Derrick E. Fouts

Derrick E. Fouts, PhD

Professor
301-795-7874

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

Bioinformatics advances. 2026-01-21; 6.1: vbag017.

cAMRah: a scalable and portable workflow for harmonized antimicrobial resistance gene prediction from bacterial genomes

Matute DL, Clarke TH, LaPointe AR, Singh I, Fouts DE
PMID: 41710351

The Journal of infectious diseases. 2025-11-14; 232.5: 1097-1107.

Escherichia coli Type III Secretion System 2 Is Associated With Patient Mortality in Bloodstream Infections

Thaden JT, Cox P, Ankrah PK, Khandelwal S, Bourgeois JS, Poteete O, Ruffin F, Arepally G, Sutton G, Brinkac L, Clarke TH, Ko DC, Fouts DE, Fowler VG
PMID: 40404560

Cell host & microbe. 2025-11-12; 33.11: 1997-1998.

Intestinal REG3 Lectins Protect against Alcoholic Steatohepatitis by Reducing Mucosa-Associated Microbiota and Preventing Bacterial Translocation

Wang L, Fouts DE, Stärkel P, Hartmann P, Chen P, Llorente C, Depew J, Moncera K, Ho SB, Brenner DA, Hooper LV, Schnabl B
PMID: 41109221

mBio. 2025-11-12; 16.11: e0198825.

Integrating genomic and Tn-Seq data to identify common in vivo fitness mechanisms across multiple bacterial species

Fouts DE, Clarke TH, Severin GB, Brown AN, Ottosen EN, Holmes CL, Moricz BS, Mason S, Sinha R, Anderson MT, DiRita V, Bachman MA, Mobley HLT
PMID: 40981419

Scientific reports. 2025-10-21; 15.1: 36634.

Identification of a novel bacteriophage attachment site into ffs, the 4.5S non-coding RNA component of the signal recognition particle

Stevens RH, Zhang H, Fouts DE
PMID: 41120537

Antibiotics (Basel, Switzerland). 2025-10-10; 14.10:

In Silico Identification and Molecular Characterization of Lentilactobacillus hilgardii Antimicrobial Peptides with Activity Against Carbapenem-Resistant Acinetobacter baumannii

Appel A, Velazco L, Alreja AB, LeClair K, Duggal AP, Vashee I, Taal AM, Gonzalez-Juarbe N, Fouts DE
PMID: 41148698

Nature. 2025-10-01; 646.8083: 180-189.

mAChR4 suppresses liver disease via GAP-induced antimicrobial immunity

Llorente C, Raya Tonetti F, Bruellman R, Brea R, Pell N, Hartmann P, Maccioni L, Han H, Cabré N, Liu J, Eguileor A, Fondevila MF, Meijnikman AS, Hsu CL, Alghafri A, Zhou R, Gao B, Duan Y, Zhang P, Febbraio MA, Taniguchi K, Newberry RD, Fouts DE, Brenner DA, Stärkel P, Karin M, Schnabl B
PMID: 40836099

The Journal of clinical investigation. 2025-07-01; 135.13:

Activation of intestinal endogenous retroviruses by alcohol exacerbates liver disease

Cabré N, Fondevila MF, Wei W, Yamazaki T, Tonetti FR, Eguileor A, Garcia-Carbonell R, Meijnikman AS, Miyamoto Y, Mayo S, Wang Y, Zhang X, Trimbuch T, Lehnardt S, Eckmann L, Fouts DE, Llorente C, Tsukamoto H, Stärkel P, Schnabl B
PMID: 40359032

Microbiology spectrum. 2025-04-15; 13.5: e0330324.

Insertion sequence-mediated phage resistance contributes to attenuated colonization of cytolytic Enterococcus faecalis variants in the gut

Fujiki J, Nakamura T, Kreimeyer H, Llorente C, Fouts DE, Schnabl B
PMID: 40231830

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

Mobley HLT, Anderson MT, Moricz BS, Severin GB, Holmes CL, Ottosen EN, Eichler T, Gupta S, Paudel S, Sinha R, Mason S, Himpsl SD, Brown AN, Gaca M, Kiser CM, Clarke TH, Fouts DE, DiRita VJ, Bachman MA
PMID: 39178317

PloS one. 2024-07-29; 19.7: e0307968.

