Thomas Sharpton

Dr. Sharpton is the Principal Investigator of the Sharpton Lab, an Associate Professor of Microbiology and Statistics at Oregon State University, and the founding director of the Oregon State University Microbiome Initiative.

Contact Information

Research Interests

  • gut microbiome function
  • metagenomics


Thomas Sharpton is an Associate Professor of Microbiology and Statistics at Oregon State University (OSU). He obtained his Ph.D. in Microbiology from the University California at Berkeley in 2009 with a Designated Emphasis in Computational Biology. From there he trained at the Gladstone Institutes as a postdoctoral fellow, wherein he pioneered computational methods to study the human microbiome. In 2013, he joined OSU and initiated an internationally recognized research program that uses systems biology methods to resolve the gut microbiome’s influence on the health, ecology, and evolution of vertebrates. So far, his laboratory has contributed to 35 publications and helped raise over $10 million of grant support. He has published in preeminent scientific journals, including Nature, PNAS, and Microbiome and serves as an editor for mSystems, an editorial advisory board member for Applied & Environmental Microbiology, and a review editor for Frontiers in Microbiology. Dr. Sharpton was recently awarded the Phi Kappa Phi Emerging Scholar Award for his efforts to define the gut microbiome’s role in health. Dr. Sharpton also serves as the Founding Director of the Oregon State University Microbiome Initiative, which seeks to transform microbiome research and training.


