Christopher Dupont, PhD

Associate Professor
858-200-1886

Chris Dupont is an Associate Professor in the Genomic Medicine, Environment & Sustainability, and Synthetic Biology groups at JCVI. His primary research focus is microbial physiology and the environmental and evolutionary influence on physiological variation. This involves work with model organisms in laboratory systems, domestication of wild microbes for model studies, and sequencing based profiling of microbial communities in a variety of environments, including organismal microbiomes. This includes metagenomic and metatranscriptomic studies of the microbiomes found in the human gut, respiratory pathways, skin, and oral surfaces.

Dr. Dupont is also working on applying synthetic biology and machine learning techniques to solve unique problems in big datasets associated with the human microbiome and the environment.

Dr. Dupont began his career at JCVI as a postdoctoral fellow. He received his PhD in oceanography from the Scripps Institution of Oceanography, as well as a bachelor's in natural resources and a master's of biological and environmental engineering from Cornell University.

Research Priorities

Systems biology of an emerging model photoautotrophic diatom
  • Characterization and regulation of CO2 concentrating mechanisms
  • Development of molecular tools for genome engineering
Genomics and physiology of marine microbes
  • Bacteria and Archaea involved in nitrification
  • Genomics of uncultivated heterotrophs
  • Assembly-centric studies of oxygen minimum zones
Organism-organism and organism-environment interactions
  • Systems biology of plant-cyanobacterial symbioses
  • Gene coexpression network analyses of both simple and complex communities
  • Coevolution of geochemistry and biological metal utilization

