberti, A., Huerta-Cepas, J., Ruscheweyh, H.J., Cuenca, M., Field, C.M., Coelho, L.P., Cruaud, C., Engelen, S., Gregory, A.C., Labadie, K., Marec, C., Pelletier, E., Royo-Llonch, M., Roux, S., Sánchez, P., Uehara, H., Zayed, A.A., Zeller, G., Carmichael, M., Dimier, C., Ferland, J., Kandels, S., Picheral, M., Pisarev, S., Poulain, J., Tara Oceans Coordinators, Acinas, S.G., 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, M.B., Wincker, P., & Sunagawa, S. 2019. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. Cell. 179:1068-1083. LINK PDF

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114.  Gregory, A.†, Zayed, A.†, Conceicao-Neto, N., Temperton, B., Bolduc, B., Alberti, A., Ardyna, M., Arkhipova, K., Carmichael, M., Cruaud, C., Dimier, C., Dominguez-Huerta, G., Ferland, J., Kandels-Lewis, S., Liu, Y., Marec, C., Pesant, S., Picheral, M., Pisarev, S., Poulain, J., Tremblay, J.-E., Vik, D., Tara Oceans Coordinators, Babin, M., Bowler, C., Culley, A.I., Vargas, C., Dutilh, B.E., Iudicone, D., Karp-Boss, L., Roux, S., Sunagawa, S., Wincker, P. & Sullivan, M.B. 2019. Marine DNA viral macro- and micro-diversity from pole to pole. Cell. 177: 1109-1123. († denotes co-first authors) LINK PDF

• The GOV2.0 viral populations are available at bitbucket (here, see the download section) or iVirus (here); for raw read availability see Suppl. Table 3.
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113. Mizuno, C., Guyomar, C., Roux, S., Lavigne, R., Rodriguez-Valera, F.,  Sullivan, M.B., Gillet, R., Forterre, P. & Krupovic, M. 2019. Numerous cultivated and uncultivated viruses encode ribosomal proteins. Nature Communications. 10:752. LINK  PDF

112. Caputi, L., Carradec, Q., Eveillard, D., Kirilovsky, A., Pelletier, E., Pierella Karlusich, J. J., Jiminez Vieira, F. R., Villar, E., Chaffron, S., Malviya, S., Scalco, E., Acinas, S., Alberti, A., Aury, J.-M., Benoiston, S., Bertrand, A., Biard, T., Bittner, L., Boccara, M., Bum, J., Brunet, C., Busseni, G.,  Carratala, A., Claustre, H., Pedro Coelho, L., Colin, S., D’Aniello, S., Da Silva, C., Del Core, M., Dore, H., Gasparini, S., Kokoszka, F., Jamet, J.-L., Lejeusne, C., Lepoivre, C., Lescot, M., Lima-Mendez, G., Lombard, F., Lukes, J., Maillet, N., Madoui, M.-A., Martinez, E., Mazzocchi, M.G.,  Neou, M., Paz-Yepes, J., Poulain, J., Ramondenc, S., Romagnan, J.-B., Roux, S., Manta, D., Sanges, R., Speich, S., Sprovieri, M., Sunagawa, S., Taillander, V., Tanaka, A., Tirichine, L., Trottier, C., Uitz, J., Veluchamy, A., Vesela, J., Vincent, F., Yau, S., Kendels-Lewis, S., Searson, S., Dimier, C., Picheral, M., Tara Oceans Coordinators, Bork, P., Boss, E., de Vargas, C., Follows, M., Grimsley, N., Guidi, L., Hingamp, P., Karsenti, E., Sordino, P., Stemmann, L., Sullivan, M.B., Tagliabue, A., Zingone, A., Garczarek, L., d’Ortenzio, F., Testor, P., Not, F., d’Alcala, M., Wincker, P., Bowler, C. & Iudicone, D. 2018. Community-Level Responses to Iron Availability in Open Ocean Planktonic Ecosystems. Global Biogeochemical Cycles. 33:391-419.  LINK  PDF

•  Awarded ‘Top cited article’ mention by the journal publisher.

111. Roux, S., Trubl, G., Goudeau, D., Nath, N., Couradeau, E., Ahlgren, N.A., Zhan, Y., Marsan, D., Chen, F., Fuhrman, J.A., Northen, T.R., Sullivan, M.B., Rich, V.I., Malmstrom, R.R., Eloe-Fadrosh, E.A. 2018. Optimizing de novo genome assembly from PCR-amplified metagenomes. PeerJ. 7:e6902 LINK  PDF

2018

110. Warwick-Dugdale, J., Solonenko, N., Moore, K., Chittick, L., Gregory, A.C., Allen, M.J., Sullivan, M.B., Temperton, B. 2018. Long-read viral metagenomics enables capture of abundant and microdiverse viral populations and their niche-defining genomic islands. PeerJ. 7:e6800. LINK  PDF

• Top-5 viewed article at PeerJ

109. Martinez, M., Woodcroft, B., Ignacio Espinoza, J. C., Zayed, A., Singleton, C., Boyd, J., Li, Y-F., Purvine, S., Maughan, H., Hodgkins, S., Anderson, D., Sederholm, M.,Temperton, B., Bolduc, B., Isogenie Project Coordinators, Saleska, S., Tyson, G. & Rich V. 2019. Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov, Ca. Cryosericia class nov, Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov. Systematic and Applied Microbiology.  42: 54-66.  LINK  PDF

108. Howard-Varona, C., Vik, D., Solonenko, N., Gazitua, C., Hobbs, Z., Honaker, R., Kinkhabwala, A. & Sullivan, M.B. 2018. Whole-Genome Sequences of Phages p000v and p000y, Which Infect the Bacterial Pathogen Shiga-Toxigenic Escherichia coli. Microbiology Resource Announcements. e01400-18.  LINK  PDF

107. Howard-Varona, C., Vik, D., Solonenko, N., Li, Y., Gazitua, C., Chittick, L., Samiec, J., Jensen, A., Anderson, P., Howard-Varona, A., Kinkhabwala, A., Abedon, S. & Sullivan, M.B. 2018. Fighting Fire with Fire: Phage Potential for the Treatment of E. coli O157 Infection. Antibiotics.  7: e101.  LINK  PDF

