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Matthew Sullivan

  • Professor, Microbiology Admin
  • IDI Thematic Program Director, OR - IDI
  • Professor, Civil, Envir & Geod Eng
  • Professor, Evol, Ecology & Org Biology
  • Riffe Bldg Room 914
    496 W. 12th Ave.
    Columbus, OH 43210
  • 614-247-1616

About

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 phtosynthetic 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 sing-cell assays to investigate questions that are critical for modeling and predicting the impoacts 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.

Research interests and areas of expertise:

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

 

 

Honors

  • May, 2013-
    May, 2018

    Marine Microbiology Initiative Investigator Award.

  • September, 2015

    Post-doctoral mentor award.

  • September, 2014

    Undergraduate mentor award.

  • October, 2013

    Kavli Fronteirs in Science Fellow.

  • August, 1998-
    August, 1999

    Fulbright Scholarship.

Chapters

2014

  • 2014. "The Phage Metagenomic Revolution." In Life in Our Phage World,

Journal Articles

2019

  • Trubl, G.; Roux, S.; Solonenko, N.; Li, Y.F. et al., 2019, "Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils." PeerJ 2019, no. 7,
  • Roux, S.; Trubl, G.; Goudeau, D.; Nath, N. et al., 2019, "Optimizing de novo genome assembly from PCR-amplified metagenomes." PeerJ 2019, no. 5,

2018

  • Pasulka, A.L.; Thamatrakoln, K.; Kopf, S.H.; Guan, Y. et al., 2018, "Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods." Environmental Microbiology 20, no. 2, 671-692 - 671-692.
  • Seeleuthner, Y.; Mondy, S.; Lombard, V.; Carradec, Q. et al., 2018, "Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans." Nature Communications 9, no. 1,

2017

  • Alberti, A.; Poulain, J.; Engelen, S.; Labadie, K. et al., 2017, "Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition." Scientific Data 4,

2015

  • Cunningham, B.; Brum, J.; Schwenck, S.; Sullivan, M.B. et al., 2015, "An inexpensive, accurate and precise wet-mount method for enumerating aquatic viruses.." Applied and Environmental Microbiology 81, no. 9,
  • de Vargas, C.; Audic, S.; Henry, N.; Decelle, J. et al., 2015, "Eukaryotic plankton diversity in the sunlit ocean." Science 348,
  • Lima-Mendez, G.; Faust, K.; Henry, N.; Decelle, J. et al., 2015, "Determinants of community structure in the global plankton interactome." SCIENCE 348, no. 6237,
  • Roux, S.; Enault, F.; Hurwitz, B.L.; Sullivan, M.B., 2015, "VirSorter: mining viral signal from microbial genomic data." PEERJ 3,
  • Villar, E.; Farrant, G.K.; Follows, M.; Garczarek, L. et al., 2015, "Environmental characteristics of Agulhas rings affect interocean plankton transport." SCIENCE 348, no. 6237,
  • Brum, J.R.; Sullivan, M.B., 2015, "Rising to the challenge: accelerated pace of discovery transforms marine virology." NATURE REVIEWS MICROBIOLOGY 13, no. 3,
  • Roux, S.; Enault, F.; Ravet, V.; Pereira, O. et al., 2015, "Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages." FRONTIERS IN MICROBIOLOGY 6,
  • Sullivan, M.B., 2015, "Viromes, Not Gene Markers, for Studying Double-Stranded DNA Virus Communities." JOURNAL OF VIROLOGY 89, no. 5,
  • 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." ISME JOURNAL 9, no. 2,
  • Lara, E.; Holmfedlt, K.; Solonenko, N.; Sà, E.L. et al., 2015, "Life-style and genome structure of marine Pseudoalteromonas siphovirus B8b isolated from the Northwestern Mediterranean Sea.." PLoS One 10, no. 1,
  • Brum, J.R.; Ignacio-Espinoza, J.C.; Roux, S.; Doulcier, G. et al., 2015, "Patterns and ecological drivers of ocean viral communities." SCIENCE 348, no. 6237,
  • 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,
  • Sunagawa, S.; Coelho, L.P.; Chaffron, S.; Kultima, J.R. et al., 2015, "Structure and function of the global ocean microbiome." SCIENCE 348, no. 6237,

2014

  • 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." PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 111, no. 29,
  • Roux, S.; Hawley, A.K.; Beltran, M.T.; Scofeld, M. et al., 2014, "Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics." eLife 2014, no. 3,
  • Roux, S.; Hawley, A.K.; Beltran, M.T.; Scofield, M. et al., 2014, "Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta- genomics." ELIFE 3,
  • Dang, V.T.; Sullivan, M.B., 2014, "Emerging methods to study bacteriophage infection at the single-cell level." FRONTIERS IN MICROBIOLOGY 5,
  • Deng, L.; Ignacio-Espinoza, J.C.; Gregory, A.C.; Poulos, B.T. et al., 2014, "Viral tagging reveals discrete populations in Synechococcus viral genome sequence space." NATURE 513, no. 7517,
  • 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, no. 8,