Serum susceptibility of Escherichia coli and its association with patient clinical outcomes

Poteete O, Cox P, Ruffin F, Sutton G, Brinkac L, Clarke TH, Fouts DE, Fowler VG, Thaden JT
PMID: 39074102

Gut microbes. 2024-02-01; 16.1: 2307586.

Fungal signature differentiates alcohol-associated liver disease from nonalcoholic fatty liver disease

Viebahn G, Hartmann P, Lang S, Demir M, Zhang X, Fouts DE, Stärkel P, Schnabl B
PMID: 38298161

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

Boonyasiri A, Brinkac LM, Jauneikaite E, White RC, Greco C, Seenama C, Tangkoskul T, Nguyen K, Fouts DE, Thamlikitkul V
PMID: 37641085

Journal of clinical microbiology. 2023-07-20; 61.7: e0019923.

Escherichia coli ST131 Associated with Increased Mortality in Bloodstream Infections from Urinary Tract Source

Brumwell A, Sutton G, Lantos PM, Hoffman K, Ruffin F, Brinkac L, Clarke TH, Adams MD, Fowler VG, Fouts DE, Thaden JT
PMID: 37338371

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

Hsu CL, Lang S, Demir M, Fouts DE, Stärkel P, Schnabl B
PMID: 36631002

Hepatology communications. 2023-02-01; 7.2: e0029.

Malassezia restricta promotes alcohol-induced liver injury

Zeng S, Hartmann P, Park M, Duan Y, Lang S, Llorente C, Wang Y, Cabré N, Fouts DE, Bacher P, Jung WH, Stärkel P, Schnabl B
PMID: 36706195

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

Filippov AA, Su W, Sergueev KV, Kevorkian RT, Snesrud EC, Srijan A, He Y, Fouts DE, Lurchachaiwong W, McGann PT, Ellison DW, Swierczewski BE, Nikolich MP
PMID: 36421303

Hepatology communications. 2022-08-01; 6.8: 2058-2069.

Intestinal virome in patients with alcohol use disorder and after abstinence

Hsu CL, Zhang X, Jiang L, Lang S, Hartmann P, Pride D, Fouts DE, Stärkel P, Schnabl B
PMID: 35368152

JAC-antimicrobial resistance. 2022-06-01; 4.3: dlac040.

Clinical challenges treating Stenotrophomonas maltophilia infections: an update

Mojica MF, Humphries R, LiPuma JJ, Mathers AJ, Rao GG, Shelburne SA, Fouts DE, van Duin D, Bonomo RA
PMID: 35529051

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

Hujer AM, Bethel CR, Taracila MA, Marshall SH, Rojas LJ, Winkler ML, Painter RE, Domitrovic TN, Watkins RR, Abdelhamed AM, D'Souza R, Mack AR, White RC, Clarke T, Fouts DE, Jacobs MR, Young K, Bonomo RA
PMID: 35435707

Journal of hepatology. 2022-04-01; 76.4: 788-799.

The fecal mycobiome in non-alcoholic fatty liver disease

Demir M, Lang S, Hartmann P, Duan Y, Martin A, Miyamoto Y, Bondareva M, Zhang X, Wang Y, Kasper P, Bang C, Roderburg C, Tacke F, Steffen HM, Goeser T, Kruglov A, Eckmann L, Stärkel P, Fouts DE, Schnabl B
PMID: 34896404

Viruses. 2022-03-29; 14.4:

Identification and Characterization of vB_PreP_EPr2, a Lytic Bacteriophage of Pan-Drug Resistant Providencia rettgeri

Mencke JL, He Y, Filippov AA, Nikolich MP, Belew AT, Fouts DE, McGann PT, Swierczewski BE, Getnet D, Ellison DW, Margulieux KR
PMID: 35458437