106. Daly, R., Roux, S., Borton, M., Morgan, D., Johnston, M., Booker, A., Hoyt, D., Meulia, T., Wolfe, R., Hanson, A., Mouser, P., Moore, J., Wunch, K., Sullivan, M.B., Wrighton, K. & Wilkins, M. 2019. Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing. Nature Microbiology. 4: 352-361.  LINK  PDF

105. Gregory, A.C., Sullivan, M.B., Segal, L.N. & Keller, B.C. 2018. Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome. Respiratory Research. 19:e174.  LINK  PDF

104. Trubl, G., Jang, H. B., Roux, S., Emerson,  J., Solonenko, N., Vik, D., Solden, L., Ellenbogen, J., Runyon, A., Bolduc, B., Woodcroft, B., Saleska, S., Tyson, G., Wrighton, K., Sullivan, M.B. & Rich, V. 2018. Soil viruses are underexplored players in ecosystem carbon processing. mSystems.  3: e00076-18.  LINK  PDF

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103. Roux, S., Adriaenssens, E.M., Dutlith, B.E., Koonin, E.V., Kropinski, A.M., Krupovic, M., Kuhn, J.H., Lavigne, R., Brister, J.R., Varsani, A., Amid, C., Aziz, R.K., Bordenstein, S.R., Bork, P., Breitbart, M., Cochrane, G.R., Daly, R.A., Desnues, C., Duhaime, M.B., Emerson, J.B., Enault, F., Fuhrman, J.A., Hingamp, P., Hugenholtz, P., Hurwitz, B.L., Ivanova, N.N., Labonte, J.M., Lee, K.-B., Malmstrom, R.R., Martinez-Garcia, M., Mizrachi, I.K., Ogata, H., Paez-Espino, D., Petit, M.-A., Putonti, C., Rattei, T., Reyes, A., Rodreigues-Valera, F., Rosario, K., Schriml, L., Schulz, F., Steward, G.F., Sullivan, M.B., Sunagawa, S., Suttle, C.A., Temperton, B., Tringe, S.G., Thurber, R.V., Webster, N.S., Whiteson, K.L., Wilhelm, S.W., Wommack, K.E., Woyke, T., Wrighton, K., Yilmaz, P., Yoshida, T., Young, M.J., Yutin, N., Allen, L.Z., Kyrpides, N.C. & Eloe-Fadrosh, E.A. 2019. Minimum Information about an Uncultivated Virus Genome (MIUViG): a community consensus on standards and best practices for describing genome sequences from uncultivated viruses. Nature Biotechnology. 37: 29-37.  LINK   PDF

102. Solden, L.M., Naas, A.E., Roux, S., Daly, R.A., Collins, W.B., Nicora, C.D., Purvine, S.O., Hoyt, D.W., Schückel, J., Jorgensen, B., Willats, W., Spalinger, D.E., Firkins, J.L., Lipton, M.S., Sullivan, M.B., Pope, P.B. & Wrighton, K.C. 2018. Interspecies cross-feedings orchestrate carbon degradation in the rumen ecosystem. Nature Microbiology. 3:1274–1284.  LINK   PDF

101. Emerson, J.B., Roux, S., Brum, J.R., Bolduc, B., Woodcroft, B.J, Jang, H.B., Singleton, C.M., Solden, L.M., Naas, A.E., Boyd, J.A., Hodgkins, S.B., Wilson, R.M., Trubl, G., Li, C., Frolking, S., Pope, P.B., Wrighton, K.C., Crill, P.M., Chanton, J.P., Saleska, S.R., Tyson, G.W., Rich, V.I. & Sullivan, M.B. 2018. Host-linked soil viral ecology along a permafrost thaw gradient. Nature Microbiology. 3:870–880.   LINK   PDF

• Highlighted 24 July, 2018 in Nature Reviews Microbiology

100. Zhong, Z., Solonenko, N.E., Gazitúa, M.C., Kenny, D.V., Mosley-Thompson, E., Rich, V.I., Van Etten, J.L., Thompson, L.G.^ & Sullivan, M.B.^ 2018. Clean low-biomass procedures and their application to ancient ice core microorganisms. Frontiers in Microbiology. 9:1094.  (^ denotes co-corresponding authors) LINK   PDF

99. Howard-Varona, C., Hargreaves, K.R., Solonenko, N.E., Markillie, L.M., White, R.A., Brewer, H.M., Ansong, C., Orr, G., Adkins, J.N. & Sullivan, M.B. 2018. Multiple mechanisms drive phage infection efficiency in nearly-identical hosts. ISMEJ. 12:1605–1618.   LINK   PDF 

• DOE EMSL press release
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• Article in Science Daily

98. Adriaenssens, E.M., Wittmann, J., Kuhn, J.H., Turner, D., Sullivan, M.B., Dutilh, B.E., Jang, H., van Zyl, L.J., Klumpp, J., Lobocka, M., Moreno Switt, A.I., Rumnieks, J., Edwards, R.A., Uchiyama, J., Alfenas-Zerbini, P., Petty, N.K., Kropinski, A.M., Barylski, J., Gillis, A., Clokie, M.R.C., Prangishvili, D., Lavigne, R., Aziz, R.K., Duffy, S., Krupovic, M., Poranen, M.M., Knezevic, P., Enault, F., Tong, Y., Oksanen, H.M. & Brister, J.R. 2018. Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Archives of Virology. 163:1125–1129.   LINK   PDF

97. Carradec, Q., Pelletier, E., Da Silva, C., Alberti, A., Seeleuthner, Y., Blanc-Mathieu, R., Lima-Mendez, G., Rocha, F., Tirichine, L., Labadie, K., Kirilovsky, A., Bertrand, A., Engelen, S., Madoui, M.A., Méheust, R., Poulain, J., Romac, S., Richter, D., Yoshikawa, G., Dimier, C., Kandels-Lewis, S., Picheral, M., Searson, S., Tara Oceans Coordinators, Jaillon, O., Aury, J.M., Karsenti, E., Sullivan, M.B., Sunagawa, S., Bork, P., Not, F., Hingamp, P., Raes, J., Guidi, L., Ogata, H., de Vargas, C., Iudicone, D., Bowler, C. & Wincker, P. 2018. A Global Ocean Atlas of Eukaryotic Genes. Nature Communications. 9:373.   LINK   PDF

