Derrick Fouts is a Professor at the Rockville Campus. Dr. Fouts has extensive experience in viral and bacteriophage genomics, bacterial genomics, comparative genomics, and metagenomics of bacterial and viral communities.

Since joining Dr. Karen Nelson's group at TIGR/JCVI in 2001, Dr. Fouts has led several microbial sequencing projects, including animal, plant and human pathogens. Many of these projects were among the first to compare multiple strains. In addition to leading projects, Dr. Fouts has developed various software tools, including applications to perform multi-genome comparisons and heuristic software (Phage Finder) to identify prophage regions in bacterial genomes. He is currently leading the effort to sequence the human virome and reference viral and bacteriophage genomes as part of the NIH sponsored, Human Microbiome Project.

Dr. Fouts received his B.S. degree (1992) in Biology with honors from Indiana University, Bloomington, and his M.S. (1994) and PhD (1997) degrees in Microbiology from the University of Illinois Urbana/Champaign Department of Microbiology. In 1997, he began postdoctoral work in Dr. Alan Collmer's lab at Cornell University.


Intestinal virome in patients with alcohol use disorder and after abstinence.
Hepatology communications. 2022-08-01; 6.8: 2058-2069.
PMID: 35368152
Clinical challenges treating Stenotrophomonas maltophilia infections: an update.
JAC-antimicrobial resistance. 2022-06-01; 4.3: dlac040.
PMID: 35529051
Imipenem/Relebactam Resistance in Clinical Isolates of Extensively Drug Resistant Pseudomonas aeruginosa: Inhibitor-Resistant β-Lactamases and Their Increasing Importance.
Antimicrobial agents and chemotherapy. 2022-05-17; 66.5: e0179021.
PMID: 35435707
Identification and Characterization of vB_PreP_EPr2, a Lytic Bacteriophage of Pan-Drug Resistant Providencia rettgeri.
Viruses. 2022-03-29; 14.4:
PMID: 35458437
Cross-Genus "Boot-Up" of Synthetic Bacteriophage in Staphylococcus aureus by Using a New and Efficient DNA Transformation Method.
Applied and environmental microbiology. 2022-02-08; 88.3: e0148621.
PMID: 34818102
Machine Learning Applied to Omics Datasets Predicts Mortality in Patients with Alcoholic Hepatitis.
Metabolites. 2022-01-05; 12.1:
PMID: 35050163
Intestinal virome and therapeutic potential of bacteriophages in liver disease.
Journal of hepatology. 2021-12-01; 75.6: 1465-1475.
PMID: 34437908
Dynamic Changes of the Fungal Microbiome in Alcohol Use Disorder.
Frontiers in physiology. 2021-07-19; 12.699253.
PMID: 34349667
Apramycin resistance in epidemic carbapenem-resistant Klebsiella pneumoniae ST258 strains.
The Journal of antimicrobial chemotherapy. 2021-07-15; 76.8: 2017-2023.
PMID: 33942093
Intestinal α1-2-Fucosylation Contributes to Obesity and Steatohepatitis in Mice.
Cellular and molecular gastroenterology and hepatology. 2021-02-22; 12.1: 293-320.
PMID: 33631374
Genomic and clinical characterisation of multidrug-resistant carbapenemase-producing ST231 and ST16 Klebsiella pneumoniae isolates colonising patients at Siriraj hospital, Bangkok, Thailand from 2015 to 2017.
BMC infectious diseases. 2021-02-04; 21.1: 142.
PMID: 33541274
A comprehensive and contemporary "snapshot" of β-lactamases in carbapenem resistant Acinetobacter baumannii.
Diagnostic microbiology and infectious disease. 2021-02-01; 99.2: 115242.
PMID: 33248392
Intestinal permeability, microbial translocation, changes in duodenal and fecal microbiota, and their associations with alcoholic liver disease progression in humans.
Gut microbes. 2020-11-09; 12.1: 1782157.
PMID: 32588725
Changes in the fecal bacterial microbiota associated with disease severity in alcoholic hepatitis patients.
Gut microbes. 2020-11-09; 12.1: 1785251.
PMID: 32684075
Intestinal Virome Signature Associated With Severity of Nonalcoholic Fatty Liver Disease.
Gastroenterology. 2020-11-01; 159.5: 1839-1852.
PMID: 32652145
AbGRI4, a novel antibiotic resistance island in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates.
The Journal of antimicrobial chemotherapy. 2020-10-01; 75.10: 2760-2768.
PMID: 32681170
Newly Named Klebsiella aerogenes (formerly Enterobacter aerogenes) Is Associated with Poor Clinical Outcomes Relative to Other Enterobacter Species in Patients with Bloodstream Infection.
Journal of clinical microbiology. 2020-08-24; 58.9:
PMID: 32493786
Monitoring Ceftazidime-Avibactam and Aztreonam Concentrations in the Treatment of a Bloodstream Infection Caused by a Multidrug-Resistant Enterobacter sp. Carrying Both Klebsiella pneumoniae Carbapenemase-4 and New Delhi Metallo-β-Lactamase-1.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2020-08-14; 71.4: 1095-1098.
PMID: 31802119
Intestinal and hepatic microbiota changes associated with chronic ethanol administration in mice.
Gut microbes. 2020-05-03; 11.3: 265-275.
PMID: 30982395
A Novel Mouse Model of Acute-on-Chronic Cholestatic Alcoholic Liver Disease: A Systems Biology Comparison With Human Alcoholic Hepatitis.
Alcoholism, clinical and experimental research. 2020-01-01; 44.1: 87-101.
PMID: 31710124
Ceftazidime-Avibactam in Combination With Fosfomycin: A Novel Therapeutic Strategy Against Multidrug-Resistant Pseudomonas aeruginosa.
The Journal of infectious diseases. 2019-07-19; 220.4: 666-676.
PMID: 31099835
Population Structure, Molecular Epidemiology, and β-Lactamase Diversity among Stenotrophomonas maltophilia Isolates in the United States.
mBio. 2019-07-02; 10.4:
PMID: 31266860
OMeta: an ontology-based, data-driven metadata tracking system.
BMC bioinformatics. 2019-01-07; 20.1: 8.
PMID: 30612540
Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel.
Frontiers in cellular and infection microbiology. 2018-06-19; 8.193.
PMID: 29971217
Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus.
Nature communications. 2017-10-16; 8.1: 837.
PMID: 29038503
HSV-1 clinical isolates with unique in vivo and in vitro phenotypes and insight into genomic differences.
Journal of neurovirology. 2017-04-01; 23.2: 171-185.
PMID: 27739035
Intestinal REG3 Lectins Protect against Alcoholic Steatohepatitis by Reducing Mucosa-Associated Microbiota and Preventing Bacterial Translocation.
Cell host & microbe. 2016-02-10; 19.2: 227-39.
PMID: 26867181
Supplementation of saturated long-chain fatty acids maintains intestinal eubiosis and reduces ethanol-induced liver injury in mice.
Gastroenterology. 2015-01-01; 148.1: 203-214.e16.
PMID: 25239591
Next generation sequencing technologies and the changing landscape of phage genomics.
Bacteriophage. 2012-07-01; 2.3: 190-199.
PMID: 23275870
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
Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice.
PLoS genetics. 2008-07-25; 4.7: e1000141.
PMID: 18654632
Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus-group plasmids, including Bacillus anthracis pXO1.
Journal of bacteriology. 2007-01-01; 189.1: 52-64.
PMID: 17041058
Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences.
Nucleic acids research. 2006-10-24; 34.20: 5839-51.
PMID: 17062630
Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry.
Journal of bacteriology. 2006-05-01; 188.9: 3402-8.
PMID: 16621835
Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain.
Journal of bacteriology. 2005-04-01; 187.7: 2426-38.
PMID: 15774886
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
Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83.
Journal of bacteriology. 2003-09-01; 185.18: 5591-601.
PMID: 12949112
A pseudomonas syringae pv. tomato DC3000 Hrp (Type III secretion) deletion mutant expressing the Hrp system of bean pathogen P. syringae pv. syringae 61 retains normal host specificity for tomato.
Molecular plant-microbe interactions : MPMI. 2003-01-01; 16.1: 43-52.
PMID: 12580281
Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor.
Proceedings of the National Academy of Sciences of the United States of America. 2002-02-19; 99.4: 2275-80.
PMID: 11854524
Translationally repressive RNA structures monitored in vivo using temperate DNA bacteriophages.
Gene. 1998-03-27; 210.1: 135-42.
PMID: 9524249
Functional recognition of fragmented operator sites by R17/MS2 coat protein, a translational repressor.
Nucleic acids research. 1997-11-15; 25.22: 4464-73.
PMID: 9358153
Site-specific phosphorylation of the human immunodeficiency virus type-1 Rev protein accelerates formation of an efficient RNA-binding conformation.
Biochemistry. 1997-10-28; 36.43: 13256-62.
PMID: 9341215
Improved method for selecting RNA-binding activities in vivo.
Nucleic acids research. 1996-04-15; 24.8: 1582-4.
PMID: 8628698