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

Assad-Garcia N, D'Souza R, Buzzeo R, Tripathi A, Oldfield LM, Vashee S, Fouts DE
PMID: 34818102

Metabolites. 2022-01-05; 12.1:

Machine Learning Applied to Omics Datasets Predicts Mortality in Patients with Alcoholic Hepatitis

Gao B, Wu TC, Lang S, Jiang L, Duan Y, Fouts DE, Zhang X, Tu XM, Schnabl B
PMID: 35050163

Journal of hepatology. 2021-12-01; 75.6: 1465-1475.

Intestinal virome and therapeutic potential of bacteriophages in liver disease

Hsu C, Hsu CL, Duan Y, Fouts DE, Schnabl B
PMID: 34437908

Frontiers in physiology. 2021-07-19; 12.699253.

Dynamic Changes of the Fungal Microbiome in Alcohol Use Disorder

Hartmann P, Lang S, Zeng S, Duan Y, Zhang X, Wang Y, Bondareva M, Kruglov A, Fouts DE, Stärkel P, Schnabl B
PMID: 34349667

The Journal of antimicrobial chemotherapy. 2021-07-15; 76.8: 2017-2023.

Apramycin resistance in epidemic carbapenem-resistant Klebsiella pneumoniae ST258 strains

Hao M, Schuyler J, Zhang H, Shashkina E, Du H, Fouts DE, Satlin M, Kreiswirth BN, Chen L
PMID: 33942093

Pharmaceuticals (Basel, Switzerland). 2021-04-16; 14.4:

In Vitro Activity of a Novel Siderophore-Cephalosporin LCB10-0200 (GT-1), and LCB10-0200/Avibactam, against Carbapenem-Resistant Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa Strains at a Tertiary Hospital in Korea

Nguyen LP, Park CS, Pinto NA, Lee H, Seo HS, Vu TN, Mai H, Pham AHT, Jang E, Cho YL, Goglin K, Nguyen K, White R, D'Souza R, Fouts DE, Yong D
PMID: 33923801

Cellular and molecular gastroenterology and hepatology. 2021-02-22; 12.1: 293-320.

Intestinal α1-2-Fucosylation Contributes to Obesity and Steatohepatitis in Mice

Zhou R, Llorente C, Cao J, Zaramela LS, Zeng S, Gao B, Li SZ, Welch RD, Huang FQ, Qi LW, Pan C, Huang Y, Zhou P, Beussen I, Zhang Y, Bryam G, Fiehn O, Wang L, Liu EH, Yu RT, Downes M, Evans RM, Goglin K, Fouts DE, Brenner DA, Bode L, Fan X, Zengler K, Schnabl B
PMID: 33631374

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

Boonyasiri A, Jauneikaite E, Brinkac LM, Greco C, Lerdlamyong K, Tangkoskul T, Nguyen K, Thamlikitkul V, Fouts DE
PMID: 33541274

Diagnostic microbiology and infectious disease. 2021-02-01; 99.2: 115242.

A comprehensive and contemporary "snapshot" of β-lactamases in carbapenem resistant Acinetobacter baumannii

Hujer AM, Hujer KM, Leonard DA, Powers RA, Wallar BJ, Mack AR, Taracila MA, Rather PN, Higgins PG, Prati F, Caselli E, Marshall SH, Clarke T, Greco C, Venepally P, Brinkac L, Kreiswirth BN, Fouts DE, Bonomo RA, Antibacterial Resistance Leadership Group (ARLG)
PMID: 33248392

Hepatology (Baltimore, Md.). 2020-12-01; 72.6: 2182-2196.