• CNRS International Magazine press release

96. Seeleuthner, Y., Mondy, S., Lombard, V., Carradec, Q., Pelletier, E., Wessner, M., Leconte, L., Mangot, J.F., Poulain, J., Labadie, K., Logares, R., Sunagawa, S., de Berardinis, V., Salanoubat, M., Dimier, C., Kandels-Lewis, S., Picheral, M., Searson, S., Pesant, S., Poulton, N., Stepanauskas, R., Bork, P., Bowler, C., Hingamp, P., Sullivan, M.B., Iudicone, D., Massana, R., Aury, J.M., Henrissat, B., Karsenti, E., Jaillon, O., Sieracki, M., de Vargas, C. & Wincker, P. 2018. Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans. Nature Communications. 9:310.  LINK   PDF

• CNRS International Magazine press release

2017

95. Pasulka, A., Thamatrakoln, K., Kopf, S., Guan, Y., Poulos, B., Moradian, A., Sweredoski, M., Hess, S., Sullivan, M.B., Bidle, K. & Orphan, V.  2017. Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods. Environmental Microbiology. 20:671–692.  LINK   PDF

94. Anderson, C.L., Sullivan, M.B. & Fernando, S.C. 2017. Dietary energy drives the dynamic response of bovine rumen viral communities. Microbiome. 5:155.  LINK   PDF

93. Roux, S., Emerson, J.B., Eloe-Fadrosh, E.A. & Sullivan, M.B. 2017. Benchmarking viromics: An in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. PeerJ. 5:e3817.  LINK   PDF

92. Roux, S., Chan, L.-K., Egan, R., Malmstrom, R.R., McMahon, K.D. & Sullivan, M.B. 2017. Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. Nature Communications. 8: 858. LINK   PDF

• Faculty of 1000 “Recommended paper” 12 Dec 2017 

91. Duhaime, M.B., Solonenko, N., Roux, S., Verberkmoes, N.C., Wichels, A. & Sullivan, M.B. 2017. Comparative omics and trait analyses of marine Pseudoalteromonas phages advance the phage OTU concept. Frontiers in Microbiology. 8:1241.  LINK   PDF

90. Silas, S., Makarova, K., Shmakov, S., Paez-Espino, D., Mohr, G., Liu, Y., Davison, M., Roux, S., Krishnamurthy, S., Fu, B., Hansen, L., Wang, D., Sullivan, M.B., Millard, A., Clokie, M., Bhaya, D., Lambowitz, A., Kyrpides, N., Koonin, E., & Fire, A. 2017. On the origin of reverse transcriptase-using CRISPR-Cas systems and their hyper-diverse, enigmatic spacer repertoires. mBio. 8:00897-17.  LINK   PDF

89. Alberti, A., Poulain, J., Engelen, S., Labadie, K., Romac, S., Ferrera, I., Albini, G., Aury, J.M., Belser, C., Bertrand, A., Cruaud, C., Da Silva, C., Azema-Dossat, C., Gavory, F., Gas, S., Guy, J., Haquelle, M., Jacoby, E., Jaillon, O., Lemainque, A., Pelletier, E., Samson, G., Wessner, M., Acinas, S., Royo-Llonch, M., Cornejo-Castillo, F., Logares, R., Fernandez-Gomez, B., Bowler, C., Cochrane, G., Amid, C., Hoopen, P.T., de Vargas, C., Grimsley, N., Desgranges, E., Kandels-Lewis, S., Ogata, H., Poulton, N., Sieracki, M., Stepanauskas, R., Sullivan, M.B., Brum, J., Duhaime, M., Poulos B., Hurwitz, B., Pesant, S., Karsenti, E. & Wincker, P. 2017. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Scientific Data. 4: 170093.  LINK   PDF

88. Vik​, D.R., Roux, S., Brum, J.R., Bolduc, B., Emerson, J.B., Padilla, C.C., Stewart, F.J. & Sullivan, M.B. 2017. Putative archaeal viruses from the mesopelagic ocean. PeerJ. 5: 3428.  LINK   PDF

87. Martínez-Hernández, F., Fornas, O., Lluesma Gomez, M., Bolduc, B., de la Cruz Peña, M.J., Martínez Martínez, J., Antón, J., Gasol, J.M., Rosselli, R., Rodríguez-Valera, F., Sullivan, M.B., Acinas, S.G. & Martinez-Garcia, M. 2017. Single-virus genomics reveals hidden cosmopolitan and abundant viruses. Nature Communications. 8: 15892.  LINK   PDF 

86. Bolduc, B.†, Jang, H.B.†, Doulcier, G., You, Z.Q., Roux, S. & Sullivan, M.B., 2017. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PeerJ. 5: 3243. († denotes co-first authors)   LINK   PDF

85. Krzysztof, S., Caputi, L., Buttigieg, P.L., D’Alelio, D., Ibarbalz, F.M., Sullivan, M.B., Chaffron, S., Bowler, C., d’Alcala’, M.R. & Iudicone, D.. 2017. Modelling plankton ecosystems in the meta-omics era. Are we ready? Marine Genomics. 32: 1-17.   LINK   PDF

84. Murata, K., Zhang, Q.F., Galaz-Montoya, J.G., Fu, C., Coleman, M.C., Osburne, M., Schmid, M., Sullivan, M.B.^, Chisholm, S.W.^, & Chiu, W.^ 2017.  Visualizing Adsorption of Cyanophage P-SSP7 onto Marine Prochlorococcus. Scientific Reports. 7: 44176.   (^ denotes co-corresponding authors) LINK   PDF  

83. Nishimura, Y., Watai, H., Honda, T., Mihara, T., Omae, K., Roux, S., Blanc-Mathieu, R., Yamamoto, K., Hingamp, P., Sako, Y., Sullivan, M.B., Goto, S., Ogata, H. & Yoshida, T. 2017.  Environmental viral genomes shed new light on virus-host interactions in the ocean. mSphere. 2:00359-16.   LINK   PDF

