Peer-reviewed publications, 2013–2026.

Mangieri N, Gaufin T, Ghatbale P, Pride DT, Picozzi C. Characterization of broad-host-range bacteriophages targeting multidrug-resistant E. coli and Shigella spp.: in vitro potential. BMC Microbiol. 2026 Feb 5;26(1):269. doi: 10.1186/s12866-025-04672-3. PMID: 41645056; PMCID: PMC13015098.

Luong T, Kharrat L, Champagne-Jorgensen K, Melendez JA, Pride D, Conrad DJ, Roach DR. Ecological partitioning enables phage-antibiotic cooperation in a human Pseudomonas infection. Nat Commun. 2026 Feb 11;17(1):2615. doi: 10.1038/s41467-026-69247-w. PMID: 41667461; PMCID: PMC13003088.

Carrillo Terrazas M, Oles RE, Loomis LR, Hsu C-Y, Vasquez Ayala A, Lee MH, Paulchakrabarti M, Pride D, Choudhury B, Nizet V, Raffatellu M, Knight R, Chu H. Antimicrobial resistance is widespread among intestinal and extra-intestinal Bacteroides fragilis strains. Infect Immun. 2025 Dec 16;93(12):e0052925. doi: 10.1128/iai.00529-25. Epub 2025 Nov 24. PMID: 41277826; PMCID: PMC12707147.

Ardalani O, Phaneuf PV, Krishnan J, Chauhan SM, Pride D, Zielinski DC, Monk JM, Nielsen LK, Palsson BO. Rare metabolic gene essentiality is a determinant of microniche adaptation in Escherichia coli. PLoS Pathog. 2025 Dec 8;21(12):e1013775. doi: 10.1371/journal.ppat.1013775. PMID: 41359686; PMCID: PMC12704874.

Kline A, Cobián Güemes AG, Yore J, Ghose C, Van Tyne D, Whiteson K, Pride DT. Current Clinical Laboratory Challenges to Widespread Adoption of Phage Therapy in the United States. Antibiotics (Basel). 2025 May 29;14(6):553. doi: 10.3390/antibiotics14060553. PMID: 40558145; PMCID: PMC12189272.

Ghatbale P, Blanc A, Sue A, Leonard J, Bates M, Garcia AG, Hensley J, Gomes Nunes DD, Hitchcock N, Shiach J, Bardaró R, Sah G, Ghose C, Whiteson KL, Schooley RT, White RA 3rd, Cobián Güemes AG, Meyer JR, Pride DT. Experimental phage evolution results in expanded host ranges against antibiotic resistant Klebsiella pneumoniae isolates. Nat Commun. 2025 Nov 19;16(1):9903. doi: 10.1038/s41467-025-66062-7. PMID: 41258013; PMCID: PMC12630596.

Monsibais AN, Tea O, Ghatbale P, Dunham SJB, Zünd M, Phan J, Lam K, Paulson M, Tran N, Suder DS, Blanc AN, Samillano C, Suh J, Atif H, Vien E, Nguyen R, Vo A, Gonen S, Pride D, Whiteson K. Enhanced suppression of Stenotrophomonas maltophilia by a three-phage cocktail: genomic insights and kinetic profiling. Antimicrob Agents Chemother. 2025 Mar 5;69(3):e0116224. doi: 10.1128/aac.01162-24. Epub 2025 Jan 22. PMID: 39840957; PMCID: PMC11881566.

Ghatbale P, Sah GP, Dunham S, Khong E, Blanc A, Monsibais A, Garcia A, Schooley RT, Cobián Güemes AG, Whiteson K, Pride DT. In vitro resensitization of multidrug-resistant clinical isolates of Enterococcus faecium and E. faecalis through phage-antibiotic synergy. Antimicrob Agents Chemother. 2025 Feb 13;69(2):e0074024. doi: 10.1128/aac.00740-24. Epub 2024 Dec 19. PMID: 39699213; PMCID: PMC11823633.

Khong E, Oh JJ, Jimenez JM, Liu R, Dunham S, Monsibais A, Rhoads A, Ghatbale P, Garcia A, Cobián Güemes AG, Blanc AN, Chiu M, Kuo P, Proost M, Kline A, Aslam S, Schooley RT, Whiteson K, Fraley SI, Pride DT. A simple solid media assay for detection of synergy between bacteriophages and antibiotics. Microbiol Spectr. 2024 May 2;12(5):e0322123. doi: 10.1128/spectrum.03221-23. Epub 2024 Mar 25. PMID: 38526142; PMCID: PMC11064537.

Cobián Güemes AG, Ghatbale P, Blanc AN, Morgan CJ, Garcia A, Leonard J, Huang L, Kovalick G, Proost M, Chiu M, Kuo P, Oh J, Karthikeyan S, Knight R, Pogliano J, Schooley RT, Pride DT. Jumbo phages are active against extensively drug-resistant eyedrop-associated Pseudomonas aeruginosa infections. Antimicrob Agents Chemother. 2023 Dec 14;67(12):e0065423. doi: 10.1128/aac.00654-23. Epub 2023 Nov 6. PMID: 37931230; PMCID: PMC10720484.