  • Rodrigues, Richard R., Gurung, Manoj, Li, Zhipeng, Garcia-Jaramillo, Manuel, Greer, Renee, Gaulke, Christopher, Bauchinger, Franziska, You, Hyekyoung, Pederson, Jacob W., Vasquez-Perez, Stephany, White, Kimberly D., Frink, Briana, Philmus, Benjamin, Jump, Donald B., Trinchieri, Giorgio, Berry, David, Sharpton, Thomas J., Dzutsev, Amiran, Morgun, Andrey, Shulzhenko, Natalia (2021) Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet-induced diabetes.. Nature communications. 12(1). doi: 10.1038/s41467-020-20313-x
  • Wong, Carmen P., Magnusson, Kathy R., Sharpton, Thomas J., Ho, Emily (2021) Effects of zinc status on age-related T cell dysfunction and chronic inflammation.. Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine. . doi: 10.1007/s10534-020-00279-5
  • Nalven, Sarah G., Ward, Collin P., Payet, Jerome P., Cory, Rose M., Kling, George W., Sharpton, Thomas J., Sullivan, Christopher M., Crump, Byron C. (2020) Experimental metatranscriptomics reveals the costs and benefits of dissolved organic matter photo-alteration for freshwater microbes.. Environmental microbiology. 22(8). doi: 10.1111/1462-2920.15121
  • Raber, Jacob, Fuentes Anaya, Andrea, Torres, Eileen Ruth S., Lee, Joanne, Boutros, Sydney, Grygoryev, Dmytro, Hammer, Austin, Kasschau, Kristin D., Sharpton, Thomas J., Turker, Mitchell S., Kronenberg, Amy (2020) Effects of Six Sequential Charged Particle Beams on Behavioral and Cognitive Performance in B6D2F1 Female and Male Mice.. Frontiers in physiology. 11. doi: 10.3389/fphys.2020.00959
  • Couch, Claire E., Arnold, Holly K., Crowhurst, Rachel S., Jolles, Anna E., Sharpton, Thomas J., Witczak, Marci F., Epps, Clinton W., Beechler, Brianna R. (2020) Bighorn sheep gut microbiomes associate with genetic and spatial structure across a metapopulation.. Scientific reports. 10(1). doi: 10.1038/s41598-020-63401-0
  • Kashyap, Amita, Rhodes, Adelaide, Kronmiller, Brent, Berger, Josie, Champagne, Ashley, Davis, Edward W., Finnegan, Mitchell V., Geniza, Matthew, Hendrix, David A., Lohr, Christiane V., Petro, Vanessa M., Sharpton, Thomas J., Wells, Jackson, Epps, Clinton W., Jaiswal, Pankaj, Tyler, Brett M., Ramsey, Stephen A. (2020) Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis.. BMC genomics. 21(1). doi: 10.1186/s12864-019-6432-4
  • Logan, Isabelle E., Bobe, Gerd, Miranda, Cristobal L., Vasquez-Perez, Stephany, Choi, Jaewoo, Lowry, Malcolm B., Sharpton, Thomas J., Morgun, Andrey, Maier, Claudia S., Stevens, Jan F., Shulzhenko, Natalia, Gombart, Adrian F. (2020) Germ-Free Swiss Webster Mice on a High-Fat Diet Develop Obesity, Hyperglycemia, and Dyslipidemia.. Microorganisms. 8(4). doi: 10.3390/microorganisms8040520
  • Schaaf, Russel M., Sharpton, Thomas J., Murray, Katrina N., Kent, Andrew D., Kent, Michael L. (2020) Retrospective analysis of the Zebrafish International Resource Center diagnostic data links Pseudocapillaria tomentosa to intestinal neoplasms in zebrafish Danio rerio (Hamilton 1822).. Journal of fish diseases. 43(11). doi: 10.1111/jfd.13233
  • Stagaman, Keaton, Sharpton, Thomas J., Guillemin, Karen (2020) Zebrafish microbiome studies make waves.. Lab animal. 49(7). doi: 10.1038/s41684-020-0573-6
  • Flannery, Jessica E., Stagaman, Keaton, Burns, Adam R., Hickey, Roxana J., Roos, Leslie E., Giuliano, Ryan J., Fisher, Philip A., Sharpton, Thomas J. (2020) Gut Feelings Begin in Childhood: the Gut Metagenome Correlates with Early Environment, Caregiving, and Behavior.. mBio. 11(1). doi: 10.1128/mBio.02780-19
  • Sharpton, Thomas J., Combrink, Leigh, Arnold, Holly K., Gaulke, Christopher A., Kent, Michael (2020) Harnessing the gut microbiome in the fight against anthelminthic drug resistance.. Current opinion in microbiology. 53. doi: 10.1016/j.mib.2020.01.017
  • Neves, A. L. A., Chen, Y., Le Cao, K.-A., Mandal, S., Sharpton, T. J., McAllister, T., Guan, L. L. (2020) Taxonomic and functional assessment using metatranscriptomics reveals the effect of Angus cattle on rumen microbial signatures.. Animal : an international journal of animal bioscience. 14(4). doi: 10.1017/S1751731119002453
  • Zhang, Yang, Bobe, Gerd, Revel, Johana S., Rodrigues, Richard R., Sharpton, Thomas J., Fantacone, Mary L., Raslan, Kareem, Miranda, Cristobal L., Lowry, Malcolm B., Blakemore, Paul R., Morgun, Andrey, Shulzhenko, Natalia, Maier, Claudia S., Stevens, Jan F., Gombart, Adrian F. (2020) Improvements in Metabolic Syndrome by Xanthohumol Derivatives Are Linked to Altered Gut Microbiota and Bile Acid Metabolism.. Molecular nutrition & food research. 64(1). doi: 10.1002/mnfr.201900789
  • Mendez, Rufa L., Miranda, Cristobal, Armour, Courtney R., Sharpton, Thomas J., Stevens, Jan Frederik, Kwon, Jung Yeon (2020) Supplementation with Sea Vegetables Palmaria mollis and Undaria pinnatifida Exerts Metabolic Benefits in Diet-Induced Obesity in Mice.. Current developments in nutrition. 4(5). doi: 10.1093/cdn/nzaa072
  • Raber, Jacob, Yamazaki, Joy, Torres, Eileen Ruth S., Kirchoff, Nicole, Stagaman, Keaton, Sharpton, Thomas, Turker, Mitchell S., Kronenberg, Amy (2019) Combined Effects of Three High-Energy Charged Particle Beams Important for Space Flight on Brain, Behavioral and Cognitive Endpoints in B6D2F1 Female and Male Mice.. Frontiers in physiology. 10. doi: 10.3389/fphys.2019.00179
