Dr. Matthew B. Sullivan's research focus is on the co-evolution of microbe and virus (phage) in environmental populations, as well as the impact of marine phages on microbe-mediated global biogeochemistry. Genomics and model-systems-based experimentation revealed that cyanobacterial phages often contain host photosynthesis genes, which are expressed during infection and act as a

diversity generator for their numerically-dominant, globally-distributed photosynthetic hosts. Using a genomic and metagenomic toolkit, we query 'wild' viral populations to identify important hypotheses that can be evaluated using model-system approaches with appropriate phage isolates. The Sullivan lab is also developing single-cell assays to investigate questions that are critical for

modeling and predicting the impacts of phage-host interactions in the wild. Specifically, these include gaining an understanding of the in situ host range of phage isolates, the metabolic capacity of to-date uncultured phage-host systems, the impacts of host growth status on phage production, and the fraction of microbial cells that are infected in wild populations.

Matthew Sullivan's Curriculum Vitae

Selected Publications

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. 2019. Phage-specific metabolic reprogramming of virocells. ISME. In press.

 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

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

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

 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

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

Gregory, A.†, Zayed, A.†, Jang, H.B., 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.

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

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

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

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 Highlighted 24 July, 2018 in Nature Reviews Microbiology

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

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 

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 

 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

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. In press. (^ = co-corresponding authors)

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. (* = co-first authors,^ = co-corresponding authors)  LINK

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  PREPRINT

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. (^=co-corresponding authors). ISMEJ. 11: 7-14.  LINK  PREPRINT

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. ISME J. 11: 284-295.  LINK

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  PREPRINT

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. (*=co-first authors)  LINK

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. (*=co-first authors) (^=co-corresponding authors)  LINK

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. 10.7554/eLife.08490.  LINK

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. doi:10.1126/science.1261498. (*=co-first authors)   LINK

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

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