Publications

Shahsavari N, Wang B, Imai Y, Mori M, Son S, Liang L, Böhringer N, Manuse S, Gates MF, Morrissette M, Corsetti R, Espinoza JL, Dupont CL, Laub MT, Lewis K
A Silent Operon of Photorhabdus luminescens Encodes a Prodrug Mimic of GTP.
mBio. 2022-06-28; 13.3: e0070022.
PMID: 35575547
Gupta J, Rathour R, Dupont C, Mishra A, Shekhar Thakur I
Biogeochemical profiling and taxonomic characterization of municipal landfill site by metagenomic sequencing.
Bioresource technology. 2022-05-01; 351.126936.
PMID: 35247565
Manck LE, Park J, Tully BJ, Poire AM, Bundy RM, Dupont CL, Barbeau KA
Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean.
The ISME journal. 2022-02-01; 16.2: 358-369.
PMID: 34341506
Nabwera HM, Espinoza JL, Worwui A, Betts M, Okoi C, Sesay AK, Bancroft R, Agbla SC, Jarju S, Bradbury RS, Colley M, Jallow AT, Liu J, Houpt ER, Prentice AM, Antonio M, Bernstein RM, Dupont CL, Kwambana-Adams BA
Interactions between fecal gut microbiome, enteric pathogens, and energy regulating hormones among acutely malnourished rural Gambian children.
EBioMedicine. 2021-11-01; 73.103644.
PMID: 34695658
Santoro EP, Borges RM, Espinoza JL, Freire M, Messias CSMA, Villela HDM, Pereira LM, Vilela CLS, Rosado JG, Cardoso PM, Rosado PM, Assis JM, Duarte GAS, Perna G, Rosado AS, Macrae A, Dupont CL, Nelson KE, Sweet MJ, Voolstra CR, Peixoto RS
Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality.
Science advances. 2021-08-13; 7.33:
PMID: 34389536
Ndhlovu GON, Abotsi RE, Shittu AO, Abdulgader SM, Jamrozy D, Dupont CL, Mankahla A, Nicol MP, Hlela C, Levin ME, Lunjani N, Dube FS
Molecular epidemiology of Staphylococcus aureus in African children from rural and urban communities with atopic dermatitis.
BMC infectious diseases. 2021-04-13; 21.1: 348.
PMID: 33849482
Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, IMG/M Data Consortium, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA
A genomic catalog of Earth's microbiomes.
Nature biotechnology. 2021-04-01; 39.4: 499-509.
PMID: 33169036
Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, IMG/M Data Consortium, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA
Publisher Correction: A genomic catalog of Earth's microbiomes.
Nature biotechnology. 2021-04-01; 39.4: 520.
PMID: 33208936
Bayer B, Saito MA, McIlvin MR, Lücker S, Moran DM, Lankiewicz TS, Dupont CL, Santoro AE
Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions.
The ISME journal. 2021-04-01; 15.4: 1025-1039.
PMID: 33230266
Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, IMG/M Data Consortium, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA
Author Correction: A genomic catalog of Earth's microbiomes.
Nature biotechnology. 2021-04-01; 39.4: 521.
PMID: 33795890
Espinoza JL, Dupont CL, O'Rourke A, Beyhan S, Morales P, Spoering A, Meyer KJ, Chan AP, Choi Y, Nierman WC, Lewis K, Nelson KE
Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach.
PLoS computational biology. 2021-03-29; 17.3: e1008857.
PMID: 33780444
Cohen NR, McIlvin MR, Moran DM, Held NA, Saunders JK, Hawco NJ, Brosnahan M, Ditullio GR, Lamborg C, McCrow JP, Dupont CL, Allen AE, Saito MA
Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean.
Nature microbiology. 2021-02-01; 6.2: 173-186.
PMID: 33398100
Gupta J, Rathour R, Dupont CL, Kaul D, Thakur IS
Genomic insights into waste valorized extracellular polymeric substances (EPS) produced by Bacillus sp. ISTL8.
Environmental research. 2021-01-01; 192.110277.
PMID: 33069701
Saito MA, Saunders JK, Chagnon M, Gaylord DA, Shepherd A, Held NA, Dupont C, Symmonds N, York A, Charron M, Kinkade DB
Development of an Ocean Protein Portal for Interactive Discovery and Education.
Journal of proteome research. 2021-01-01; 20.1: 326-336.
PMID: 32897077
Stuart RK, Pederson ERA, Weyman PD, Weber PK, Rassmussen U, Dupont CL
Bidirectional C and N transfer and a potential role for sulfur in an epiphytic diazotrophic mutualism.
The ISME journal. 2020-12-01; 14.12: 3068-3078.
PMID: 32814866
Nguyen MH, Kaul D, Muto C, Cheng SJ, Richter RA, Bruno VM, Liu G, Beyhan S, Sundermann AJ, Mounaud S, Pasculle AW, Nierman WC, Driscoll E, Cumbie R, Clancy CJ, Dupont CL
Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients.
Microbial genomics. 2020-12-01; 6.12:
PMID: 33245689
Breier JA, Jakuba MV, Saito MA, Dick GJ, Grim SL, Chan EW, McIlvin MR, Moran DM, Alanis BA, Allen AE, Dupont CL, Johnson R
Revealing ocean-scale biochemical structure with a deep-diving vertical profiling autonomous vehicle.
Science robotics. 2020-11-25; 5.48:
PMID: 33239321
Saunders JK, Gaylord DA, Held NA, Symmonds N, Dupont C, Dupont CL, Shepherd A, Kinkade DB, Saito MA
METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies-Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses.
Journal of proteome research. 2020-11-06; 19.11: 4718-4729.
PMID: 32897080
Zhang F, Rossignol P, Huang T, Wang Y, May A, Dupont C, Orbovic V, Irish VF