82. Howard-Varona, C.†, Hargreaves, K.R.†, Abedon, S.T. & Sullivan, M.B. 2017. Lysogeny in nature – mechanisms, impact and ecology of temperate phages. ISMEJ. 16:1-10.  († denotes co-first authors)   LINK   PDF

81. Poulos, B.T., John, S.G., & Sullivan, M.B. 2017. Iron Chloride Flocculation of Bacteriophages from Seawater. Bacteriophages: Methods and Protocols. 1681.  LINK   PDF

• for updated protocol see protocols.io)

80. Kang, D.-W.†, Adams, J.B.†, Gregory, A.C.†, Borody, T., Chittick, L., Fasano, A., Khoruts, A., Geis, E., Maldonado, J., McDonough-Means, S., Pollard, E.L., Roux, S., Sadowsky, M.J., Schwarzberg Lipson, K., Sullivan, M.B.^, Caporaso, J.G.^ & Krajmalnik-Brown, R.^ 2017. Microbiota transfer alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome. 5:10.  († denotes co-first authors) (^ denotes co-corresponding authors)   LINK   PDF

• short 10-minute video for parents from James Adams M.D., available at http://autism.asu.edu

79. Simmonds, P., Adams, M.J., Benko, M., Breitbart, M., Brister, J.R., Carstens, E.B., Davison, A.J., Delwart, E., Gorbalenya, A.E., Harrach, B., Hull, R., King, A.M.Q., Koonin, E.V., Krupovic, M., Kuhn, J.H., Lefkowitz, E.J., Nibert, M.L., Orton, R., Roosinck, M.J., Sabanadzovic, S., Sullivan, M.B., Suttle, C.A., Tesh, R.B., van der Vlugt, R.A., Varsani, A., & Zerbini, F.M. 2017. Virus taxonomy in the age of metagenomics. Nature Reviews in Microbiology. 15:161-168.   LINK   PDF

78. Enault, F., Briet, A., Bouteille, L., Roux, S., & Sullivan, M.B., Petit, M.A. 2017. Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses. ISMEJ. 11:237-247.   LINK   PDF

77. Bolduc, B., Youens-Clark, K., Roux, S., Hurwitz, B.L.^, & Sullivan, M.B.^ 2017. iVirus: facilitating new insights into viral ecology with software and community datasets imbedded in a cyberinfrastructure. ISMEJ. 11:7-14.   (^ denotes co-corresponding authors)  LINK   PDF

• iVirus highlighted in CyVerse
• CyVerse coverage of OSU’s Viromics Workshop

76. Howard-Varona. C., Roux, S., Dore, H., Solonenko, N., Holmfeldt, K., Markillie, L.M., Orr, G., & Sullivan, M.B. 2017. Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus. ISMEJ. 11: 284-295.   LINK   PDF

• EMSL press release

2016

75. Sullivan, M.B., Weitz, J.S., & Wilhelm, S. 2016. Crystal Ball: Viral ecology comes of age. Environmental Microbiology Reports. 9: 33-35.   LINK   PDF

74. Paez-Espino, D., Chen, I-M A., Palaniappan, K.,  Ratner, A., Chu, K., Szeto, E., Pillay, M., Huang, J., Markowitz, V.M., Nielsen, T., Huntemann, M., Reddy, T.B.K., Pavlopoulos, G.A., Sullivan, M.B., Campbell, B.J., Chen, F., McMahon, K., Hallam, S.J., Denef, V., Cavicchioli, R., Caffrey, S.M., Streit, W.R., Webster, J., Handley, K., Salekdeh, G.H., Tsesmetzis, N., Setubal, J.C., PopeP.B., Liu, W-T., Rivers, A.R., Ivanova, N.N. & Kyrpides, N.C. 2016. IMG/VR: A database of cultured and uncultured DNA Viruses 1 and Retroviruses. Nucleic Acids Research. 45: D457-D465.   LINK   PDF

73. Gregory, A.C., Solonenko, S.A., Ignacio-Espinoza, J.C., LaButti, K., Copeland, A., Sudek, S., Maitland, A., Chittick, L., dos Santos, F., Weitz, J.S., Worden, A.Z., Woyke, T., Sullivan, M.B. 2016. Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer. BMC Genomics. 17: 930.   LINK   PDF

• Host range data available here.

72. Roux, S. Solonenko, N. Dang, V.T. Poulos, B.T. Schwenck, S.M. Goldsmith, D.B. Coleman, M.L. Breitbart, M. Sullivan, M.B. 2016. Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. PeerJ. 4: e2777.   LINK   PDF

71. Roux, S., Brum, J.R., Dutilh, B.E., Sunagawa, S., Duhaime, M.B., Loy, A., Poulos, B.T., Solonenko, N., Lara, E., Poulain, J., Pesant, S., Kandels-Lewis, S., Dimier, C., Picheral, M., Searson, S., Cruaud, C., Alberti, A.,  Duarte, C.M.M.,  Gasol, J.M.M.,  Vaqué, D., Tara Oceans Coordinators, Bork, P.,  Acinas, S.G., Wincker, P. & Sullivan, M.B. 2016. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature. 537: 689-693.   LINK   PDF   THE GOV DATASET

• Highlighted 03 Oct 2016 in Nature Reviews Genetics  
• Nature podcast, 22 Sept 2016: A sea of viruses
• OSU press release
• Article in The Science Explorer
• Article in The Institute of Marine Sciences News
• Article in Environmental Research Web’s blog
• Article in Seeker Magazine

70. Holmfeldt, K.^, Solonenko, N., Howard-Varona, C., Moreno, M., Malmstrom, R.R., Blow, M.J. & Sullivan, M.B.^ 2016. Large-scale maps of variable infection efficiencies in aquatic Bacteriodetes phage-host model systems. Environmental Microbiology. 18: 3949-3961.  (^ denotes co-corresponding authors)   LINK   PDF

69. Trubl, G, Solonenko, N., Chittick, L., Solonenko, S., Rich, V.I., & Sullivan, M.B. 2016.  Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient. PeerJ. 4:e1999.   LINK   PDF

68. Duhaime, M.B., Wichels, A., & Sullivan, M.B. 2016. Six Pseudoalteromonas strains isolated from surface waters of Kabeltonne, offshore Helgoland, North Sea. Genome Announcements. 4:e01697-15.   LINK   PDF