Intestinal Virome in Patients With Alcoholic Hepatitis

Jiang L, Lang S, Duan Y, Zhang X, Gao B, Chopyk J, Schwanemann LK, Ventura-Cots M, Bataller R, Bosques-Padilla F, Verna EC, Abraldes JG, Brown RS, Vargas V, Altamirano J, Caballería J, Shawcross DL, Ho SB, Louvet A, Lucey MR, Mathurin P, Garcia-Tsao G, Kisseleva T, Brenner DA, Tu XM, Stärkel P, Pride D, Fouts DE, Schnabl B
PMID: 32654263

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

Maccioni L, Gao B, Leclercq S, Pirlot B, Horsmans Y, De Timary P, Leclercq I, Fouts D, Schnabl B, Stärkel P
PMID: 32588725

Gut microbes. 2020-11-09; 12.1: 1785251.

Changes in the fecal bacterial microbiota associated with disease severity in alcoholic hepatitis patients

Lang S, Fairfied B, Gao B, Duan Y, Zhang X, Fouts DE, Schnabl B
PMID: 32684075

Gastroenterology. 2020-11-01; 159.5: 1839-1852.

Intestinal Virome Signature Associated With Severity of Nonalcoholic Fatty Liver Disease

Lang S, Demir M, Martin A, Jiang L, Zhang X, Duan Y, Gao B, Wisplinghoff H, Kasper P, Roderburg C, Tacke F, Steffen HM, Goeser T, Abraldes JG, Tu XM, Loomba R, Stärkel P, Pride D, Fouts DE, Schnabl B
PMID: 32652145

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

Chan AP, Choi Y, Clarke TH, Brinkac LM, White RC, Jacobs MR, Bonomo RA, Adams MD, Fouts DE
PMID: 32681170

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

Wesevich A, Sutton G, Ruffin F, Park LP, Fouts D, Fouts DE, Fowler VG, Thaden JT
PMID: 32493786

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

Yasmin M, Fouts DE, Jacobs MR, Haydar H, Marshall SH, White R, D'Souza R, Lodise TP, Rhoads DD, Hujer AM, Rojas LJ, Hoyen C, Perez F, Edwards A, Bonomo RA
PMID: 31802119

Microbiology resource announcements. 2020-07-23; 9.30:

Complete Genome Sequence of Broad-Host-Range Staphylococcus aureus Myophage ESa1

D'Souza R, Filippov AA, Sergueev KV, He Y, Ward AM, Goglin K, Vashee S, Nikolich MP, Fouts DE
PMID: 32703841

Gut microbes. 2020-05-03; 11.3: 265-275.

Intestinal and hepatic microbiota changes associated with chronic ethanol administration in mice

Bluemel S, Wang L, Kuelbs C, Moncera K, Torralba M, Singh H, Fouts DE, Schnabl B
PMID: 30982395

Antimicrobial agents and chemotherapy. 2020-04-21; 64.5:

ARGONAUT II Study of the In Vitro Activity of Plazomicin against Carbapenemase-Producing Klebsiella pneumoniae

Jacobs MR, Good CE, Hujer AM, Abdelhamed AM, Rhoads DD, Hujer KM, Rudin SD, Domitrovic TN, Connolly LE, Krause KM, Patel R, Arias CA, Kreiswirth BN, Rojas LJ, D'Souza R, White RC, Brinkac LM, Nguyen K, Singh I, Fouts DE, van Duin D, Bonomo RA, Antibacterial Resistance Leadership Group
PMID: 32152078

Microbiology resource announcements. 2020-04-16; 9.16:

Complete Genome Sequence of Staphylococcus aureus Phage SA75, Isolated from Goat Feces

D'Souza R, White RC, Buzzeo R, Goglin K, Vashee S, Lee Y, Son B, Ryu S, Fouts DE
PMID: 32299871

Hepatology (Baltimore, Md.). 2020-02-01; 71.2: 522-538.

