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.

Publications

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 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
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
COVID-19 pandemic reveals the peril of ignoring metadata standards.
Scientific data. 2020-06-19; 7.1: 188.
PMID: 32561801
Intestinal and hepatic microbiota changes associated with chronic ethanol administration in mice.
Gut microbes. 2020-05-03; 11.3: 265-275.
PMID: 30982395
OMeta: an ontology-based, data-driven metadata tracking system.
BMC bioinformatics. 2019-01-07; 20.1: 8.
PMID: 30612540
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
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
Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry.
Journal of bacteriology. 2006-05-01; 188.9: 3402-8.
PMID: 16621835
Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences.
Nucleic acids research. 2006-01-01; 34.3: 5839-51.
PMID: 17062630
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
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

LOCUST

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

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PanOCT

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

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Phage_Finder

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

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Genomics of Non-Tuberculosis Mycobacteria

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GGRaSP

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

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PanACEA

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

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CRACKLE: Carbapenems in Klebsiella pneumoniae and Other Enterobacteriaceae

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Designer Phage

Synthetic Engineering of Bacteriophage for Treatment of Wound Infections

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Chronic Wound Microbiome

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Bacterial Translocation and Changes in the Intestinal Microbiome in Mouse Models of Liver Disease

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Genomic Analysis of Multidrug Resistance in Esbl-Positive and Carbapenem-Resistant Bacterial Pathogens

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Influence of Genetic Variation and AMR in Enterobacter and E. coli Bloodstream Infections (BSI)

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Genomics of Acinetobacter baumannii

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Viral Synthetic Genomics to Engineer Large dsDNA Viruses

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

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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.

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Antimicrobial Resistance from Combat Wounds

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Asymptomatic Bacteriuria: Microbiome and Metaproteome

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

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Leptospira Genomics and Human Health

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

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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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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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Bacteriophage and Antibacterial Resistant Infections
13-Nov-2019
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

09-Jul-2019
Collaborator Release

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

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