Matthew Sullivan

Matthew Sullivan

Matthew Sullivan



Riffe Lab

Areas of Expertise

  • Phage Ecology and Evolution
  • Phage-host Interaction biology
  • Phage Discovery through (meta)genomics


  • B.S. Long Island University, 1997
  • M. Phil. Queens University of Belfast, 1998
  • Ph.D. MIT/WHOI, 2004
  • Postdoc, MIT, 2004-2007

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

Prochlorococcus cyanophages.

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 

  • DOE EMSL press release
  • OSU press release
  • Article in Science Daily
  • 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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