Reprogramming of Stem Cell Activity to Convert Thorns into Branches.
Current biology : CB. 2020-08-03; 30.15: 2951-2961.e5.
PMID: 32559443
Espinoza JL, Shah N, Singh S, Nelson KE, Dupont CL
Applications of weighted association networks applied to compositional data in biology.
Environmental microbiology. 2020-08-01; 22.8: 3020-3038.
PMID: 32436334
Kaul D, Rathnasinghe R, Ferres M, Tan GS, Barrera A, Pickett BE, Methe BA, Das SR, Budnik I, Halpin RA, Wentworth D, Schmolke M, Mena I, Albrecht RA, Singh I, Nelson KE, García-Sastre A, Dupont CL, Medina RA
Author Correction: Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection.
Nature communications. 2020-06-16; 11.1: 3132.
PMID: 32546784
Kaul D, Rathnasinghe R, Ferres M, Tan GS, Barrera A, Pickett BE, Methe BA, Das SR, Das S, Budnik I, Halpin RA, Wentworth D, Schmolke M, Mena I, Albrecht RA, Singh I, Nelson KE, García-Sastre A, Dupont CL, Medina RA
Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection.
Nature communications. 2020-05-21; 11.1: 2537.
PMID: 32439901
Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J
Genetic tool development in marine protists: emerging model organisms for experimental cell biology.
Nature methods. 2020-05-01; 17.5: 481-494.
PMID: 32251396
Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J
Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology.
Nature methods. 2020-05-01; 17.5: 551.
PMID: 32296171
Williams MR, Cau L, Wang Y, Kaul D, Sanford JA, Zaramela LS, Khalil S, Butcher AM, Zengler K, Horswill AR, Dupont CL, Hovnanian A, Gallo RL
Interplay of Staphylococcal and Host Proteases Promotes Skin Barrier Disruption in Netherton Syndrome.
Cell reports. 2020-03-03; 30.9: 2923-2933.e7.
PMID: 32130897
O'Rourke A, Beyhan S, Choi Y, Morales P, Chan AP, Espinoza JL, Dupont CL, Meyer KJ, Spoering A, Lewis K, Nierman WC, Nelson KE
Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling.
Antimicrobial agents and chemotherapy. 2020-02-21; 64.3:
PMID: 31907190
Smith SR, Dupont CL, McCarthy JK, Broddrick JT, Oborník M, Horák A, Füssy Z, Cihlář J, Kleessen S, Zheng H, McCrow JP, Hixson KK, Araújo WL, Nunes-Nesi A, Fernie A, Nikoloski Z, Palsson BO, Allen AE
Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom.
Nature communications. 2019-10-07; 10.1: 4552.
PMID: 31591397
Broddrick JT, Du N, Smith SR, Tsuji Y, Jallet D, Ware MA, Peers G, Matsuda Y, Dupont CL, Mitchell BG, Palsson BO, Allen AE
Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum.
The New phytologist. 2019-05-01; 222.3: 1364-1379.
PMID: 30636322
Weiss H, Hertzberg VS, Dupont C, Espinoza JL, Levy S, Nelson K, Norris S, FlyHealthy Research Team
The Airplane Cabin Microbiome.
Microbial ecology. 2019-01-01; 77.1: 87-95.
PMID: 29876609
Espinoza JL, Harkins DM, Torralba M, Gomez A, Highlander SK, Jones MB, Leong P, Saffery R, Bockmann M, Kuelbs C, Inman JM, Hughes T, Craig JM, Nelson KE, Dupont CL
Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease.
mBio. 2018-11-27; 9.6:
PMID: 30482830
Gomez A, Espinoza JL, Harkins DM, Leong P, Saffery R, Bockmann M, Torralba M, Kuelbs C, Kodukula R, Inman J, Hughes T, Craig JM, Highlander SK, Jones MB, Dupont CL, Nelson KE
Host Genetic Control of the Oral Microbiome in Health and Disease.
Cell host & microbe. 2017-09-13; 22.3: 269-278.e3.
PMID: 28910633
Matsuda Y, Hopkinson BM, Nakajima K, Dupont CL, Tsuji Y
Mechanisms of carbon dioxide acquisition and CO2 sensing in marine diatoms: a gateway to carbon metabolism.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 2017-09-05; 372.1728:
PMID: 28717013
McCarthy JK, McCarthy JK, Smith SR, McCrow JP, Tan M, Zheng H, Beeri K, Roth RA, Roth R, Lichtle C, Lichtle C, Goodenough U, Bowler C, Bowler CP, Dupont CL, Dupont CL, Allen AE
Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom.
The Plant cell. 2017-08-01; 29.8: 2047-2070.
PMID: 28765511
Smith SR, Gillard JT, Kustka AB, McCrow JP, Badger JH, Zheng H, New AM, Dupont CL, Obata T, Fernie AR, Allen AE
Correction: Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation.
PLoS genetics. 2017-03-29; 13.3: e1006688.
PMID: 28355217
Llorens-Marès T, Liu Z, Allen LZ, Rusch DB, Craig MT, Dupont CL, Bryant DA, Casamayor EO
Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly.
The ISME journal. 2017-01-01; 11.1: 201-211.
PMID: 27392085
Levering J, Dupont CL, Allen AE, Palsson BO, Zengler K
Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels.
mSystems. 2017-01-01; 2.1:
PMID: 28217746
Smith SR, Gillard JT, Kustka AB, McCrow JP, Badger JH, Zheng H, New AM, Dupont CL, Obata T, Fernie AR, Allen AE
Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation.
PLoS genetics. 2016-12-01; 12.12: e1006490.
PMID: 27973599
Llorens-Marès T, Yooseph S, Goll J, Hoffman J, Vila-Costa M, Borrego CM, Dupont CL, Casamayor EO
Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics.
The ISME journal. 2015-07-01; 9.7: 1648-61.
PMID: 25575307