2013

  • Allers, E.; Moraru, C.; Duhaime, M.B.; Beneze, E. et al., 2013, "Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses." ENVIRONMENTAL MICROBIOLOGY 15, no. 8,
  • Holmfeldt, K.; Solonenko, N.; Shah, M.; Corrier, K. et al., 2013, "Twelve previously unknown phage genera are ubiquitous in global oceans." PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 110, no. 31,
  • Hurwitz, B.L.; Deng, L.; Poulos, B.T.; Sullivan, M.B., 2013, "Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics." ENVIRONMENTAL MICROBIOLOGY 15, no. 5,
  • Solonenko, S.A.; Ignacio-Espinoza, J.C.; Alberti, A.; Cruaud, C. et al., 2013, "Sequencing platform and library preparation choices impact viral metagenomes." BMC GENOMICS 14,
  • Allers, E.; Wright, J.J.; Konwar, K.M.; Howes, C.G. et al., 2013, "Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean." ISME JOURNAL 7, no. 2,
  • 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, no. 5,
  • Weitz, J.S.; Poisot, T.; Meyer, J.R.; Flores, C.O. et al., 2013, "Phage-bacteria infection networks.." Trends in Microbiology 21, no. 2,
  • Zhao, Y.L.; Temperton, B.; Thrash, J.C.; Schwalbach, M.S. et al., 2013, "Abundant SAR11 viruses in the ocean.." Nature 494, no. 7437,
  • Hurwitz, B.L.; Hallam, S.J.; Sullivan, M.B., 2013, "Metabolic reprogramming by viruses in the sunlit and dark ocean." GENOME BIOLOGY 14, no. 11,
  • Labrie, S.J.; Frois-Moniz, K.; Osburne, M.S.; Kelly, L. et al., 2013, "Genomes of marine cyanopodoviruses reveal multiple origins of diversity.." Environmental Microbiology 15, no. 5,
  • Solonenko, S.A.; Sullivan, M.B., 2013, "Preparation of Metagenomic Libraries from Naturally Occurring Marine Viruses." MICROBIAL METAGENOMICS, METATRANSCRIPTOMICS, AND METAPROTEOMICS 531,
  • Ceyssens, P.J.; Aertsen, A.; Donovan, D.M.; Lavigne, R. et al., 2013, "Meeting report of the European Molecular Biology Organization (EMBO) Symposium 'Viruses of Microbes II', Brussels, July 2012." RESEARCH IN MICROBIOLOGY 164, no. 7,
  • 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." ISME JOURNAL 7, no. 9,
  • 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, no. 2,

2012

  • Duhaime, M.B.; Sullivan, M.B., 2012, "Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline." VIROLOGY 434, no. 2,
  • Holmfeldt, K.; Odic, D.; Sullivan, M.B.; Middelboe, M. et al., 2012, "Cultivated Single-Stranded DNA Phages That Infect Marine Bacteroidetes Prove Difficult To Detect with DNA-Binding Stains." APPLIED AND ENVIRONMENTAL MICROBIOLOGY 78, no. 3,
  • Deng, L.; Gregory, A.; Yilmaz, S.; Poulos, B.T. et al., 2012, "Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging." MBIO 3, no. 6,
  • 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 MICROBIOLOGY 14, no. 9,
  • 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, no. 8,

2011

  • Marine, R.; Polson, S.W.; Ravel, J.; Hatfull, G. et al., 2011, "Evaluation of a Transposase Protocol for Rapid Generation of Shotgun High-Throughput Sequencing Libraries from Nanogram Quantities of DNA." APPLIED AND ENVIRONMENTAL MICROBIOLOGY 77, no. 22,
  • Karsenti, E.; Acinas, S.G.; Bork, P.; Bowler, C. et al., 2011, "A Holistic Approach to Marine Eco-Systems Biology." PLOS BIOLOGY 9, no. 10,
  • John, S.G.; Mendez, C.B.; Deng, L.; Poulos, B. et al., 2011, "A simple and efficient method for concentration of ocean viruses by chemical flocculation." ENVIRONMENTAL MICROBIOLOGY REPORTS 3, no. 2,

