Karen E. Nelson, Ph.D. is the President of the J. Craig Venter Institute (JCVI). Prior to being appointed President, she held a number of other positions at the Institute, including Director of JCVI's Rockville Campus, and Director of Human Microbiology and Metagenomics in the Department of Human Genomic Medicine at JCVI. Dr. Nelson received her undergraduate degree from the University of the West Indies, and her Ph.D. from Cornell University. She has authored or co-authored over 200 peer reviewed publications, edited three books, and is currently Editor-in-Chief of the journal Microbial Ecology.

Dr. Nelson is an elected member of the National Academy of Sciences. Other honors include being named ARCS Scientist of the Year 2017; a Fellow of the American Academy of Microbiology; being inducted into the Indian National Academy of Sciences in 2018; and being appointed an Honorary Professor at the University of the West Indies as well as a Helmholtz International Fellow.

Dr. Nelson has extensive experience in microbial ecology, microbial genomics, microbial physiology and metagenomics. Dr. Nelson has led several genomic and metagenomic efforts, and led the first human metagenomics study that was published in 2006. Additional ongoing studies in her group include metagenomic approaches to study the ecology of the gastrointestinal tract of humans and animals, studies on the relationship between the microbiome and various human and animal disease conditions, reference genome sequencing and analysis primarily for the human body, and other -omics studies.

Research Priorities

Microbiome in health and disease
  • Interrogating microbiome profiles and host microbe interactions
Emergence of Antimicrobial Resistance
  • Understanding the intricate play between infectious species, gene transfer and the emergence of resistance
Understanding Resistance mechanisms in microbial species
  • Deep investigations into how microbes respond to different types of drugs
Identification of novel species
  • In different environments including the oral cavity, plants, and artic sediments

Publications

An unsupervised learning approach to identify novel signatures of health and disease from multimodal data.
Genome medicine. 2020-01-10; 12.1: 7.
PMID: 31924279
Microbial metagenome of urinary tract infection.
Scientific reports. 2018-03-12; 8.1: 4333.
PMID: 29531289
Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease.
Clinical and translational gastroenterology. 2018-01-18; 9.1: e132.
PMID: 29345635
Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.
Cell metabolism. 2017-05-02; 25.5: 1054-1062.e5.
PMID: 28467925
Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies.
BMC genomics. 2017-04-13; 18.1: 296.
PMID: 28407798
The Human Microbiome and Cancer.
Cancer prevention research (Philadelphia, Pa.). 2017-04-01; 10.4: 226-234.
PMID: 28096237
The blood DNA virome in 8,000 humans.
PLoS pathogens. 2017-03-22; 13.3: e1006292.
PMID: 28328962
A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome.
Scientific reports. 2016-08-25; 6.31731.
PMID: 27558918
Library preparation methodology can influence genomic and functional predictions in human microbiome research.
Proceedings of the National Academy of Sciences of the United States of America. 2015-11-10; 112.45: 14024-9.
PMID: 26512100
Microbiome analysis of stool samples from African Americans with colon polyps.
PloS one. 2013-01-01; 8.12: e81352.
PMID: 24376500
Microbiome in human health and disease.
Science progress. 2013-01-01; 96.Pt 2: 153-70.
PMID: 23901633
Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes.
Proceedings of the National Academy of Sciences of the United States of America. 2012-06-19; 109.25: 9692-8.
PMID: 22615407
Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease.
Journal of hepatology. 2012-06-01; 56.6: 1283-92.
PMID: 22326468
Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.
BMC bioinformatics. 2012-03-19; 13.42.
PMID: 22429538
Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis.
BMC genomics. 2010-09-07; 11.488.
PMID: 20819230
Bacterial diversity in the oral cavity of 10 healthy individuals.
The ISME journal. 2010-08-01; 4.8: 962-74.
PMID: 20336157
Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus.
Journal of bacteriology. 2008-08-01; 190.15: 5455-63.
PMID: 18556790
Population diversity and dynamics of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis in the upper respiratory tracts of adults, determined by a nonculture strategy.
Infection and immunity. 2008-05-01; 76.5: 1889-96.
PMID: 18316382
Metagenomic analysis of the human distal gut microbiome.
Science (New York, N.Y.). 2006-06-02; 312.5778: 1355-9.
PMID: 16741115
Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences.
Journal of bacteriology. 2006-04-01; 188.7: 2364-74.
PMID: 16547022
Molecular analysis of the bacterial microbiota in the human stomach.
Proceedings of the National Academy of Sciences of the United States of America. 2006-01-17; 103.3: 732-7.
PMID: 16407106
Diversity of the human intestinal microbial flora.
Science (New York, N.Y.). 2005-06-10; 308.5728: 1635-8.
PMID: 15831718
Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species.
PLoS biology. 2005-01-01; 3.1: e15.
PMID: 15660156

