Chris Dupont is an Associate Professor in the Microbial and Environmental Genomics group 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.

Dr. Dupont is also working on applying synthetic biology and machine learning techniques to solve unique problems in big dataset 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

Genomic insights into waste valorized extracellular polymeric substances (EPS) produced by Bacillus sp. ISTL8.
Environmental research. 2020-10-16; 192.110277.
PMID: 33069701
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. 2020-09-23;
PMID: 32897080
Development of an Ocean Protein Portal for Interactive Discovery and Education.
Journal of proteome research. 2020-09-08;
PMID: 32897077
Bidirectional C and N transfer and a potential role for sulfur in an epiphytic diazotrophic mutualism.
The ISME journal. 2020-08-19;
PMID: 32814866
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
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
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
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
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
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
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
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.
The ISME journal. 2012-06-01; 6.6: 1186-99.
PMID: 22170421
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

Nitrifying Archaea and Bacteria

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Global Ocean Sampling Expedition (GOS)

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Engineering Diatoms to Optimize Production of Desired Products

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Engineering a Mobile Exo-Symbiont for Crop Improvement

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Molecular Toolkit for Diatom Genetic Engineering

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Diatom Carbon Concentrating Mechanisms

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Co-Evolution of Planet and Biota

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Resolving the Bottleneck in Antibiotic Discovery

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Using Nature’s Resources for More Sustainable Agriculture

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Revolutionizing the Future of Dental Care

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Eliminating Ocean Microplastics with Microbes

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Virulence and Drug Resistance of Burkholderia Isolated from ISS

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

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Assembly-Enabled Genome-Resolved Examinations of Microbiomes

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The Ferret Upper Respiratory Microbiome

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

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Seasonal Succession in the High Arctic

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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

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