2010

  • Henn, M.R.; Sullivan, M.B.; Stange-Thomann, N.; Osburne, M.S. et al., 2010, "Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes." PLOS ONE 5, no. 2,
  • Liu, X.; Zhang, Q.; Murata, K.; Baker, M.L. et al., 2010, "Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus." NATURE STRUCTURAL & MOLECULAR BIOLOGY 17, no. 7,
  • Sullivan, M.B.; Huang, K.H.; Ignacio-Espinoza, J.C.; Berlin, A.M. et al., 2010, "Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments." ENVIRONMENTAL MICROBIOLOGY 12, no. 11,

2009

  • Sullivan, M.B.; Krastins, B.; Hughes, J.L.; Kelly, L. et al., 2009, "The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial 'mobilome'." ENVIRONMENTAL MICROBIOLOGY 11, no. 11,

2008

  • Sullivan, M.B.; Coleman, M.L.; Quinlivan, V.; Rosenkrantz, J.E. et al., 2008, "Portal protein diversity and phage ecology." ENVIRONMENTAL MICROBIOLOGY 10, no. 10,
  • Dammeyer, T.; Bagby, S.C.; Sullivan, M.B.; Chisholm, S.W. et al., 2008, "Efficient phage-mediated pigment biosynthesis in oceanic cyanabacteria." CURRENT BIOLOGY 18, no. 6,

2007

  • Moore, L.R.; Coe, A.; Zinser, E.R.; Saito, M.A. et al., 2007, "Culturing the marine cyanobacterium Prochlorococcus." LIMNOLOGY AND OCEANOGRAPHY-METHODS 5,
  • Lindell, D.; Jaffe, J.D.; Coleman, M.L.; Futschik, M.E. et al., 2007, "Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution." NATURE 449, no. 7158,
  • Breitbart, M.; Thompson, L.R.; Suttle, C.A.; Sullivan, M.B., 2007, "Exploring the Vast Diversity of Marine Viruses." OCEANOGRAPHY 20, no. 2,

2006

  • DeLong, E.F.; Preston, C.M.; Mincer, T.; Rich, V. et al., 2006, "Community genomics among stratified microbial assemblages in the ocean's interior." SCIENCE 311, no. 5760,
  • Sullivan, M.B.; Lindell, D.; Lee, J.A.; Thompson, L.R. et al., 2006, "Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts." PLOS BIOLOGY 4, no. 8,
  • Coleman, M.L.; Sullivan, M.B.; Martiny, A.C.; Steglich, C. et al., 2006, "Genomic islands and the ecology and evolution of Prochlorococcus." SCIENCE 311, no. 5768,

2005

  • Sullivan, M.B.; Coleman, M.L.; Weigele, P.; Rohwer, F. et al., 2005, "Three Prochlorococcus cyanophage genomes: Signature features and ecological interpretations." PLOS BIOLOGY 3, no. 5,
  • Paul, J.H.; Sullivan, M.B., 2005, "Marine phage genomics: what have we learned?." CURRENT OPINION IN BIOTECHNOLOGY 16, no. 3,
  • Sullivan, M.B.; Coleman, M.L.; Weigele, P.; Rohwer, F. et al., 2005, "Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations.." PLoS biology. 3, no. 5,

2004

  • Lindell, D.; Sullivan, M.B.; Johnson, Z.I.; Tolonen, A.C. et al., 2004, "Transfer of photosynthesis genes to and from Prochlorococcus viruses." PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101, no. 30,

2003

  • Sullivan, M.B.; Waterbury, J.B.; Chisholm, S.W., 2003, "Cyanophages infecting the oceanic cyanobacterium Prochlorococcus." NATURE 424, no. 6952,
  • Sullivan, M.B.; Waterbury, J.B.; Chisholm, S.W., 2003, "Erratum: Cyanophages infecting the oceanic cyanobacterium Prochlorococcus (Nature (2000) 424 (1047-1051))." Nature 426, no. 6966, 584 - 584.
  • Rocap, G.; Larimer, F.W.; Lamerdin, J.; Malfatti, S. et al., 2003, "Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation." NATURE 424, no. 6952,

2002

  • Paul, J.H.; Sullivan, M.B.; Segall, A.M.; Rohwer, F., 2002, "Marine phage genomics." COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY 133, no. 4,

1998

  • 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, no. 2,

Unknown

  • Brum, J.R.; Hurwitz, B.; Schofield, O.; Ducklow, H. et al., "Seasonal time bombs: Dominant temperate viruses affect Southern Ocean microbial dynamics.." ISME Journal
  • Dang, V.; Howard-Varona, C.; Schwenck, S.; Sullivan, M.B., "Variably lytic infection dynamics of large Bacteroidetes podovirus phi38:1 against two Cellulophaga baltica host strains.." Environmental Microbiology
  • Poulos, B.T.; John, S.G.; Sullivan, M.B., "Iron Chloride Flocculation of Bacteriophages from Seawater.." Bacteriophages: Methods and Protocols