Research Priorities

Microbiome in health and disease
  • Interrogating microbiome profiles and host microbe interactions
Emergence of Antimicrobial Resistance
  • Understanding the intricate play between infectious species, gene transfer and the emergence of resistance
Understanding Resistance mechanisms in microbial species
  • Deep investigations into how microbes respond to different types of drugs
Identification of novel species
  • In different environments including the oral cavity, plants, and artic sediments

Identifying Healthy Aging Biomarkers

This study aims to identify specific biomarkers that correlate with longevity and healthy aging using genomics and proteomics approaches.

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Characterizing the Microbial Communities in Caribbean Environments

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Gut Microbiome Sysbiosis in Childhood Acute Lymphoblastic Leukemia (ALL) Patients

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Effect of Xylitol Consumption on the Oral Microbiome

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Leonardo da Vinci DNA Project

This project utilizes genomics approaches to confirm the identity of the remains purported to be that of Leonardo da Vinci as well as to characterize the microbial population on aging artwork.

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Relationship Between the Oral Microbiome and Caries Status of Young Twins

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Proteomics for UTI diagnosis

Understanding host-pathogen interactions is critical when it comes to improving diagnostic approaches to urinary tract infections. 

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Human Microbiome Project

The Human Microbiome Project involves characterizing human microbial isolates using whole genome shotgun sequencing.

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Understanding Dissemination Routes of Antibiotic Resistance During Early Life

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Zoo in You Traveling Exhibition

Our bodies are home to trillions of bacteria. This project provides an education resource to middle and high school aged children who are interested in science and medicine.

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

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Human Hair Microbiota

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Comprehensive Genome Sequencing of Nontyphoidal Salmonellae

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Genome Sequencing of Atypical Disease-associated and Emerging Infectious Disease Isolates of C. Jejuni, and Related Species

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The Nasopharynx Microbiome and Pneumococcal Vaccination in Filipino and South African Infants

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Gut Microbiome-Based Metagenomic Signature for Detection of Advanced Fibrosis in Nonalcoholic Fatty Liver Disease

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Progression of Esophageal Cancer

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Seasonal Succession in the High Arctic

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Transmission Kinetics of RSV Infection

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Howler Monkey Microbiome

Gastrointestinal microbial community composition and habitat structure in howler monkeys (Alouatta pigra).

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Vervet Microbiome

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Western Lowland Gorilla Microbiome

The gastrointestinal microbiota composition and function of free range wild Western Lowland Gorillas mirrors macro-ecological patterns.

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Vaginal Microbiome Project

A metagenomics approach to understanding the relationship between the vaginal microbiome, bacterial vaginosis, vaginal health and preterm birth.

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Mouse Microbiome

Enteric dysbiosis associated with a mouse model of alcoholic liver disease. The translocation of bacteria and bacterial products into the circulation contributes to alcoholic liver disease.

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Bovine Rumen Microbiome

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The Montastraea faveolata Microbiome

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Coral Pathogen Vibrio coralliilyticus

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Bottlenose Dolphin Microbiome

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Chicken Cecum Microbiome

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