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


VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes.
BMC bioinformatics. 2022-10-12; 23.1: 419.
PMID: 36224545
A Silent Operon of Photorhabdus luminescens Encodes a Prodrug Mimic of GTP.
mBio. 2022-06-28; 13.3: e0070022.
PMID: 35575547
Biogeochemical profiling and taxonomic characterization of municipal landfill site by metagenomic sequencing.
Bioresource technology. 2022-05-01; 351.126936.
PMID: 35247565
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
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
Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality.
Science advances. 2021-08-13; 7.33:
PMID: 34389536
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
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
Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach.
PLoS computational biology. 2021-03-29; 17.3: e1008857.
PMID: 33780444
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
Genomic insights into waste valorized extracellular polymeric substances (EPS) produced by Bacillus sp. ISTL8.
Environmental research. 2021-01-01; 192.110277.
PMID: 33069701
Development of an Ocean Protein Portal for Interactive Discovery and Education.
Journal of proteome research. 2021-01-01; 20.1: 326-336.
PMID: 32897077
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
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
Revealing ocean-scale biochemical structure with a deep-diving vertical profiling autonomous vehicle.
Science robotics. 2020-11-25; 5.48:
PMID: 33239321
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
Reprogramming of Stem Cell Activity to Convert Thorns into Branches.
Current biology : CB. 2020-08-03; 30.15: 2951-2961.e5.
PMID: 32559443
Applications of weighted association networks applied to compositional data in biology.
Environmental microbiology. 2020-08-01; 22.8: 3020-3038.
PMID: 32436334
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
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
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
Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling.
Antimicrobial agents and chemotherapy. 2020-02-21; 64.3:
PMID: 31907190
Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom.
Nature communications. 2019-10-07; 10.1: 4552.
PMID: 31591397
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
The Airplane Cabin Microbiome.
Microbial ecology. 2019-01-01; 77.1: 87-95.
PMID: 29876609
Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease.
mBio. 2018-11-27; 9.6:
PMID: 30482830
Host Genetic Control of the Oral Microbiome in Health and Disease.
Cell host & microbe. 2017-09-13; 22.3: 269-278.e3.
PMID: 28910633
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
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
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
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
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
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
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
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
Assembly of eukaryotic algal chromosomes in yeast.
Journal of biological engineering. 2013-12-10; 7.1: 30.
PMID: 24325901
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
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
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
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.
The ISME journal. 2012-06-01; 6.6: 1186-99.
PMID: 22170421
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
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
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
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
Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases.
Environmental microbiology. 2008-07-01; 10.7: 1831-43.
PMID: 18412551
Ni uptake and limitation in marine Synechococcus strains.
Applied and environmental microbiology. 2008-01-01; 74.1: 23-31.
PMID: 17951444
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
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
World Oral Health Day 2020
Innovative Research Programs - Microplastics
Global Ocean Sampling: Microplastics

Top scientists join forces to study leading theory behind long COVID

Several JCVI scientists will be contributing to the newly launched Long Covid Research Initiative — a collaboration of researchers, clinicians, and patients working to rapidly study and treat long Covid.

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

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