Publications

Reviews

1) Jones M.B., Highlander S.K., Anderson E.L., Li W., Dayrit M., Klitgord N., Fabani M.M., Seguritan V., Green J., Pride D.T., Yooseph S., Biggs W., Nelson K.E., and Venter J.C. 2015. Library preparation methodology can influence genomic and functional predictions in human microbiome research. Proc Natl Acad Sci U S A. 112(45): 14024-9. PMID 26512100.

2) Hwang, J.H., Lyes M., Sladewski K., McEachern E., Mathew D.P., Das S., Moshensky ., Bapat S., Pride D.T., Ongkeko W.M., and Crotty-Alexander L.E. 2016. Electronic cigarette inhalation alters innate immunity and airway cytokines while increasing the virulence of colonizing bacteria. 94(6): 667-79. PMID 26804311.

3) Duan Y., Llorente C., Lang S., Brandl K., Chu H., Jiang L., White R.C., Clarke T.H., Nguyen K., Torralba M., Shao Y., Liu J., Hernandez-Morales A., Lessor L., Rahman I.R., Miyamoto Y., Ly M., Gao B., Sun W., Kiesel R., Hutmacher F., Lee S., Ventura-Cots M, Bosques-Padilla F., Verna E.C., Abraldes J.G., Brown R.S. Jr., Vargas V., Altamirano J., Caballería J., Shawcross D.L., Ho S.B., Louvet A, Lucey M.R., Mathurin P., Garcia-Tsao G., Bataller R., Tu X.M., Eckmann L., van der Donk W.A., Young R., Lawley T.D., Stärkel P, Pride D., Fouts D.E., Schnabl B. 2019. Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease. Nature. 575(7783):505-511. PMID 31723265.

4) Jiang L., Lang S., Duan Y., Zhang X., Gao B., Chopyk J., Schwanemann L.K., Ventura-Cots M., Bataller R., Bosques-Padilla F., Verna E.C., Abraldes J.G., Brown R.S. Jr., Vargas V., Altamirano J., Caballería J., Shawcross D.L., Ho S.B., Louvet A., Lucey M.R., Mathurin P., Garcia-Tsao G., Kisseleva T., Brenner D.A., Tu X.M., Stärkel P., Pride D., Fouts D.E., Schnabl B. 2020. Intestinal Virome in Patients with Alcoholic Hepatitis. Hepatology. PMID 32654263.

5) Lang S., Demir M., Martin A., Jiang L., Zhang X., Duan Y., Gao B., Wisplinghoff H., Kasper P., Roderburg C., Tacke F., Steffen H.M., Goeser T., Abraldes J.G., Tu X.M., Loomba R., Stärkel P., Pride D., Fouts D.E., Schnabl B. Intestinal Virome Signature Associated with Severity of Nonalcoholic Fatty Liver Disease. 2020. Gastroenterology. 159(5):1839-1852. PMID 32652145.

6) Oliver A, LaMere B, Weihe C, Wandro S, Lindsay KL, Wadhwa PD, Mills DA, Pride DT, Fiehn O, Northen T, de Raad M, Li H, Martiny JBH, Lynch S, Whiteson K. 2020. Cervicovaginal Microbiome Composition is Associated with Metabolic Profiles in Healthy Pregnancy. mBio. 11(4):e01851-20. PMID 32843557.

Collaborations

1) Abeles, S.R, and Pride D.T. 2014. Molecular bases and role of viruses in the human microbiome. J. Mol. Biol. PMID 25020228.

2) Edlund, A., Santiago-Rodriguez T.M., Boehm T.K., and Pride D.T. 2015. Bacteriophage and their potential roles in the human oral cavity. J Oral Microbiol. 7: 27423. PMID 25861745.

Primary Peer Reviewed Publications

1)   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.

2)   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.

3)   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.

4) 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.

5) 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

6) 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.

7)   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.

8) 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.

9) 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.

10)   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.

11)   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.

12) 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.

13) 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.

14) 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.

15) 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.

16) 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.

17) 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.

18) 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.