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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
PLoS pathogens. 2024-08-23; 20.8: e1012495.
Fitness factor genes conserved within the multi-species core genome of Gram-negative Enterobacterales species contribute to bacteremia pathogenesis
PloS one. 2024-07-29; 19.7: e0307968.
Serum susceptibility of Escherichia coli and its association with patient clinical outcomes
Gut microbes. 2024-02-01; 16.1: 2307586.
Fungal signature differentiates alcohol-associated liver disease from nonalcoholic fatty liver disease
BMC infectious diseases. 2023-08-28; 23.1: 556.
Characteristics and genomic epidemiology of colistin-resistant Enterobacterales from farmers, swine, and hospitalized patients in Thailand, 2014-2017
Journal of clinical microbiology. 2023-07-20; 61.7: e0019923.
Escherichia coli ST131 Associated with Increased Mortality in Bloodstream Infections from Urinary Tract Source
Hepatology (Baltimore, Md.). 2023-06-01; 77.6: 2073-2083.
Any alcohol use in NAFLD patients is associated with significant changes to the intestinal virome
Hepatology communications. 2023-02-01; 7.2: e0029.
Malassezia restricta promotes alcohol-induced liver injury
Antibiotics (Basel, Switzerland). 2022-11-19; 11.11:
Design of a Bacteriophage Cocktail Active against Shigella Species and Testing of Its Therapeutic Potential in Galleria mellonella
Hepatology communications. 2022-08-01; 6.8: 2058-2069.
Intestinal virome in patients with alcohol use disorder and after abstinence
JAC-antimicrobial resistance. 2022-06-01; 4.3: dlac040.
Clinical challenges treating Stenotrophomonas maltophilia infections: an update
Antimicrobial agents and chemotherapy. 2022-05-17; 66.5: e0179021.
Imipenem/Relebactam Resistance in Clinical Isolates of Extensively Drug Resistant Pseudomonas aeruginosa: Inhibitor-Resistant β-Lactamases and Their Increasing Importance
Journal of hepatology. 2022-04-01; 76.4: 788-799.
The fecal mycobiome in non-alcoholic fatty liver disease
Viruses. 2022-03-29; 14.4:
Identification and Characterization of vB_PreP_EPr2, a Lytic Bacteriophage of Pan-Drug Resistant Providencia rettgeri
Applied and environmental microbiology. 2022-02-08; 88.3: e0148621.
Cross-Genus "Boot-Up" of Synthetic Bacteriophage in Staphylococcus aureus by Using a New and Efficient DNA Transformation Method
Metabolites. 2022-01-05; 12.1:
Machine Learning Applied to Omics Datasets Predicts Mortality in Patients with Alcoholic Hepatitis
Journal of hepatology. 2021-12-01; 75.6: 1465-1475.
Intestinal virome and therapeutic potential of bacteriophages in liver disease
Frontiers in physiology. 2021-07-19; 12.699253.
Dynamic Changes of the Fungal Microbiome in Alcohol Use Disorder
The Journal of antimicrobial chemotherapy. 2021-07-15; 76.8: 2017-2023.
Apramycin resistance in epidemic carbapenem-resistant Klebsiella pneumoniae ST258 strains
Cellular and molecular gastroenterology and hepatology. 2021-02-22; 12.1: 293-320.
Intestinal α1-2-Fucosylation Contributes to Obesity and Steatohepatitis in Mice
BMC infectious diseases. 2021-02-04; 21.1: 142.
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
Diagnostic microbiology and infectious disease. 2021-02-01; 99.2: 115242.
A comprehensive and contemporary "snapshot" of β-lactamases in carbapenem resistant Acinetobacter baumannii
Hepatology (Baltimore, Md.). 2020-12-01; 72.6: 2182-2196.
Intestinal Virome in Patients With Alcoholic Hepatitis
Gut microbes. 2020-11-09; 12.1: 1782157.
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: 1785251.
Changes in the fecal bacterial microbiota associated with disease severity in alcoholic hepatitis patients
Gastroenterology. 2020-11-01; 159.5: 1839-1852.
Intestinal Virome Signature Associated With Severity of Nonalcoholic Fatty Liver Disease
The Journal of antimicrobial chemotherapy. 2020-10-01; 75.10: 2760-2768.
AbGRI4, a novel antibiotic resistance island in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates
Journal of clinical microbiology. 2020-08-24; 58.9:
Newly Named Klebsiella aerogenes (formerly Enterobacter aerogenes) Is Associated with Poor Clinical Outcomes Relative to Other Enterobacter Species in Patients with Bloodstream Infection
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2020-08-14; 71.4: 1095-1098.
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
Gut microbes. 2020-05-03; 11.3: 265-275.
Intestinal and hepatic microbiota changes associated with chronic ethanol administration in mice
Antimicrobial agents and chemotherapy. 2020-04-21; 64.5:
ARGONAUT II Study of the In Vitro Activity of Plazomicin against Carbapenemase-Producing Klebsiella pneumoniae
Microbiology resource announcements. 2020-04-16; 9.16:
Complete Genome Sequence of Staphylococcus aureus Phage SA75, Isolated from Goat Feces
Hepatology (Baltimore, Md.). 2020-02-01; 71.2: 522-538.