Intestinal Fungal Dysbiosis and Systemic Immune Response to Fungi in Patients With Alcoholic Hepatitis

Lang S, Duan Y, Liu J, Torralba MG, Kuelbs C, Ventura-Cots M, Abraldes JG, Bosques-Padilla F, Verna EC, Brown RS, Vargas V, Altamirano J, Caballería J, Shawcross D, Lucey MR, Louvet A, Mathurin P, Garcia-Tsao G, Ho SB, Tu XM, Bataller R, Stärkel P, Fouts DE, Schnabl B
PMID: 31228214

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

Furuya S, Argemi J, Uehara T, Katou Y, Fouts DE, Schnabl B, Dubuquoy L, Belorkar A, Vadigepalli R, Kono H, Bataller R, Rusyn I
PMID: 31710124

Nature. 2019-11-13; 575.7783: 505-511.

Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease

Duan Y, Llorente C, Lang S, Brandl K, Chu H, Jiang L, White RC, Clarke TH, Nguyen K, Torralba M, Shao Y, Liu J, Hernandez-Morales A, Lessor L, Rahman IR, Miyamoto Y, Ly M, Gao B, Sun W, Kiesel R, Hutmacher F, Lee S, Ventura-Cots M, Bosques-Padilla F, Verna EC, Abraldes JG, Brown RS, Vargas V, Altamirano J, Caballería J, Shawcross DL, Ho SB, Louvet A, Lucey MR, Mathurin P, Garcia-Tsao G, Bataller R, Tu XM, Eckmann L, van der Donk WA, Young R, Lawley TD, Stärkel P, Pride D, Fouts DE, Schnabl B
PMID: 31723265

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

Papp-Wallace KM, Zeiser ET, Becka SA, Park S, Wilson BM, Winkler ML, D'Souza R, Singh I, Sutton G, Fouts DE, Chen L, Kreiswirth BN, Ellis-Grosse EJ, Drusano GL, Perlin DS, Bonomo RA
PMID: 31099835

mBio. 2019-07-02; 10.4:

Population Structure, Molecular Epidemiology, and β-Lactamase Diversity among Stenotrophomonas maltophilia Isolates in the United States

Mojica MF, Rutter JD, Taracila M, Abriata LA, Fouts DE, Papp-Wallace KM, Walsh TJ, LiPuma JJ, Vila AJ, Bonomo RA
PMID: 31266860

mBio. 2019-03-26; 10.2:

Rapid Replacement of Acinetobacter baumannii Strains Accompanied by Changes in Lipooligosaccharide Loci and Resistance Gene Repertoire

Adams MD, Wright MS, Karichu JK, Venepally P, Fouts DE, Chan AP, Richter SS, Jacobs MR, Bonomo RA
PMID: 30914511

mSphere. 2019-03-13; 4.2:

Emergence of New Delhi Metallo-β-Lactamase (NDM-5) in Klebsiella quasipneumoniae from Neonates in a Nigerian Hospital

Brinkac LM, White R, D'Souza R, Nguyen K, Obaro SK, Fouts DE
PMID: 30867330

BMC bioinformatics. 2019-01-07; 20.1: 8.

OMeta: an ontology-based, data-driven metadata tracking system

Singh I, Kuscuoglu M, Harkins DM, Sutton G, Fouts DE, Nelson KE
PMID: 30612540

Diagnostic microbiology and infectious disease. 2018-11-01; 92.3: 253-258.

Sequence heterogeneity of the PenA carbapenemase in clinical isolates of Burkholderia multivorans

Becka SA, Zeiser ET, Marshall SH, Gatta JA, Nguyen K, Singh I, Greco C, Sutton GG, Fouts DE, LiPuma JJ, Papp-Wallace KM
PMID: 29983287

BMC bioinformatics. 2018-06-27; 19.1: 246.

PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes

Clarke TH, Brinkac LM, Inman JM, Sutton G, Fouts DE
PMID: 29945570

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

Santos LA, Adhikarla H, Yan X, Wang Z, Fouts DE, Vinetz JM, Alcantara LCJ, Hartskeerl RA, Goris MGA, Picardeau M, Reis MG, Townsend JP, Zhao H, Ko AI, Wunder EA
PMID: 29971217

Scientific reports. 2018-06-05; 8.1: 8656.

