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.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.

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. 

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.

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).

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).

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.

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.

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.

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) 

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. 

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. 

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. 

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)

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. 

 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.  

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)  

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.

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. 

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)  The GOV2.0 viral populations are available at bitbucket (see the download section) or iVirus; 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. 

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.  

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.  

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. 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) 

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.   

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.  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. 

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.  (^ = 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)  

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.  

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. 

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.  

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. 

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)  

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)  

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.  

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) 

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

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