Intestinal Fungal Dysbiosis and Systemic Immune Response to Fungi in Patients With Alcoholic Hepatitis
Alcoholism, clinical and experimental research. 2020-01-01; 44.1: 87-101.
A Novel Mouse Model of Acute-on-Chronic Cholestatic Alcoholic Liver Disease: A Systems Biology Comparison With Human Alcoholic Hepatitis
Nature. 2019-11-13; 575.7783: 505-511.
Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease
The Journal of infectious diseases. 2019-07-19; 220.4: 666-676.
Ceftazidime-Avibactam in Combination With Fosfomycin: A Novel Therapeutic Strategy Against Multidrug-Resistant Pseudomonas aeruginosa
mBio. 2019-07-02; 10.4:
Population Structure, Molecular Epidemiology, and β-Lactamase Diversity among Stenotrophomonas maltophilia Isolates in the United States
mSphere. 2019-03-13; 4.2:
Emergence of New Delhi Metallo-β-Lactamase (NDM-5) in Klebsiella quasipneumoniae from Neonates in a Nigerian Hospital
BMC bioinformatics. 2019-01-07; 20.1: 8.
OMeta: an ontology-based, data-driven metadata tracking system
BMC bioinformatics. 2018-06-27; 19.1: 246.
PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes
Frontiers in cellular and infection microbiology. 2018-06-19; 8.193.
Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel
Nature communications. 2017-10-16; 8.1: 837.
Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus
The Journal of clinical investigation. 2017-06-30; 127.7: 2829-2841.
Intestinal fungi contribute to development of alcoholic liver disease
Journal of neurovirology. 2017-04-01; 23.2: 171-185.
HSV-1 clinical isolates with unique in vivo and in vitro phenotypes and insight into genomic differences
PLoS neglected tropical diseases. 2016-02-18; 10.2: e0004403.
What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira
Cell host & microbe. 2016-02-10; 19.2: 227-39.
Intestinal REG3 Lectins Protect against Alcoholic Steatohepatitis by Reducing Mucosa-Associated Microbiota and Preventing Bacterial Translocation
Genome announcements. 2015-01-22; 3.1:
Genome Sequences of the Listeria ivanovii subsp. ivanovii Type Strain and Two Listeria ivanovii subsp. londoniensis Strains
Gastroenterology. 2015-01-01; 148.1: 203-214.e16.
Supplementation of saturated long-chain fatty acids maintains intestinal eubiosis and reduces ethanol-induced liver injury in mice
Pathogens (Basel, Switzerland). 2014-04-10; 3.2: 280-308.
Leptospiral pathogenomics
Bacteriophage. 2012-07-01; 2.3: 190-199.
Next generation sequencing technologies and the changing landscape of phage genomics
Journal of hepatology. 2012-06-01; 56.6: 1283-92.
Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease
Archives of virology. 2011-01-01; 156.1: 25-35.
Clostridium perfringens bacteriophages ΦCP39O and ΦCP26F: genomic organization and proteomic analysis of the virions
PLoS genetics. 2008-07-25; 4.7: e1000141.
Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice
Journal of bacteriology. 2007-01-01; 189.1: 52-64.
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
Nucleic acids research. 2006-10-24; 34.20: 5839-51.
Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences
Journal of bacteriology. 2006-05-01; 188.9: 3402-8.
Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry
Journal of bacteriology. 2005-04-01; 187.7: 2426-38.
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
PLoS biology. 2005-01-04; 3.1: e15.
Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species
PLoS biology. 2004-10-01; 2.10: e303.
Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)
Nucleic acids research. 2004-04-28; 32.8: 2386-95.
Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species
Science (New York, N.Y.). 2004-04-02; 304.5667: 66-74.
Environmental genome shotgun sequencing of the Sargasso Sea
Journal of bacteriology. 2003-09-01; 185.18: 5591-601.
Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83
Nature. 2003-05-01; 423.6935: 81-6.
The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria
Molecular plant-microbe interactions : MPMI. 2003-01-01; 16.1: 43-52.
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
Proceedings of the National Academy of Sciences of the United States of America. 2002-02-19; 99.4: 2275-80.
Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor
Gene. 1998-03-27; 210.1: 135-42.
Translationally repressive RNA structures monitored in vivo using temperate DNA bacteriophages
Nucleic acids research. 1997-11-15; 25.22: 4464-73.
Functional recognition of fragmented operator sites by R17/MS2 coat protein, a translational repressor
Biochemistry. 1997-10-28; 36.43: 13256-62.
Site-specific phosphorylation of the human immunodeficiency virus type-1 Rev protein accelerates formation of an efficient RNA-binding conformation
Nucleic acids research. 1996-04-15; 24.8: 1582-4.
Improved method for selecting RNA-binding activities in vivo
PanOCT
PanOCT is a program written in PERL for pan-genomic analysis of closely related prokaryotic species or strains.
GGRaSP
An R-package for selecting representative genomes using Gaussian mixture models.
Phage_Finder
Phage_Finder is a heuristic computer program written in PERL to identify prophage regions within bacterial genomes.
PanACEA
PanACEA is a tool for Pan-Genome visualization, which utilizes locally-computed interactive web-pages to view ordered pan-genome data.
LOCUST
A custom sequence locus typer for classifying microbial genotypic and phenotypic attributes.
Designer Phage
Synthetic Engineering of Bacteriophage for Treatment of Wound InfectionsViral 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.