A custom sequence locus typer for classifying microbial genotypic and phenotypic attributes.


PanOCT is a program written in PERL for pan-genomic analysis of closely related prokaryotic species or strains.


Phage_Finder is a heuristic computer program written in PERL to identify prophage regions within bacterial genomes.


An R-package for selecting representative genomes using Gaussian mixture models.


PanACEA is a tool for Pan-Genome visualization, which utilizes locally-computed interactive web-pages to view ordered pan-genome data.

Designer Phage

Synthetic Engineering of Bacteriophage for Treatment of Wound Infections


Viral Synthetic Genomics to Engineer Large dsDNA Viruses

Rapid engineering of large dsDNA viruses using synthetic genomics assembly tools.

Genomics, Biomarkers and Mechanisms of Healing in Chronic Wounds

Utilize genomics approaches to identify the microbial composition and functional elements in non-healing and chronic wounds.

Asymptomatic Bacteriuria: Microbiome and Metaproteome

We use genomics approaches to detect the presence of bacteria with known inflammatory responses in asymptomatic patients. 

Vaginal Microbiome Project

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

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.

Bacteriophage and Antibacterial Resistant Infections
Press Release

J. Craig Venter Institute and UC San Diego Develop Phage Treatment as Potential Cure for Alcoholic Liver Disease

Team targeted specific toxin-producing strains of the bacterium, Enterococcus faecalis, which is shown to be responsible for most liver damage

Collaborator Release

Combining Antibiotics, Researchers Deliver One-Two Punch against Ubiquitous Bacterium

CWRU/Cleveland VA findings in mouse models could make inroads against superbugs