David R. Nelson

  • Professor
  • Phone: 401.874.5902
  • Email: dnelson@uri.edu
  • Office Location: CBLS, Rm 381


David Nelson is a microbiologist. He received an AB (Bacteriology) from University of California, Los Angeles (UCLA); an MS (Bacteriology) from the University of Wisconsin, Madison (studied the ecology and physiology of Methanosarcina sp. UBS with J.G. Zeikus); a Ph.D. (Microbiology) from UCLA (studied the physiology of Bdellovibrio bacteriovorus with S.C. Rittenberg); and conducted his postdoctoral training in the Department of Microbiology and Immunology at the University of California, Berkeley (studied the molecular biology of fruiting body formation in Myxococcus xanthus with D.R. Zusman).

Dr. Nelson joined the URI faculty in 1982 as a member of the Department of Microbiology, which eventually became the Department of Cell and Molecular Biology (CMB). Dr. Nelson is now a Professor of Microbiology in CMB. In 2002, Dr. Nelson founded the URI Center for Genomics and DNA Sequencing with grant funding from NSF and served as the director until 2021. This facility is now part of the Rhode Island INBRE Molecular Informatics Core. Dr. Nelson also served as the Director of Graduate Education for CMB (2009-2012) and then as the Coordinator for the BES Graduate Specialization in CMB (2013-2014). Additionally, Dr. Nelson served as an editorial board member (2005-2020), associate editor (2008-2015), and section editor (2015-2020) for BMC Microbiology. He was also the recipient of the College of Environment and Life Sciences Research Scientist of the Year Award (2001), the URI Excellence Award (Intellectual Property, 2012), and an additional three URI Intellectual Property Awards (2013, 2014, 2019).


Since joining the URI faculty, the Nelson lab research interests have included bacterial responses to stress (e.g., starvation, heat shock, etc.) in Myxococcus xanthus, Borrelia burgdorferi, and Vibrio anguillarum; mechanisms of pathogenesis in V. anguillarum, Flavobacterium columnare, and Vibrio coralliilyticus; and mechanisms of probiotic activity in Phaeobacter inhibens and other probiotic bacteria. Our current research focuses on the molecular basis for pathogen-host-probiont interactions in the V. coralliilyticus-Eastern Oyster-P. inhibens system. This work is being carried out in collaboration with the laboratories of Marta Gomez-Chiarri (FAVS) and David Rowley (BPS). We also have ongoing research on the molecular basis for pathogen-host-probiont interactions in the V. coralliilyticus-coral (Astrangia poculata)-Pseudoalteromonas rubra system This work is being carried out in collaboration with the laboratories of Koty Sharp (Roger Williams University) and David Rowley (BPS).


  • Ph.D., Microbiology, University of California, Los Angeles, 1979
  • M.S., Bacteriology, University of Wisconsin, Madison, 1974
  • A.B., Bacteriology, University of California, Los Angeles, 1972

Selected Publications

Takyi E, LaPorte J, Sohn S, Stevick RJ, Witkop EM, Gregg LS, Chesler-Poole A, Small J, White MM, Giray C, Rowley DC, Nelson DR, Gomez-Chiari M. 2023. Development and evaluation of a formulation of probiont Phaeobacter inhibens S4 for the management of vibriosis in bivalve hatcheries. Aqua Fish & Fisheries. 2023:1-12. https://doi.org/10.1002/aff2.112.

LaPorte JP, Spinard EJ, Cavanagh D, Gomez-Chiarri M, Rowley DC, Mekalanos JJ, Mittraparp-Arthorn P, Nelson DR. 2023. Draft Genome Sequence of Vibrio parahaemolyticus PSU5579, Isolated during an Outbreak of Acute Hepatopancreatic Necrosis Disease in Thailand. Microbiol Resour Announc. 16;12(2):e0087322. doi: https://doi.org/10.1128/mra.00873-22. PubMed PMID: 36656017; PubMed Central PMCID: PMC9933731.

Bhuta R, DeNardo B, Wang J, Atoyan J, Zhang Y, Nelson D, Shapiro J. Durable changes in the gut microbiome in survivors of childhood acute lymphoblastic leukemia. Pediatr Blood Cancer. 2021 Dec;68(12):e29308. doi: 10.1002/pbc.29308. Epub 2021 Aug 31. PMID: 34467651.

Gomez-Chiarri M, Modak T, Roberts E, Stevik R, Nelson D, Rowley D. 2019. Immune responses of American oysters to bacterial and parasitic challenge. Fish & Shellfish Immunol. 91:462-463. doi: https://doi.org/10.1016/j.fsi.2019.04.266.

Zhao W, Yuan T, Piva C, Spinard EJ, Schuttert C, Rowley DC and Nelson DR. 2019. The probiotic bacterium, Phaeobacter inhibens, down-regulates virulence factor transcription in the shellfish pathogen, Vibrio coralliilyticus, by N-acyl homoserine lactone production. Appl Envir Microbiol 85: e01545-18. https://doi.org/10.1128/AEM.01545-18.

Mou X, Spinard EJ, Hillman SL, Nelson DR. 2017. Isocitrate dehydrogenase mutation in Vibrio anguillarum results in virulence attenuation and immunoprotection in rainbow trout (Oncorhynchus mykiss). BMC Microbiol. 17(1): 217. doi: 10.1186/s12866-017-1124-1.

Zhao, W., Dao, C., Karim, M., Gomez-Chiarri, M., Rowley, D., and Nelson, D.R. 2016. Contributions of tropodithietic acid and biofilm formation to the probiotic activity of Phaeobacter inhibens. BMC Microbiol. 16:1 doi:https://doi.org/10.1186/s12866-015-0617-z

Mou, X., Spinard, E.J., Driscoll, M.V., Zhao, W., and Nelson, D.R. 2013. H-NS is a Negative Regulator of the two hemolysin/cytotoxin gene clusters in Vibrio anguillarum. Infect Immun. 81:3566-3576. doi: 10.1128/IAI.00506-13