67. Guidi, L.†, Chaffron, S.†, Bittner, L.†, Eveillard, D.†, Larhlimi, A., Roux, S., Darzi, Y., Audic, S., Berline, L., Brum, J.R., Coelho, L.P., Espinoza, J.C., Malviya, S., Sunagawa, S., Dimier, C., Kandels-Lewis, S., Picheral, M., Poulain, J., Searson, S., Tara Oceans Consortium Coordinators, Stemmann, L., Not, F., Hingamp, P., Speich, S., Follows, M., Karp-Boss, L., Boss, E., Ogata, H., Pesant, S., Weissenbach, J.,, Wincker, P., Acinas, S.G., Bork, P., de Vargas, C., Iudicone, D., Sullivan, M.B., Raes, J., Karsenti, E., Bowler, C., & Gorsky, G. 2016. Plankton networks driving carbon export in the oligotrophic ocean. Nature. 532:465-470.  († denotes co-first authors)   LINK   PDF

• Highlighted 22 February 2016 in Nature Reviews Microbiology 14: 194.
• OSU press release
  
• In-depth coverage in Environmental Monitor

66. Brum J.R.†, Ignacio-Espinoza, J.C.†, Kim, E-H.†, Trubl, G., Jones, R., Roux, S., VerBerkmoes, N.C., Rich, V.I.^, & Sullivan, M.B.^ 2016. Illuminating structural proteins in viral “dark matter” with metaproteomics. PNAS. 113: 2436-2441.  († denotes co-first authors) (^ denotes co-corresponding authors)   LINK   PDF

65. Krupovic, M., Dutilh, B.E., Adriaenssens, E.M., Wittmann, J., Vogensen, F.K., Sullivan M.B., Rumnieks, J., Prangishvili, D., Lavigne, R., Kropinski, A.M., Klumpp, J., Gillis, A., Enault, F., Edwards, R.A., Duffy, S., Clokie, M.R., Barylski, J., Ackermann, H.W., & Kuhn, J.H. 2016. Taxonomy of prokaryotic viruses: update from the ICTVbacterial and archaeal viruses subcommittee. Archives of Virology. 161:1096-9.   LINK  PDF

2015

64. Labonté, J.M., Swan, B.K., Poulos, B., Luo, H., Koren, S., Hallam, S.J., Sullivan, M.B., Woyke, T., Wommack, K.E. & Stepanauskas, R. 2015. Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton. ISMEJ. 9: 2386-99.   LINK   PDF

63. Pesant, S., Not, F., Picheral, M., Kandels-Lewis, S., Le Bescot, N., Gorsky, G., Iudicone, D., Karsenti, E., Speich, S., Troublé, R., Dimier, C., Searson, S. & Tara Oceans Consortium Coordinators. 2015. Open science resources for the discovery and analysis of Tara Oceans data. Scientific Data. 2: 150023.   LINK   PDF

62. Dang, V., Howard-Varona, C., Schwenck, S. & Sullivan, M.B. 2015. Variably lytic infection dynamics of large Bacteroidetes podovirus phi38:1 against two Cellulophaga baltica host strains. Environmental Microbiology. 17: 4659–4671.   LINK   PDF

61. Roux, S., Hallam, S.J., Woyke, T., & Sullivan, M.B. 2015. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. eLife. 4:e08490.   LINK   PDF

• VirSorter Curated Dataset: Predicted viral sequences with automatic annotation, virus-host matrix, and Genome Clustering network.
• Highlighted 14 Aug 2015 in Nature Reviews Microbiology 13: 526-527.
• Article in Wired

60. Brum, J.R., Hurwitz, B., Schofield, O., Ducklow, H., & Sullivan, M.B. 2015. Seasonal time bombs: Dominant temperate viruses affect Southern Ocean microbial dynamics. ISMEJ. 10:437–449.   LINK   PDF

59. Brum, J.R.†, Ignacio-Espinoza, J.C.†, Roux, S.†, Doulcier, G., Acinas, S.G., Alberti, A., Chaffron, S., Cruaud, C., de Vargas, C., Gasol, J.M., Gorsky, G., Gregory, A.C., Guidi, L., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Poulos, B.T., Schwenck, S.M., Speich, S., Dimier, C., Kandels-Lewis, S., Picheral, M., Searson, S., Tara Oceans Coordinators, Bork, P., Bowler, C., Sunagawa, S., Wincker, P., Karsenti, E., & Sullivan, M.B. 2015. Patterns and ecological drivers of ocean viral communities. Science. 348: 1261498. († denotes co-first authors)   LINK   PDF

• TOV 43 dataset: virome predicted proteins, protein clusters, and viral populations
• Article in Quanta Magazine by Carl Zimmer (21 May 2015)
• Interview on NPR Science Friday with Ira Flatow (21 May 2015)
• Part of a Tara Oceans Special Issue on Ocean Plankton (references #55-59 here) that was highlighted in the New York Times (21 May 2015), the BBC News (22 May 2015) and Nature Reviews Microbiology (8 June 2015)

58. de Vargas, C.†, Audic, S.†, Henry, N.†, Decelle, J.†, Mahé, F.†, Logares, R., Lara, E., Berney, C., Le Bescot, N., Probert, I., Carmichael, M., Poulain, J., Romac, S., Colin, S., Aury, J.-M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., Flegontova, O., Guidi, L., Horák, A., Jaillon, O., Lima-Mendez, G., Lukeš, J., Malviya, S., Morard, R., Mulot, M., Scalco, E., Siano, R., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Tara Ocean Coordinators, Acinas, S.G., Bork, P., Bowler, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Raes, J., Sieracki, M.E., Speich, S., Stemmann, L., Sunagawa, S., Weissenbach, J., Wincker, P., & Karsenti, E. 2015. Eukaryotic plankton diversity in the sunlit ocean. Science. 348: 1261605. († denotes co-first authors)   LINK   PDF

