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Thomas Sharpton in front of blue backdrop

Thomas J. Sharpton

Associate Professor
Department of Microbiology
Department of Statistics

Thomas J. Sharpton

Associate Professor
Department of Microbiology
Department of Statistics



Ph.D., University of California, Berkeley

B.A. Oregon State University, 2003


Dr. Thomas Sharpton’s research is broadly directed towards ascertaining how commensal microbiota and their genomic characteristics (i.e., the microbiome) relate to health. His laboratory specializes in the development and application of high-throughput computational and statistical tools that characterize microbiome biology, and investigates how microbiomes are distributed across space, time, and host physiology. The Sharpton lab aims to develop testable hypotheses about how hosts and their microbiome interact, and strives to understand the evolutionary and ecological processes that influence community assembly, maintenance, and function within a host. Ultimately, this knowledge will be used to discover disease mechanisms, identify predicative and diagnostic biomarkers of disease, and develop tools to treat disease through manipulation of the microbiome. All of the data resources and software that his lab develops are freely available. Dr. Sharpton has spent many years conducting bioinformatic investigations of host-microbe interactions. As a Ph.D. student at the University of California, Berkeley, he conducted comparative genomic investigations of pathogenic fungi to identify evolutionary and ecological processes that contribute to human disease. His postdoctoral research at the J. David Gladstone Institutes focused on the development and application of high-throughput computational procedures and data resources to characterize the diversity of microbiomes from metagenomic data. While there, he developed several novel bioinformatics algorithms and data resources (e.g., PhylOTU, the Sifting Families database, shotmap), which he has used to explore the diversity and function of various microbiomes, especially those associated with the global ocean and the human body. Current research in the Sharpton lab includes the development of bioinformatics tools that improve the analysis of microbiome function, investigations into the relationship between gut microbiome diversity and inflammatory bowel disease, and characterization of the composition of the oral microbiome associated with ancient human populations (e.g., the Khoesan) to ascertain how humans and their microbiomes have coevolved.

Research Interests

  • Microbiome Ecology
  • Evolution and Function
  • Biostatistics
  • Genomics and Metagenomics
  • Data Integration
  • Big Data Analysis
  • Machine Learning
  • Network Informatics


  • Armour, C.R., Nayfach, S., Pollard, K.S. and Sharpton, T.J. 2019 A Metagenomic Meta-Analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome. mSystems, 4 (4) DOI: 10.1128/mSystems.00332-18
  • Morelan, I.A., Gaulke, C.K., Sharpton, T.J., Thurber, R. Vega, and Denver, D.R. 2019. Microbiome variation in an intertidal sea anemone across latitudes and symbiotic states. Frontiers in Mar. Sci. 6:7.
  • Flannery, J. Callaghan, B., Sharpton, T., Fisher, P., and Pfeifer, J. 2019. Is adolescence the missing developmental link in Microbiome-Gut-Brain axis communication? Dev. Psychobiol. PMID: 30690712.
  • Kirchoff, N.S., Udell, M.A.R., and Sharpton, T.J. 2019. The gut microbiome correlates with conspecific aggression in a small population of rescued dogs (Canis familiaris). PeerJ. PMID: 30643689.
  • Gaulke, C.A., Martins, M.L., Watral, V.G., Humphreys, I.R., Spagnoli, S.T., Kent, M.L., and Sharpton, T.J. 2019. A longitudinal assessment of host-microbe-parasite interactions resolves the zebrafish gut microbiome's link to Pseudocapillaria tomentosa infection and pathology. Microbiome. PMID 30678738.
  • Gaulke, C.A., Rolshoven, J., Wong, C.P., Hudson, L.G., Ho, E., and Sharpton, T.J. 2018. Marginal zinc deficiency and environmentally relevant concentrations of arsenic elicit combined effects on the gut microbiome. mSphere. 3(6):pii:e00521.
  • Gaulke, C.A. and Sharpton, T.J. 2018. The influence of ethnicity and geography on human gut microbiome composition. Nat. Med. 24(10):1495-1496.
  • Kent, M.L., Gaulke, G.A., Watral, V., and Sharpton, T.J. 2018. Pseudocapillaria tomentosa in laboratory zebrafish (Danio rerio): Patterns of infection and dose response. Dis. Aquat. Org. (in press).
  • Wang, L., Shantz, A.A., Payet, J., Sharpton, T.J., Foster, A., Burkepile, D.E., and Vega-Thurber, R. 2018. Corals and their microbiomes are differentially affected by exposure to elevated nutrients and a natural thermal anomaly. Frontiers of Mar. Sci. 5:101.
  • Allan, E.R.O., Tennessen, J.A., Sharpton, T.J. and Blouin, M.S. 2018. Allelic variation in a single genomic region alters the microbiome of the snail Biomphalaria glabrata. J. Hered. Mar 16. PMID 29566237.