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Chris Dupont is a 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.
Related Information
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
Publications
BMC microbiology. 2025-12-12; 26.1: 34.
Environmental and skin-nasal microbiome variation in South African children with atopic dermatitis
The Journal of infectious diseases. 2025-09-30;
Blood cultures contain populations of genetically diverse Candida albicans strains that may differ in echinocandin tolerance and fitness
The Lancet. Infectious diseases. 2025-05-01; 25.5: e294-e306.
Targeting the SARS-CoV-2 reservoir in long COVID
Stroke. 2024-10-01; 55.10: e266-e268.
Unveiling Molecular Diversity in Cerebral Thrombi via Spatial Transcriptomics
mBio. 2024-08-14; 15.8: e0003824.
Marine bacteria Alteromonas spp. require UDP-glucose-4-epimerase for aggregation and production of sticky exopolymer
Nucleic acids research. 2024-08-12; 52.14: e63.
Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing
Frontiers in public health. 2024-08-09; 12.1399731.
Whole-genome sequencing-based genetic diversity, transmission dynamics, and drug-resistant mutations in Mycobacterium tuberculosis isolated from extrapulmonary tuberculosis patients in western Ethiopia
PloS one. 2024-07-25; 19.7: e0304060.
Pangenome and genomic signatures linked to the dominance of the lineage-4 of Mycobacterium tuberculosis isolated from extrapulmonary tuberculosis patients in western Ethiopia
PNAS nexus. 2024-04-01; 3.4: pgae126.
Host-microbiome associations in saliva predict COVID-19 severity
Science (New York, N.Y.). 2024-03-22; 383.6689: 1344-1349.
Efficient formation of single-copy human artificial chromosomes
The ISME journal. 2024-01-08; 18.1:
Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron
Environmental microbiology. 2023-12-01; 25.12: 2761-2775.
Plastics select for distinct early colonizing microbial populations with reproducible traits across environmental gradients
ACS synthetic biology. 2023-11-17; 12.11: 3215-3228.
Validating a Promoter Library for Application in Plasmid-Based Diatom Genetic Engineering
Molecular biology and evolution. 2023-10-04; 40.10:
Genus-Wide Transcriptional Landscapes Reveal Correlated Gene Networks Underlying Microevolutionary Divergence in Diatoms
Cold Spring Harbor perspectives in biology. 2023-10-03;
Microbial Catalysis for CO2 Sequestration: A Geobiological Approach
Nature immunology. 2023-10-01; 24.10: 1778.
Author Correction: SARS-CoV-2 reservoir in post-acute sequelae of COVID-19 (PASC)
Nature immunology. 2023-10-01; 24.10: 1616-1627.
SARS-CoV-2 reservoir in post-acute sequelae of COVID-19 (PASC)
Nature communications. 2023-09-22; 14.1: 5918.
Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures
PloS one. 2023-08-03; 18.8: e0289557.
Comparison of DNA concentration and bacterial pathogen PCR detection when using two DNA extraction kits for nasopharyngeal/oropharyngeal samples
Cell reports. 2023-05-30; 42.5: 112494.
Competition between skin antimicrobial peptides and commensal bacteria in type 2 inflammation enables survival of S. aureus
PNAS nexus. 2022-11-01; 1.5: pgac239.
Differential network analysis of oral microbiome metatranscriptomes identifies community scale metabolic restructuring in dental caries
BMC bioinformatics. 2022-10-12; 23.1: 419.
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
Proceedings of the National Academy of Sciences of the United States of America. 2022-09-13; 119.37: e2200014119.
Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean
mBio. 2022-06-28; 13.3: e0070022.
A Silent Operon of Photorhabdus luminescens Encodes a Prodrug Mimic of GTP
Bioresource technology. 2022-05-01; 351.126936.
Biogeochemical profiling and taxonomic characterization of municipal landfill site by metagenomic sequencing
The ISME journal. 2022-02-01; 16.2: 358-369.
Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean
EBioMedicine. 2021-11-01; 73.103644.
Interactions between fecal gut microbiome, enteric pathogens, and energy regulating hormones among acutely malnourished rural Gambian children
Science advances. 2021-08-13; 7.33:
Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality
BMC infectious diseases. 2021-04-13; 21.1: 348.