57. Lima-Mendez, G.†, Faust, K.†, Henry, N.†, Decelle, J., Colin, S., Carcillo, F., Chaffron, S., Ignacio-Espinosa, J.C., Roux, S.,Vincent, F., Bittner, L., Darzi, Y., Wang, J., Audic, S., Berline, L., Bontempi, G., Cabello, A.M., Coppola, L., Cornejo-Castillo, F.M., d’Ovidio, F., De Meester, L., Ferrera, I., Garet-Delmas, M.-J., Guidi, L., Lara, E., Pesant, S., Royo-Llonch, M., Salazar, G., Sánchez, P., Sebastian, M., Souffreau, C., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Tara Oceans Coordinators, Gorsky, G., Not, F., Ogata, H., Speich, S., Stemmann, L., Weissenbach, J., Wincker, P., Acinas, S.G., Sunagawa, S., Bork, P., Sullivan, M.B.,Karsenti, E., Bowler, C., de Vargas, C., & Raes, J. 2015. Determinants of community structure in the global plankton interactome. Science. 348: 1262073.  († denotes co-first authors)   LINK   PDF

56. Villar, E., Farrant, G.K., Follows, M., Garczarek, L., Speich, S., Audic, S., Bittner, L., Blanke, B., Brum, J.R., Brunet, C., Casotti, R., Chase, A., Dolan, J.R., d’Ortenzio, F., Gattuso, J.-P., Grima, N., Guidi, L., Hill, C.N., Jahn, O., Jamet, J.-L., Le Goff, H., Lepoivre, C., Malviya, S., Pelletier, E., Romagnan, J.-B., Roux, S., Santini, S., Scalco, E., Schwenck, S.M., Tanaka, A., Testor, P., Vannier, T., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Tara Oceans Coordinators, Acinas, S.G., Bork, P., Boss, E., de Vargas, C., Gorsky, G., Ogata, H., Pesant, S., Sullivan, M.B., Sunagawa, S., Wincker, P., Karsenti, E., Bowler, C., Not, F., Hingamp, P., & Iudicone, D. 2015. Environmental characteristics of Agulhas rings affect interocean plankton transport. Science. 348:1261447.   LINK   PDF

55. Sunagawa, S.†, Coelho, L.P.†, Chaffron, S.†, Kultima, J.R., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D.R., Alberti, A., Cornejo-Castillo, F.M., Costea, P.I., Cruaud, C., d’Ovidio, F., Engelen, S., Ferrera, I., Gasol, J.M., Guidi, L., Hildebrand, F., Kokoszka, F., Lepoivre, C., Lima-Mendez, G., Poulain, J., Poulos, B.T., 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, M.B., Weissenbach, J., Wincker, P., Karsenti, E., Raes, J., Acinas, S.G., & Bork, P. 2015. Structure and function of the global ocean microbiome. Science. 348:1261359.  († denotes co-first authors)  LINK   PDF

54. Roux, S., Enault, F., Hurwitz, B.L., & Sullivan, M.B. 2015. VirSorter: mining viral signal from microbial genomic data. PeerJ. 3:e985.  LINK   PDF

• Selected in PeerJ Top Microbiology Papers – August 2015
  

53. Roux, S., Enault, F., Ravet, V., Pereira, O., & Sullivan, M.B. 2015. Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages. Frontiers in Microbiology. 6:199.   LINK   PDF

52. Cunningham, B., Brum, J., Schwenck, S., Sullivan, M.B., & John, S. 2015. An inexpensive, accurate and precise wet-mount method for enumerating aquatic viruses. Applied Environmental Microbiology. 81:2995-3000.   LINK   PDF

51. Sullivan, M.B. 2015. Viromes, not gene markers for studying dsDNA viral communities. J Virology. 89:2459-2461.   LINK   PDF

50. Lara, E., Holmfedlt, K., Solonenko, N., Sà, E.L., Ignacio-Espinoza, J.C., Cornejo-Castillo, F.M., Verberkmoes, N.C., Vaqué, D., Sullivan, M.B., & Acinas, S.G. 2015. Life-style and genome structure of marine Pseudoalteromonas siphovirus B8b isolated from the Northwestern Mediterranean Sea. PLoS One. 10:e0114829.   LINK   PDF

49. Brum, J.R., & Sullivan, M.B. 2015. Rising to the challenge: accelerated pace of discovery transforms marine virology. Nature Reviews Microbiology. 13:147–159.   LINK   PDF

48. Hurwitz, B.L., Brum, J.R., & Sullivan, M.B. 2015. Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome. ISMEJ. 9:472–484.   LINK   PDF

2014

47. Dang, V.T. & Sullivan, M.B. 2014. Emerging methods to study bacteriophage infection at the single-cell level. Frontiers in Microbiology. 5:724.   LINK   PDF

46. Sullivan, M.B. 2014. The Phage Metagenomic Revolution. Life in Our Phage World. 2:55-70.   Amazon

45. Roux, S., Hawley, A.K., Beltran, M.T., Scofield, M., Schwientek, P., Stepanauskas, R., Woyke, T., Hallam, S.J., & Sullivan, M.B. 2014. Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. eLife.3:e03125.   LINK   PDF

• Highlighted in Nature Reviews in Microbiology
• Highlighted in eLife

44. Hurwitz, B.L., Westveld, A.H., Brum, J.R., & Sullivan, M.B. 2014. Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses. PNAS. 111:10714–10719.   LINK   PDF

43. Deng, L.†, Ignacio-Espinoza, J.C.†, Gregory, A., Poulos, B.T., Weitz, J.S., Hugenholtz, P., & Sullivan, M.B. 2014. Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature. 513:242–245.  († denotes co-first authors)   LINK   PDF

42. Holmfeldt, K.†, Howard-Varona, C.†, Solonenko, N., & Sullivan, M.B. 2014. Contrasting genomic patterns and infection strategies of two co-existing Bacteroidetes podovirus genera. Environmental Microbiology. 16:2501–2513.  († denotes co-first authors)  LINK   PDF

2013

41. Hurwitz, B.L., Hallam, S.J., & Sullivan, M.B. 2013. Metabolic reprogramming by viruses in the sunlit and dark ocean. Genome Biology. 14:R123.   LINK   PDF

40. Solonenko, S.A. & Sullivan, M.B. 2013. Preparation of metagenomic libraries from naturally occurring marine viruses. Methods in Enzymology. Microbial Metagenomics, Metatranscriptomics, and Metaproteomics edition. 531:143–165.   LINK   PDF