Chopyk J, Cobián Güemes AG, Ramirez-Sanchez C, Attai H, Ly M, Jones MB, Liu R, Liu C, Yang K, Tu XM, Abeles SR, Nelson K, Pride DT. Common antibiotics, azithromycin and amoxicillin, affect gut metagenomics within a household. BMC Microbiol. 2023 Aug 2;23(1):206. doi: 10.1186/s12866-023-02949-z. PMID: 37528343; PMCID: PMC10394940.

Borin JM, Liu R, Wang Y, Wu TC, Chopyk J, Huang L, Kuo P, Ghose C, Meyer JR, Tu XM, Schnabl B, Pride DT. Fecal virome transplantation is sufficient to alter fecal microbiota and drive lean and obese body phenotypes in mice. Gut Microbes. 2023 Jan-Dec;15(1):2236750. doi: 10.1080/19490976.2023.2236750. PMID: 37475473; PMCID: PMC10364654.

Sah GP, Kovalick G, Chopyk J, Kuo P, Huang L, Ghatbale P, Das P, Realegeno S, Knight R, Gilbert JA, Pride DT. Characterization of SARS-CoV-2 Distribution and Microbial Succession in a Clinical Microbiology Testing Facility during the SARS-CoV-2 Pandemic. Microbiol Spectr. 2023 Mar 14;11(2):e0450922. doi: 10.1128/spectrum.04509-22. Epub ahead of print. PMID: 36916973; PMCID: PMC10100919.

Tamma PD, Souli M, Billard M, Campbell J, Conrad D, Ellison DW, Evans B, Evans SR, Greenwood-Quaintance KE, Filippov AA, Geres HS, Hamasaki T, Komarow L, Nikolich MP, Lodise TP, Nayak SU, Norice-Tra C, Patel R, Pride D, Russell J, Van Tyne D, Chambers HF, Fowler Jr VG, Schooley RT; Antibacterial Resistance Leadership Group. Safety and microbiological activity of phage therapy in persons with cystic fibrosis colonized with Pseudomonas aeruginosa: study protocol for a phase 1b/2, multicenter, randomized, double-blind, placebo-controlled trial. Trials. 2022 Dec 28;23(1):1057. doi: 10.1186/s13063-022-07047-5. PMID: 36578069; PMCID: PMC9795609.

Chan SK, Zhao Z, Penziner S, Khong E, Pride D, Schooley RT, Steinmetz NF. Isolation of a Peptide That Binds to Pseudomonas aeruginosa Lytic Bacteriophage. ACS Omega. 2022 Oct 12;7(42):38053-38060. doi: 10.1021/acsomega.2c05539. PMID: 36312416; PMCID: PMC9609082.

Wandro S, Ghatbale P, Attai H, Hendrickson C, Samillano C, Suh J, Dunham SJB, Pride DT, Whiteson K. Phage Cocktails Constrain the Growth of Enterococcus. mSystems. 2022 Aug 30;7(4):e0001922. doi: 10.1128/msystems.00019-22. Epub 2022 Jun 28. PMID: 35762793; PMCID: PMC9426582.

Attai H, Wilde J, Liu R, Chopyk J, Garcia AG, Allen-Vercoe E, Pride D. Bacteriophage-Mediated Perturbation of Defined Bacterial Communities in an In Vitro Model of the Human Gut. Microbiol Spectr. 2022 Jun 29;10(3):e0113522. doi: 10.1128/spectrum.01135-22. Epub 2022 May 31. PMID: 35638779; PMCID: PMC9241613.

Hsu CL, Zhang X, Jiang L, Lang S, Hartmann P, Pride D, Fouts DE, Stärkel P, Schnabl B. Intestinal virome in patients with alcohol use disorder and after abstinence. Hepatol Commun. 2022 Aug;6(8):2058-2069. doi: 10.1002/hep4.1947. Epub 2022 Apr 2. PMID: 35368152; PMCID: PMC9315129.

Suh GA, Lodise TP, Tamma PD, Knisely JM, Alexander J, Aslam S, Barton KD, Bizzell E, Totten KMC, Campbell JL, Chan BK, Cunningham SA, Goodman KE, Greenwood-Quaintance KE, Harris AD, Hesse S, Maresso A, Nussenblatt V, Pride D, Rybak MJ, Sund Z, van Duin D, Van Tyne D, Patel R; Antibacterial Resistance Leadership Group. Considerations for the Use of Phage Therapy in Clinical Practice. Antimicrob Agents Chemother. 2022 Mar 15;66(3):e0207121. doi: 10.1128/AAC.02071-21. Epub 2022 Jan 18. PMID: 35041506; PMCID: PMC8923208.

Penziner S, Schooley RT, Pride DT. Animal Models of Phage Therapy. Front Microbiol. 2021 Jan 28;12:631794. doi: 10.3389/fmicb.2021.631794. PMID: 33584632; PMCID: PMC7876411.

Pride D. The Viruses Inside You. Sci Am. 2020 Dec 1;323(6):46. doi: 10.1038/scientificamerican1220-46. PMID: 39014744.