Molecular epidemiology of Staphylococcus aureus in African children from rural and urban communities with atopic dermatitis
Nature biotechnology. 2021-04-01; 39.4: 499-509.
A genomic catalog of Earth's microbiomes
The ISME journal. 2021-04-01; 15.4: 1025-1039.
Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions
Nature biotechnology. 2021-04-01; 39.4: 520.
Publisher Correction: A genomic catalog of Earth's microbiomes
Nature biotechnology. 2021-04-01; 39.4: 521.
Author Correction: A genomic catalog of Earth's microbiomes
PLoS computational biology. 2021-03-29; 17.3: e1008857.
Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach
Nature microbiology. 2021-02-01; 6.2: 173-186.
Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean
Journal of proteome research. 2021-01-01; 20.1: 326-336.
Development of an Ocean Protein Portal for Interactive Discovery and Education
Environmental research. 2021-01-01; 192.110277.
Genomic insights into waste valorized extracellular polymeric substances (EPS) produced by Bacillus sp. ISTL8
The ISME journal. 2020-12-01; 14.12: 3068-3078.
Bidirectional C and N transfer and a potential role for sulfur in an epiphytic diazotrophic mutualism
Microbial genomics. 2020-12-01; 6.12:
Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients
Science robotics. 2020-11-25; 5.48:
Revealing ocean-scale biochemical structure with a deep-diving vertical profiling autonomous vehicle
Journal of proteome research. 2020-11-06; 19.11: 4718-4729.
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
Current biology : CB. 2020-08-03; 30.15: 2951-2961.e5.
Reprogramming of Stem Cell Activity to Convert Thorns into Branches
Environmental microbiology. 2020-08-01; 22.8: 3020-3038.
Applications of weighted association networks applied to compositional data in biology
Nature communications. 2020-06-16; 11.1: 3132.
Author Correction: Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection
Nature communications. 2020-05-21; 11.1: 2537.
Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection
Nature methods. 2020-05-01; 17.5: 481-494.
Genetic tool development in marine protists: emerging model organisms for experimental cell biology
Nature methods. 2020-05-01; 17.5: 551.
Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology
Cell reports. 2020-03-03; 30.9: 2923-2933.e7.
Interplay of Staphylococcal and Host Proteases Promotes Skin Barrier Disruption in Netherton Syndrome
Antimicrobial agents and chemotherapy. 2020-02-21; 64.3:
Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling
PloS one. 2020-02-19; 15.2: e0227152.
Genomic and phenotypic characterization of Burkholderia isolates from the potable water system of the International Space Station
Synthetic biology (Oxford, England). 2020-02-05; 5.1: ysaa001.
Universal loop assembly: open, efficient and cross-kingdom DNA fabrication
mSphere. 2020-01-29; 5.1:
Influence of Substrate Concentration on the Culturability of Heterotrophic Soil Microbes Isolated by High-Throughput Dilution-to-Extinction Cultivation
Nature communications. 2019-10-07; 10.1: 4552.
Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom
The New phytologist. 2019-05-01; 222.3: 1364-1379.
Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum
Annual review of marine science. 2019-01-03; 11.131-158.
Planktonic Marine Archaea
Microbial ecology. 2019-01-01; 77.1: 87-95.
The Airplane Cabin Microbiome
mBio. 2018-11-27; 9.6:
Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease
Nature communications. 2018-05-22; 9.1: 2017.
Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm
Molecular biology and evolution. 2018-05-01; 35.5: 1160-1175.
Genomic Changes Associated with the Evolutionary Transitions of Nostoc to a Plant Symbiont
Cell host & microbe. 2017-09-13; 22.3: 269-278.e3.
Host Genetic Control of the Oral Microbiome in Health and Disease
Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 2017-09-05; 372.1728:
Mechanisms of carbon dioxide acquisition and CO2 sensing in marine diatoms: a gateway to carbon metabolism
The Plant cell. 2017-08-01; 29.8: 2047-2070.
Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom
Proceedings of the National Academy of Sciences of the United States of America. 2017-07-18; 114.29: E6015-E6024.
Diatom centromeres suggest a mechanism for nuclear DNA acquisition
Journal of experimental botany. 2017-06-01; 68.14: 3937-3948.