39. Ignacio-Espinoza, J.C., Solonenko, S.A., & Sullivan, M.B. 2013. The global virome: Not as big as we thought? Current Opinion in Virology. 3:566–571.   LINK   PDF

38. Holmfeldt, K., Solonenko, N., Shah, M., Corrier, K., Riemann, L., VerBerkmoes, N.C., & Sullivan, M.B. 2013. Twelve previously unknown phage genera are ubiquitous in global oceans. PNAS. 110:12798-12803.   LINK   PDF

37. Solonenko, S.A., Ignacio-Espinoza, J.C., Alberti, A., Cruaud, C., Hallam, S., Konstantinidis, K., Tyson, G., Wincker, P., & Sullivan, M.B. 2013. Sequencing platform and library preparation choices impact viral metagenomes. BMC Genomics. 14:320.   LINK   PDF

36. Brum, J.R., Schenck, R.O., & Sullivan, M.B. 2013. Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses. ISMEJ. 7:1738–1751.   LINK   PDF

35. Ceyssens, P.J., Aertsen, A., Donovan, D.M., Lavigne, R., Sullivan, M.B., Debarbieux, L., & Vaneechoutte, M. 2013. Meeting report of the European Molecular Biology Organization (EMBO) symposium ‘Viruses of Microbes II’, Brussels, July 2012. Res. Microbiol. 164:799–805.   LINK   PDF

34. Zhao, Y.L.†, Temperton, B.†, Thrash, J.C., Schwalbach, M.S., Vergin, K.L., Landry, Z.C., Ellisman, M., Deerinck, T., Sullivan, M.B., & Giovannoni, S.J. 2013. Abundant SAR11 viruses in the ocean. Nature. 494:357-360.  († denotes co-first authors)   LINK   PDF

33. Allers, E.†, Moraru, C.†, Duhaime, M.B., Beneze, E., Solonenko, N., Barrero-Canosa, J., Amann, R.^{^}, & Sullivan, M.B.^{^} 2013. Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses. Environmental Microbiology. 15:2306–2318.  († denotes co-first authors) (^ denotes co-corresponding authors)   LINK   PDF

32. Hurwitz, B.L. & Sullivan, M.B. 2013. The Pacific Ocean Virome (POV): A marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One. 8:e57355.   LINK   PDF

• POV protein clusters download

31. Labrie, S.J., Frois-Moniz, K., Osburne, M.S., Kelly, L., Roggensack, S.E., Sullivan, M.B., Gearin, G., Zeng, Q., Fitzgerald, M., Henn, M.R., & Chisholm, S.W. 2013. Genomes of marine cyanopodoviruses reveal multiple origins of diversity. Environmental Microbiology. 15:1356-1376.  LINK  PDF

30. Weitz, J.S., Poisot, T., Meyer, J.R., Flores, C.O., Valverde, S., Sullivan, M.B., & Hochberg, M.E. 2013. Phage-bacteria infection networks. Trends in Microbiology. 21:82-91. LINK PDF

2012

29. Duhaime, M.B. & Sullivan, M.B. 2012. Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline. Virology. 434:181-186. LINK PDF

28. Deng, L., Gregory, A., Yilmaz, S., Poulos, B.T., Hugenholtz, P., & Sullivan, M.B. 2012. Contrasting life strategies of viruses that infect photo- and heterotrophic bacteria, as revealed by viral tagging. mBio. 3:e00373-12.   LINK   PDF

• Faculty of 1000 Prime recommended this article “of special significance” on 27 Aug 2013

27. Allers, E.†, Wright, J.J.†, Konwar, K.M., Howes, C.G., Beneze, E., Hallam, S.J.^{^}, & Sullivan, M.B.^{^} 2012. Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean. ISMEJ. 7:256-268.  († denotes co-first authors) (^ denotes co-corresponding authors) LINK   PDF

26. Hurwitz, B.L., Deng, L., Poulos, B.T., & Sullivan, M.B. 2012. Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environmental Microbiology. 15:1428–1440.   LINK   PDF

25. Duhaime, M.B., Deng, L., Poulos, B.T., & Sullivan, M.B. 2012. Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: A rigorous assessment and optimization of the linker amplification method. Environmental Microbiolgy. 14:2526-2537. LINK   PDF

24. Ignacio-Espinoza, J.C. & Sullivan, M.B. 2012. Phylogenomics of T4 cyanophages: Lateral gene transfer in the ‘core’ and origins of host genes. Environmental Microbiology. 14:2113-2126.   LINK   PDF

23. Holmfeldt, K., Odic, D., Sullivan, M.B., Middelboe, M., & Riemann, L. 2012. Cultivated single-stranded DNA phages that infect marine Bacteroidetes prove difficult to detect with DNA-binding stains. Applied Environmental Microbiology. 78:892-894. LINK   PDF

2011

22. Marine, R., Polson, S.W., Ravel, J., Hatfull, G., Russell, D., Sullivan, M.B., Syed, F., Dumas, M., & Wommack, K.E. 2011. Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA. Applied Environmental Microbiology. 77:8071-8079. LINK   PDF

21. Karsenti, E., Acinas, S.G., Bork, P., Bowler, C., De Vargas, C., Raes, J., Sullivan, M.B, Arendt, D., Benzoni, F., Claverie, J.M., Follows, M., Gorsky, G., Hingamp, P., Iudicone, D., Jaillon, O., Kandels-Lewis, S., Krzic, U., Not, F., Ogata, H., Pesant, S., Reynaud, E.G., Sardet, C., Sieracki, M.E., Speich, S., Velayoudon, D., Weissenbach, J., Wincker, P., & the Tara Oceans Consortium. 2011. A holistic approach to marine eco-systems biology. PLoS Biology. 9:e1001177.   LINK   PDF

20. John, S.G., Mendez, C.B., Deng, L., Poulos, B., Kauffman, A.K.M., Kern, S., Brum, J., Polz, M.F., Boyle, E.A., & Sullivan, M.B. 2011. A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environmental Microbiology Reports. 3:195-202.   LINK   PDF