Multidrug resistant pathogens respond differently to the presence of co-pathogen, commensal, probiotic and host cells

Chan AP, Choi Y, Brinkac LM, Krishnakumar R, Depew J, Kim M, Hinkle MK, Lesho EP, Fouts DE
PMID: 29872152

F1000Research. 2018-05-01; 7.521.

Enterobacterhormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes

Sutton GG, Brinkac LM, Clarke TH, Fouts DE
PMID: 30430006

Nature communications. 2017-10-16; 8.1: 837.

Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus

Llorente C, Jepsen P, Inamine T, Wang L, Bluemel S, Wang HJ, Loomba R, Bajaj JS, Schubert ML, Sikaroodi M, Gillevet PM, Xu J, Kisseleva T, Ho SB, Depew J, Du X, Sørensen HT, Vilstrup H, Nelson KE, Brenner DA, Fouts DE, Schnabl B
PMID: 29038503

The Journal of clinical investigation. 2017-06-30; 127.7: 2829-2841.

Intestinal fungi contribute to development of alcoholic liver disease

Yang AM, Inamine T, Hochrath K, Chen P, Wang L, Llorente C, Bluemel S, Hartmann P, Xu J, Koyama Y, Kisseleva T, Torralba MG, Moncera K, Beeri K, Chen CS, Freese K, Hellerbrand C, Lee SM, Hoffman HM, Mehal WZ, Garcia-Tsao G, Mutlu EA, Keshavarzian A, Brown GD, Ho SB, Bataller R, Stärkel P, Fouts DE, Schnabl B
PMID: 28530644

Bioinformatics (Oxford, England). 2017-06-01; 33.11: 1725-1726.

LOCUST: a custom sequence locus typer for classifying microbial isolates

Brinkac LM, Beck E, Inman J, Venepally P, Fouts DE, Sutton G
PMID: 28130240

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

Danaher RJ, Fouts DE, Chan AP, Choi Y, Depew J, McCorrison JM, Nelson KE, Wang C, Miller CS
PMID: 27739035

mBio. 2016-12-13; 7.6:

Comprehensive Genome Analysis of Carbapenemase-Producing Enterobacter spp.: New Insights into Phylogeny, Population Structure, and Resistance Mechanisms

Chavda KD, Chen L, Fouts DE, Sutton G, Brinkac L, Jenkins SG, Bonomo RA, Adams MD, Kreiswirth BN
PMID: 27965456

PLoS neglected tropical diseases. 2016-02-18; 10.2: e0004403.

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang YF, Galloway RL, Haake DA, Haft DH, Hartskeerl R, Ko AI, Levett PN, Matsunaga J, Mechaly AE, Monk JM, Nascimento AL, Nelson KE, Palsson B, Peacock SJ, Picardeau M, Ricaldi JN, Thaipandungpanit J, Wunder EA, Yang XF, Zhang JJ, Vinetz JM
PMID: 26890609

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

Wang L, Fouts DE, Stärkel P, Hartmann P, Chen P, Llorente C, Depew J, Moncera K, Ho SB, Brenner DA, Hooper LV, Schnabl B
PMID: 26867181

Genome biology. 2015-07-21; 16.1: 143.

A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii

Chan AP, Sutton G, Depew J, Krishnakumar R, Choi Y, Huang XZ, Beck E, Harkins DM, Kim M, Lesho EP, Nikolich MP, Fouts DE
PMID: 26195261

Genome announcements. 2015-01-22; 3.1:

Genome Sequences of the Listeria ivanovii subsp. ivanovii Type Strain and Two Listeria ivanovii subsp. londoniensis Strains

Hupfeld M, Fouts DE, Loessner MJ, Klumpp J
PMID: 25614561

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

Chen P, Torralba M, Tan J, Embree M, Zengler K, Stärkel P, van Pijkeren JP, Depew J, Loomba R, Ho SB, Bajaj JS, Mutlu EA, Keshavarzian A, Tsukamoto H, Nelson KE, Fouts DE, Schnabl B
PMID: 25239591

BMC bioinformatics. 2014-11-19; 15.1: 357.

NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly

McCorrison JM, Venepally P, Singh I, Fouts DE, Lasken RS, Methé BA
PMID: 25407910

Pathogens (Basel, Switzerland). 2014-04-10; 3.2: 280-308.

Leptospiral pathogenomics

Lehmann JS, Matthias MA, Vinetz JM, Fouts DE
PMID: 25437801

Virology journal. 2013-06-06; 10.181.

Sequencing viral genomes from a single isolated plaque

Depew J, Zhou B, McCorrison JM, Wentworth DE, Purushe J, Koroleva G, Fouts DE
PMID: 23742765

PloS one. 2012-11-07; 7.11: e48289.

Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen

Fouts DE, Szpakowski S, Purushe J, Torralba M, Waterman RC, MacNeil MD, Alexander LJ, Nelson KE
PMID: 23144861

Journal of translational medicine. 2012-08-28; 10.174.

Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury

Fouts DE, Pieper R, Szpakowski S, Pohl H, Knoblach S, Suh MJ, Huang ST, Ljungberg I, Sprague BM, Lucas SK, Torralba M, Nelson KE, Groah SL
PMID: 22929533

Bacteriophage. 2012-07-01; 2.3: 190-199.

Next generation sequencing technologies and the changing landscape of phage genomics

Klumpp J, Fouts DE, Sozhamannan S
PMID: 23275870

Journal of hepatology. 2012-06-01; 56.6: 1283-92.

Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease

Fouts DE, Torralba M, Nelson KE, Brenner DA, Schnabl B
PMID: 22326468

Archives of virology. 2011-01-01; 156.1: 25-35.

Clostridium perfringens bacteriophages ΦCP39O and ΦCP26F: genomic organization and proteomic analysis of the virions

Seal BS, Fouts DE, Simmons M, Garrish JK, Kuntz RL, Woolsey R, Schegg KM, Kropinski AM, Ackermann HW, Siragusa GR
PMID: 20963614

Journal of bacteriology. 2008-08-01; 190.15: 5455-63.

Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus

Deboy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, Emerson JB, Mohamoud Y, Watkins K, Henrissat B, Gilbert HJ, Nelson KE
PMID: 18556790

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

Fouts DE, Tyler HL, Deboy RT, Daugherty S, Ren Q, Badger JH, Durkin AS, Huot H, Shrivastava S, Kothari S, Dodson RJ, Mohamoud Y, Khouri H, Roesch LF, Krogfelt KA, Struve C, Triplett EW, Methé BA
PMID: 18654632

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

Rasko DA, Rosovitz MJ, Økstad OA, Fouts DE, Jiang L, Cer RZ, Kolstø AB, Gill SR, Ravel J
PMID: 17041058

Nucleic acids research. 2006-10-24; 34.20: 5839-51.

Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences

Fouts DE
PMID: 17062630

Journal of bacteriology. 2006-05-01; 188.9: 3402-8.

Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry

Fouts DE, Rasko DA, Cer RZ, Jiang L, Fedorova NB, Shvartsbeyn A, Vamathevan JJ, Tallon L, Althoff R, Arbogast TS, Fadrosh DW, Read TD, Gill SR
PMID: 16621835

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

Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty SC, Madupu R, Angiuoli SV, Durkin AS, Haft DH, Vamathevan J, Khouri H, Utterback T, Lee C, Dimitrov G, Jiang L, Qin H, Weidman J, Tran K, Kang K, Hance IR, Nelson KE, Fraser CM
PMID: 15774886

PLoS biology. 2005-01-04; 3.1: e15.

Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species

Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, Deboy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Sullivan SA, Shetty JU, Ayodeji MA, Shvartsbeyn A, Schatz MC, Badger JH, Fraser CM, Nelson KE
PMID: 15660156

PLoS biology. 2004-10-01; 2.10: e303.

Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)

Ward N, Larsen Ø, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Methé B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, Deboy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, Eisen JA
PMID: 15383840

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

Nelson KE, Fouts DE, Mongodin EF, Ravel J, Deboy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT, Peterson J, White O, Nelson WC, Nierman W, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Haft DH, Selengut J, Van Aken S, Khouri H, Fedorova N, Forberger H, Tran B, Kathariou S, Wonderling LD, Uhlich GA, Bayles DO, Luchansky JB, Fraser CM
PMID: 15115801

Science (New York, N.Y.). 2004-04-02; 304.5667: 66-74.

Environmental genome shotgun sequencing of the Sargasso Sea

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO
PMID: 15001713

Journal of bacteriology. 2003-09-01; 185.18: 5591-601.

Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83

Nelson KE, Fleischmann RD, Deboy RT, Paulsen IT, Fouts DE, Eisen JA, Daugherty SC, Dodson RJ, Durkin AS, Gwinn M, Haft DH, Kolonay JF, Nelson WC, Mason T, Tallon L, Gray J, Granger D, Tettelin H, Dong H, Galvin JL, Duncan MJ, Dewhirst FE, Fraser CM
PMID: 12949112

Nature. 2003-05-01; 423.6935: 81-6.

The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria

Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, Deboy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE, White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, Kolstø AB, Fraser CM
PMID: 12721629

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

Fouts DE, Badel JL, Ramos AR, Rapp RA, Collmer A
PMID: 12580281

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

Fouts DE, Abramovitch RB, Alfano JR, Baldo AM, Buell CR, Cartinhour S, Chatterjee AK, D'Ascenzo M, Gwinn ML, Lazarowitz SG, Lin NC, Martin GB, Rehm AH, Schneider DJ, van Dijk K, Tang X, Collmer A
PMID: 11854524

Gene. 1998-03-27; 210.1: 135-42.

Translationally repressive RNA structures monitored in vivo using temperate DNA bacteriophages

Fouts DE, Celander DW
PMID: 9524249

Nucleic acids research. 1997-11-15; 25.22: 4464-73.

Functional recognition of fragmented operator sites by R17/MS2 coat protein, a translational repressor

Fouts DE, True HL, Celander DW
PMID: 9358153

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

Fouts DE, True HL, Cengel KA, Celander DW
PMID: 9341215

Nucleic acids research. 1996-04-15; 24.8: 1582-4.

Improved method for selecting RNA-binding activities in vivo

Fouts DE, Celander DW
PMID: 8628698

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.

Multidrug-Resistant Klebsiella pneumoniae from Pediatric Sepsis Patients in Nigeria

LOCUST

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

Genomics of Non-Tuberculosis Mycobacteria

CRACKLE: Carbapenems in Klebsiella pneumoniae and Other Enterobacteriaceae

Designer Phage

Synthetic Engineering of Bacteriophage for Treatment of Wound Infections

Video

Seeking Funding

Chronic Wound Microbiome

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

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

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

Genomics of Acinetobacter baumannii

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.

Antimicrobial Resistance from Combat Wounds

Asymptomatic Bacteriuria: Microbiome and Metaproteome

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

Leptospira Genomics and Human Health

Past Project

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

Past Project

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

Past Project

Vaginal Microbiome Project

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

Past Project

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.

Past Project

Bovine Rumen Microbiome

Past Project

Toby Clarke, MS

Bioinformatics Engineer

Stephanie Mounaud

Scientific Project Manager

Hayley Nordstrom, MS

Staff Scientist

Lily Velazco

Bacteriophage and Antibacterial Resistant Infections
12-Sep-2023
Press Release

J. Craig Venter Institute scientists awarded five-year, $5.7M grant from NIH to develop phage treatment

Phage research accelerates with the rise of antibiotic resistance to address increasingly prevalent and difficult to treat bacterial infections

11-Dec-2019
Blog

Venter Institute Researchers Tackle the Growing Concern of Antibiotic Resistant Bacterial Infections with Genomic, Phage Approaches

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

08-May-2019
The San Diego Union-Tribune

Genetically modified bacteria-killing viruses used on patient for first time