The diversity of CO2-concentrating mechanisms in marine diatoms as inferred from their genetic content
Frontiers in microbiology. 2017-05-30; 8.949.
Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond
PLoS genetics. 2017-03-29; 13.3: e1006688.
Correction: Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation
The ISME journal. 2017-01-01; 11.1: 201-211.
Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly
mSystems. 2017-01-01; 2.1:
Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels
PLoS genetics. 2016-12-01; 12.12: e1006490.
Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation
Frontiers in microbiology. 2016-07-06; 7.1043.
Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem
The ISME journal. 2015-07-01; 9.7: 1648-61.
Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics
The ISME journal. 2015-05-01; 9.5: 1076-92.
Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities
Nature communications. 2015-04-21; 6.6925.
Designer diatom episomes delivered by bacterial conjugation
PloS one. 2014-02-27; 9.2: e89549.
Functional tradeoffs underpin salinity-driven divergence in microbial community composition
Journal of biological engineering. 2013-12-10; 7.1: 30.
Assembly of eukaryotic algal chromosomes in yeast
Proceedings of the National Academy of Sciences of the United States of America. 2013-06-25; 110.26: E2390-9.
Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum
The New phytologist. 2013-04-01; 198.2: 398-407.
Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season
Nucleic acids research. 2012-11-01; 40.20: 10375-83.
Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast
The ISME journal. 2012-06-01; 6.6: 1186-99.
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage
Nature biotechnology. 2011-09-18; 29.10: 915-21.
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets
Proceedings of the National Academy of Sciences of the United States of America. 2011-03-08; 108.10: 3830-7.
Efficiency of the CO2-concentrating mechanism of diatoms
Proceedings of the National Academy of Sciences of the United States of America. 2010-06-08; 107.23: 10567-72.
History of biological metal utilization inferred through phylogenomic analysis of protein structures
Applied and environmental microbiology. 2009-08-01; 75.15: 5047-57.
Coastal strains of marine Synechococcus species exhibit increased tolerance to copper shock and a distinctive transcriptional response relative to those of open-ocean strains
Environmental microbiology. 2009-06-01; 11.6: 1376-85.
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. 2008-07-01; 10.7: 1831-43.
Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases
Applied and environmental microbiology. 2008-01-01; 74.1: 23-31.
Ni uptake and limitation in marine Synechococcus strains
Proceedings of the National Academy of Sciences of the United States of America. 2007-05-01; 104.18: 7705-10.
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. 2006-11-21; 103.47: 17822-7.
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. 2006-09-05; 103.36: 13555-9.
Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment
Projects
Center for Innovative Recycling and Circular Economy
CIRCLE will focus on addressing the pressing issues of air pollution reduction, agricultural and food waste treatment, and plastic waste disposal through disruptive solutions—challenges that transcend national borders and require a multidisciplinary approach.Video
News
J. Craig Venter Institute awarded 5-year, $5M grant to lead Center for Innovative Recycling and Circular Economy (CIRCLE)
CIRCLE is one of the six new NSF Global Centers focused on advancing bioeconomy research to solve global challenges
Groundbreaking study reveals oral microbiome’s role in immune response and COVID-19 severity
Newly developed AI model shows that saliva is a better predictor of COVID-19 severity than existing blood tests
Scientists develop method to efficiently construct single-copy human artificial chromosomes (HACs)
This new tool will allow scientists to work in mammalian systems in ways only previously available in bacteria and yeast
HACs have wide potential research applications to synthetic biologists and may eventually aid in delivering DNA in clinical applications
New LongCOVID research launched by PolyBio’s global consortium of scientists
Funding will deepen research on the persistence of the SARS-CoV-2 virus in LongCOVID patients and launch new clinical trials
PolyBio Research Foundation Consortium & colleagues publishes Nature position paper on SARS-CoV-2 reservoir in Long COVID/PASC
What are the Drivers of Chronic Infectious Disease?
A $1 million grant from the Steven & Alexandra Cohen Foundation will launch a UC San Diego-led national effort to more deeply study tissue samples from patients with conditions ranging from long COVID-19 and relapsed Lyme disease to chronic fatigue syndrome
The Tissue Analysis Pipeline will be directed by scientists at UC San Diego and the J. Craig Venter Institute
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.
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
Ocean Microplastics Explained
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