Dupont CL, McCrow JP, Valas R, Moustafa A, Walworth N, Goodenough U, Roth R, Hogle SL, Bai J, Johnson ZI, Mann E, Palenik B, Barbeau KA, Venter JC, Allen AE
Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities.
The ISME journal. 2015-05-01; 9.5: 1076-92.
PMID: 25333462
Karas BJ, Diner RE, Lefebvre SC, McQuaid J, Phillips AP, Noddings CM, Brunson JK, Valas RE, Deerinck TJ, Jablanovic J, Gillard JT, Beeri K, Ellisman MH, Glass JI, Hutchison CA, Smith HO, Venter JC, Allen AE, Dupont CL, Weyman PD
Designer diatom episomes delivered by bacterial conjugation.
Nature communications. 2015-04-21; 6.6925.
PMID: 25897682
Dupont CL, Larsson J, Yooseph S, Ininbergs K, Goll J, Asplund-Samuelsson J, McCrow JP, Celepli N, Allen LZ, Ekman M, Lucas AJ, Hagström Å, Thiagarajan M, Brindefalk B, Richter AR, Andersson AF, Tenney A, Lundin D, Tovchigrechko A, Nylander JA, Brami D, Badger JH, Allen AE, Rusch DB, Hoffman J, Norrby E, Friedman R, Pinhassi J, Venter JC, Bergman B
Functional tradeoffs underpin salinity-driven divergence in microbial community composition.
PloS one. 2014-02-27; 9.2: e89549.
PMID: 24586863
Karas BJ, Molparia B, Jablanovic J, Hermann WJ, Lin YC, Dupont CL, Tagwerker C, Yonemoto IT, Noskov VN, Chuang RY, Allen AE, Glass JI, Hutchison CA, Smith HO, Venter JC, Weyman PD
Assembly of eukaryotic algal chromosomes in yeast.
Journal of biological engineering. 2013-12-10; 7.1: 30.
PMID: 24325901
McLean JS, Lombardo MJ, Badger JH, Edlund A, Novotny M, Yee-Greenbaum J, Vyahhi N, Hall AP, Yang Y, Dupont CL, Ziegler MG, Chitsaz H, Allen AE, Yooseph S, Tesler G, Pevzner PA, Friedman RM, Nealson KH, Venter JC, Lasken RS
Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.
Proceedings of the National Academy of Sciences of the United States of America. 2013-06-25; 110.26: E2390-9.
PMID: 23754396
Konotchick T, Dupont CL, Valas RE, Badger JH, Allen AE
Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season.
The New phytologist. 2013-04-01; 198.2: 398-407.
PMID: 23488966
Tagwerker C, Dupont CL, Karas BJ, Ma L, Chuang RY, Benders GA, Ramon A, Novotny M, Montague MG, Venepally P, Brami D, Schwartz A, Andrews-Pfannkoch C, Gibson DG, Glass JI, Smith HO, Venter JC, Hutchison CA
Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast.
Nucleic acids research. 2012-11-01; 40.20: 10375-83.
PMID: 22941652
Dupont CL, Rusch DB, Yooseph S, Lombardo MJ, Richter RA, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH, Halpern AL, Lasken RS, Nealson K, Friedman R, Venter JC
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.
The ISME journal. 2012-06-01; 6.6: 1186-99.
PMID: 22170421
Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets.
Nature biotechnology. 2011-09-18; 29.10: 915-21.
PMID: 21926975
Dupont CL, Butcher A, Valas RE, Bourne PE, Caetano-Anollés G
History of biological metal utilization inferred through phylogenomic analysis of protein structures.
Proceedings of the National Academy of Sciences of the United States of America. 2010-06-08; 107.23: 10567-72.
PMID: 20498051
Stuart RK, Dupont CL, Johnson DA, Paulsen IT, Palenik B
Coastal strains of marine Synechococcus species exhibit increased tolerance to copper shock and a distinctive transcriptional response relative to those of open-ocean strains.
Applied and environmental microbiology. 2009-08-01; 75.15: 5047-57.
PMID: 19502430
Todd JD, Curson AR, Dupont CL, Nicholson P, Johnston AW
The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi.
Environmental microbiology. 2009-06-01; 11.6: 1376-85.
PMID: 19220400
Dupont CL, Neupane K, Shearer J, Palenik B
Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases.
Environmental microbiology. 2008-07-01; 10.7: 1831-43.
PMID: 18412551
Dupont CL, Barbeau K, Palenik B
Ni uptake and limitation in marine Synechococcus strains.
Applied and environmental microbiology. 2008-01-01; 74.1: 23-31.
PMID: 17951444
Palenik B, Grimwood J, Aerts A, Rouzé P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, Napoli C, Gendler K, Manuell A, Tai V, Vallon O, Piganeau G, Jancek S, Heijde M, Jabbari K, Bowler C, Lohr M, Robbens S, Werner G, Dubchak I, Pazour GJ, Ren Q, Paulsen I, Delwiche C, Schmutz J, Rokhsar D, Van de Peer Y, Moreau H, Grigoriev IV
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation.
Proceedings of the National Academy of Sciences of the United States of America. 2007-05-01; 104.18: 7705-10.
PMID: 17460045
Dupont CL, Yang S, Palenik B, Bourne PE
Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry.
Proceedings of the National Academy of Sciences of the United States of America. 2006-11-21; 103.47: 17822-7.
PMID: 17098870
Palenik B, Ren Q, Dupont CL, Myers GS, Heidelberg JF, Badger JH, Madupu R, Nelson WC, Brinkac LM, Dodson RJ, Durkin AS, Daugherty SC, Sullivan SA, Khouri H, Mohamoud Y, Halpin R, Paulsen IT
Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment.
Proceedings of the National Academy of Sciences of the United States of America. 2006-09-05; 103.36: 13555-9.
PMID: 16938853