• Minor correction concerning buffer recipes:   PDF

2010

19. Sullivan, M.B., Huang, K.H., Ignacio-Espinoza, J.C., Berlin, A.M., Kelly, L., Weigele, P.R., DeFrancesco, A.S., Kern, S.E., Thompson, L.R., Young, S., Yandava, C., Fu, R., Krastins, B., Chase, M., Sarracino, D., Osburne, M.S., Henn, M.R., & Chisholm, S.W. 2010. Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments. Environmental Microbiology. 12:3035-3056. LINK PDF

18. Liu, X.A., Zhang, Q.F., Murata, K., Baker, M.L., Sullivan, M.B., Fu, C., Dougherty, M.T., Schmid, M.F., Osburne, M.S., Chisholm, S.W., & Chiu, W. 2010. Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Nature Structural and Molecular Biology. 17:830-836. LINK PDF

17. Henn, M.R., Sullivan, M.B., Stange-Thomann, N., Osburne, M.S., Berlin, A.M., Kelly, L., Yandava, C., Kodira, C., Zeng, Q.D., Weiand, M., Sparrow, T., Saif, S., Giannoukos, G., Young, S.K., Nusbaum, C., Birren, B.W., & Chisholm, S.W. 2010. Analysis of high-throughput sequencing and annotation strategies for phage genomes. PLoS One. 5:e9083. LINK PDF

2009

16. Sullivan, M.B., Krastins, B., Hughes, J.L., Kelly, L., Chase, M., Sarracino, D., Chisholm, S.W. 2009. The genome and structural proteome of an ocean siphovirus: A new window into the cyanobacterial ‘mobilome’. Environmental Microbiology. 11:2935-2951. LINK PDF

2008

15. Sullivan, M.B., Coleman, M.L., Quinlivan, V., Rosenkrantz, J.E., DeFrancesco, A.S., Tan, G., Fu, R., Lee, J.A., Waterbury, J.B., Bielawski, J.P., & Chisholm, S.W. 2008. Portal protein diversity and phage ecology. Environmental Microbiology. 10:2810-2823. LINK PDF

14. Dammeyer, T., Bagby, S.C., Sullivan, M.B., Chisholm, S.W., Frankenberg-Dinkel, N. 2008. Efficient phage-mediated pigment biosynthesis in oceanic cyanobacteria. Current Biology. 18:442-448. LINK PDF

2007

13. Lindell, D., Jaffe, J.D., Coleman, M.L., Futschik, M.E., Axmann, I.M., Rector, T., Kettler, G., Sullivan, M.B., Steen, R., Hess, W.R., Church, G.M., & Chisholm, S.W. 2007. Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature. 449:83-86. LINK PDF

12. Moore, L.R., Coe, A., Zinser, E.R., Saito, M.A., Sullivan, M.B., Lindell, D., Frois-Moniz, K., Waterbury, J., & Chisholm, S.W. 2007. Culturing the marine cyanobacterium Prochlorococcus. Limnology and Oceanographic Methods. 5:353-362. LINK PDF

11. Breitbart, M., Thompson, L.R., Suttle, C.A., & Sullivan, M.B. 2007. Exploring the vast diversity of marine viruses. Oceanography. 20:135-139. LINK PDF

2006

10. Sullivan, M.B., Lindell, D., Lee, J.A., Thompson, L.R., Bielawski, J.P., & Chisholm, S.W. 2006. Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biology. 4:1344-1357. LINK PDF

• Faculty of 1000 “must read” 6 July 2006
• Science (21 Jul 06) & Nat. Rev. Micro. (Sept 06, v.4) Literature Highlight
• 1 of 4 refs in Goldenfield & Woese, 2007. Nature 445:369

9. Coleman, M.L., Sullivan, M.B., Martiny, A.C., Steglich, C., Barry, K., DeLong, E.F., & Chisholm, S.W. 2006. Genomic islands and the ecology and evolution of Prochlorococcus. Science. 311:1768-1770. LINK PDF

8. DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R., Chisholm, S.W., & Karl, D.M. 2006. Community genomics among stratified microbial assemblages in the ocean’s interior. Science. 311:496-503. LINK PDF

• Faculty of 1000 “Recommended paper” 17 Feb 2006

2005

7. Sullivan, M.B., Coleman, M.L., Weigele, P., Rohwer, F., & Chisholm, S.W. 2005. Three Prochlorococcus cyanophage genomes: Signature features and ecological interpretations. PLoS Biology. 3:790-806. LINK PDF

• Nature Reviews Microbiology, Highlight of the Literature (July 2005, vol. 3, 520)

6. Paul, J.H., & Sullivan, M.B. 2005. Marine phage genomics: What have we learned? Current Opinion in Biotechnology. 16:299-307. LINK PDF

2004

5. Lindell, D., Sullivan, M.B., Johnson, Z.I., Tolonen, A.C., Rohwer, F., & Chisholm, S.W. 2004. Transfer of photosynthesis genes to and from Prochlorococcus viruses. PNAS. 101:11013-11018. LINK PDF

2003

4. Sullivan, M.B., Waterbury, J.B., & Chisholm, S.W. 2003. Cyanophages infecting the oceanic cyanobacterium Prochlorococcus. Nature. 424:1047-1051. LINK PDF

3. Rocap, G., Larimer, F.W., Lamerdin, J., Malfatti, S., Chain, P., Ahlgren, N.A., Arellano, A., Coleman, M., Hauser, L., Hess, W.R., Johnson, Z.I., Land, M., Lindell, D., Post, A.F., Regala, W., Shah, M., Shaw, S.L., Steglich, C., Sullivan, M.B., Ting, C.S., Tolonen, A., Webb, E.A., Zinser, E.R., & Chisholm, S.W. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature. 424:1042-1047. LINK PDF

2002

2. Paul, J.H., Sullivan, M.B., Segall, A.M., & Rohwer, F. 2002. Marine phage genomics. CBPB. 133:463-476. LINK PDF

1998

1. Kana, T.M., Sullivan, M.B., Cornwell, J.C., & Groszkowski, K.M. 1998. Denitrification in estuarine sediments determined by membrane inlet mass spectrometry. Limnology and Oceanography. 43:334-339. LINK PDF

 

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