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 Jr, 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. Intestinal Virome in Patients With Alcoholic Hepatitis. Hepatology. 2020 Dec;72(6):2182-2196. doi: 10.1002/hep.31459. Epub 2020 Oct 10. PMID: 32654263; PMCID: PMC8159727.

Chopyk, J., Akrami K., Bavly T., Shin J.H., Schwanemann L.K., Ly M., Kalai R., Xu Y., Kelley S.T., Malhotra A., Torriani F.J., Sweeney D.A., and Pride D.T. 2020. Temporal variations in bacterial community diversity and composition throughout intensive care unit renovations. Microbiome. 8(1): 86. PMID 32513256.

Schulfer, A., Santiago-Rodriguez T.M., Ly M., Borin J.M., Chopyk J., Blaser M.J., and Pride D.T. 2020. Fecal Viral Community Responses to High-Fat Diet in Mice. mSphere. 5(1): e00833-19. PMID 32102942.

Ghose, C., Ly M., Schwanemann L.K., Shin J.H., Atab K., Barr J.J., Little M., Schooley R.T., Chopyk J., and Pride, D.T. 2019. The virome of cerebrospinal fluid: viruses where we once thought there were none. Front Microbiol. 10: 2061. PMID 31555247.

Jung, C.E., Chopyk J., Shin J.H., Lukacz E.S., Brubaker L., Schwanemann L.K., Knight R., Wolfe A.J., and Pride, D.T. 2019. Benchmarking urine storage and collection conditions for evaluating the female urinary microbiome. Scientific Reports. 9: 13409. PMID 31527753.

Pannaraj, P.S., Ly M., Cerini C., Saavedra M., Aldrovandi G.M., Saboory A.A., Johnson K.M., and Pride, D.T. 2018. Shared and Distinct Features of Human Milk and Infant Stool Viromes. Front Microbiol. 9: 1162. PMID 29910789.

Ly, M. Jones, M.B., Abeles, S.R., Santiago-Rodriguez, T.M., Gao, J., Chan, I.C., Ghose, C., and Pride, D.T. 2016. Transmission of viruses via our microbiomes. Microbiome. PMID 27912785.

Abeles, S.R., Jones, M.B., Santiago-Rodriguez, T.M., Ly, M., Klitgord, N., Yooseph, S., Nelson, K.E., and Pride, D.T. 2016. Microbial diversity in individuals and their household contacts following typical antibiotic courses. Microbiome. PMID 27473422.

Santiago-Rodriguez, T.M., Ly M., Daigneault M.C., Brown I.H., McDonald J.A., Bonilla N., Allen-Vercoe E., and Pride D.T. 2015. Chemostat culture systems support diverse bacteriophage communities from human feces. Microbiome. 3: 58. PMID 26549756.

Abeles, S.R., Ly M., Santiago-Rodriguez T.M., and Pride D.T. 2015. Effects of long term antibiotic therapy on human oral and fecal viromes. PLoS One. 10: e0134941. PMID 26309137.

Santiago-Rodriguez, T.M. Naidu M., Jones M.B., Ly M., and Pride D.T. 2015. Identification of staphylococcal phage with reduced transcription in human blood through transcriptome sequencing. Front Microbiol. PMID 26074882.

Santiago-Rodriguez, T.M., Ly M., Bonilla N., and Pride D.T. 2015. The human urine virome in association with urinary tract infections. Front Microbiol. 6:14. PMID 25667584.

Lum, A.G., Santiago-Rodriguez T.M., Naidu M., Boehm T.K., and Pride D.T. 2015. Global transcription of CRISPR loci in the human oral cavity. BMC Genomics. 16: 401. PMID 25994215.

Santiago-Rodriguez, T.M., Naidu M., Abeles S.R., Boehm T.K., Ly M., and Pride D.T. 2015. Transcriptome analysis of bacteriophage communities in periodontal health and disease. BMC Genomics. 16(1): 549. PMID 26215258.

Abeles, S.R., Robles-Sikisaka, R., Ly M., Lum, A.G., Salzman, J., Boehm T.K., and Pride D.T. 2014. Human oral viruses are personal, persistent, and gender consistent. ISME J. 9: 1753-1767. PMID 24646696

Ly, M., Abeles S.R., Boehm T.K., Robles-Sikisaka R., Naidu M., Santiago-Rodriguez T., and Pride D.T. 2014. Altered oral viral ecology in association with periodontal disease. MBio. 5: e01133-14. PMID 24846382.

Robles-Sikisaka, R., Naidu M., Ly M., Salzman J., Abeles S.R., Boehm T.K., and Pride D.T. 2014. Conservation of streptococcal CRISPRs on human skin and saliva. BMC Microbiol. 14: 146. PMID 24903519.

Naidu, M., Robles-Sikisaka, R., Abeles S.R., Boehm T.K., and Pride D.T. 2014. Characterization of bacteriophage communities and CRISPR profiles from dental plaque. BMC Microbiol. 14:175. PMID 24981669. Highly Accessed.

Robles-Sikisaka, R., Ly M., Boehm T., Naidu M., Salzman J., and Pride D.T. 2013. Association between living environment and human oral viral ecology. ISME J. PMID 23598790.