Improving Algal Genetics for Biofuels and Biological Chemical Production

Global Ocean Sampling Expedition (GOS)

Video

Engineering a Mobile Exo-Symbiont for Crop Improvement

Engineering Diatoms to Optimize Production of Desired Products

Nitrifying Archaea and Bacteria

Co-Evolution of Planet and Biota

Diatom Carbon Concentrating Mechanisms

Molecular Toolkit for Diatom Genetic Engineering

Functional Genomic Investigations of Iron and Carbon Cycle Coupling in Select Keystone Marine Bacteria Heterotrophs

Resolving the Bottleneck in Antibiotic Discovery

Using Nature’s Resources for More Sustainable Agriculture

Seeking Funding

Revolutionizing the Future of Dental Care

Video

Seeking Funding

Eliminating Ocean Microplastics with Microbes

Video

Virulence and Drug Resistance of Burkholderia Isolated from ISS

Center for Research on the Respiratory Microbiota of African Children (ReMAC)

Assembly-Enabled Genome-Resolved Examinations of Microbiomes

The Ferret Upper Respiratory Microbiome

Past Project

Signature Infiltration and Maintenance on Plasmid Elements creating a Forensic Microbial System (SIMPLE-FMS)

Past Project

Seasonal Succession in the High Arctic

Past Project
World Oral Health Day 2020
Innovative Research Programs - Microplastics
Global Ocean Sampling: Microplastics
26-May-2020
Press Release

Maintaining a Healthy Upper Respiratory Tract Microbiome May Help Prevent Secondary Infections in Influenza A Patients

An influenza-impacted upper respiratory tract microbiome may invite opportunistic bacterial pathogens

18-Feb-2020
Blog

Characterization of Bacteria from the International Space Station Drinking Water

27-Jun-2019
Blog

Human Microbiome Research has Massive Potential for Health Applications

26-Sep-2018
Blog

Ocean Microplastics Explained

24-May-2018
Collaborator Release

Researchers identify bacteria and viruses ejected from the ocean

Certain types of bacteria and viruses are readily ejected into the atmosphere when waves break while others less likely to be transported into the air