  • Jiang, Duo, Armour, Courtney R., Hu, Chenxiao, Mei, Meng, Tian, Chuan, Sharpton, Thomas J., Jiang, Yuan (2019) Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities.. Frontiers in genetics. 10. doi: 10.3389/fgene.2019.00995
  • Kirchoff, Nicole S., Udell, Monique A. R., Sharpton, Thomas J. (2019) The gut microbiome correlates with conspecific aggression in a small population of rescued dogs (Canis familiaris).. PeerJ. 7. doi: 10.7717/peerj.6103
  • Li, Yuanfei, Li, Yuqi, Jin, Wei, Sharpton, Thomas J., Mackie, Roderick I., Cann, Isaac, Cheng, Yanfen, Zhu, Weiyun (2019) Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of Pecoramyces sp. F1 in Monoculture and Co-culture With a Syntrophic Methanogen.. Frontiers in microbiology. 10. doi: 10.3389/fmicb.2019.00435
  • Kent, Michael L., Watral, Virginia, Gaulke, Christopher A., Sharpton, Thomas J. (2019) Further evaluation of the efficacy of emamectin benzoate for treating Pseudocapillaria tomentosa (Dujardin 1843) in zebrafish Danio rerio (Hamilton 1822).. Journal of fish diseases. 42(10). doi: 10.1111/jfd.13057
  • Armour, Courtney R., Nayfach, Stephen, Pollard, Katherine S., Sharpton, Thomas 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
  • Flannery, Jessica, Callaghan, Bridget, Sharpton, Thomas, Fisher, Philip, Pfeifer, Jennifer (2019) Is adolescence the missing developmental link in Microbiome-Gut-Brain axis communication?. Developmental psychobiology. 61(5). doi: 10.1002/dev.21821
  • Gaulke, Christopher A., Martins, Mauricio L., Watral, Virginia G., Humphreys, Ian R., Spagnoli, Sean T., Kent, Michael L., Sharpton, Thomas J. (2019) A longitudinal assessment of host-microbe-parasite interactions resolves the zebrafish gut microbiome's link to Pseudocapillaria tomentosa infection and pathology.. Microbiome. 7(1). doi: 10.1186/s40168-019-0622-9
  • Burns, A. R., Watral, V., Sichel, S., Spagnoli, S., Banse, A. V., Mittge, E., Sharpton, T. J., Guillemin, K., Kent, M. L. (2018) Transmission of a common intestinal neoplasm in zebrafish by cohabitation.. Journal of fish diseases. 41(4). doi: 10.1111/jfd.12743
  • Gaulke, Christopher A., Rolshoven, John, Wong, Carmen P., Hudson, Laurie G., Ho, Emily, Sharpton, Thomas J. (2018) Marginal Zinc Deficiency and Environmentally Relevant Concentrations of Arsenic Elicit Combined Effects on the Gut Microbiome.. mSphere. 3(6). doi: 10.1128/mSphere.00521-18
  • Kent, Michael L., Gaulke, Christopher A., Watral, Virginia, Sharpton, Thomas J. (2018) Pseudocapillaria tomentosa in laboratory zebrafish Danio rerio: patterns of infection and dose response.. Diseases of aquatic organisms. 131(2). doi: 10.3354/dao03286
  • Allan, Euan R. O., Tennessen, Jacob A., Sharpton, Thomas J., Blouin, Michael S. (2018) Allelic Variation in a Single Genomic Region Alters the Microbiome of the Snail Biomphalaria glabrata.. The Journal of heredity. 109(5). doi: 10.1093/jhered/esy014
  • Gaulke, Christopher A., Sharpton, Thomas J. (2018) The influence of ethnicity and geography on human gut microbiome composition.. Nature medicine. 24(10). doi: 10.1038/s41591-018-0210-8
  • Torres, Eileen Ruth S., Akinyeke, Tunde, Stagaman, Keaton, Duvoisin, Robert M., Meshul, Charles K., Sharpton, Thomas J., Raber, Jacob (2018) Effects of Sub-Chronic MPTP Exposure on Behavioral and Cognitive Performance and the Microbiome of Wild-Type and mGlu8 Knockout Female and Male Mice.. Frontiers in behavioral neuroscience. 12. doi: 10.3389/fnbeh.2018.00140
  • Sharpton, Thomas J. (2018) Role of the Gut Microbiome in Vertebrate Evolution.. mSystems. 3(2). doi: 10.1128/mSystems.00174-17
  • Gaulke, Christopher A., Arnold, Holly K., Humphreys, Ian R., Kembel, Steven W., O'Dwyer, James P., Sharpton, Thomas J. (2018) Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota.. mBio. 9(5). doi: 10.1128/mBio.01348-18
  • Conley, Melissa N., Roberts, Cooper, Sharpton, Thomas J., Iwaniec, Urszula T., Hord, Norman G. (2017) Increasing dietary nitrate has no effect on cancellous bone loss or fecal microbiome in ovariectomized rats.. Molecular nutrition & food research. 61(5). doi: 10.1002/mnfr.201600372
  • Foster, Zachary S. L., Sharpton, Thomas J., Grunwald, Niklaus J. (2017) Metacoder: An R package for visualization and manipulation of community taxonomic diversity data.. PLoS computational biology. 13(2). doi: 10.1371/journal.pcbi.1005404
  • Cheng, Yanfen, Wang, Ying, Li, Yuanfei, Zhang, Yipeng, Liu, Tianyi, Wang, Yu, Sharpton, Thomas J., Zhu, Weiyun (2017) Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing.. Frontiers in microbiology. 8. doi: 10.3389/fmicb.2017.02165
  • Wilson, Alexandria K., Watral, Virginia G., Kent, Michael L., Sharpton, Thomas J., Gaulke, Christopher A. (2017) Draft Genome Sequence of Pseudomonas sp. Strain DrBHI1 (Phylum Proteobacteria).. Genome announcements. 5(39). doi: 10.1128/genomeA.01090-17
  • Sharpton, Thomas, Lyalina, Svetlana, Luong, Julie, Pham, Joey, Deal, Emily M., Armour, Courtney, Gaulke, Christopher, Sanjabi, Shomyseh, Pollard, Katherine S. (2017) Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice.. mSystems. 2(5). doi: 10.1128/mSystems.00036-17
  • Gaulke, Christopher A., Barton, Carrie L., Proffitt, Sarah, Tanguay, Robert L., Sharpton, Thomas J. (2016) Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish.. PloS one. 11(5). doi: 10.1371/journal.pone.0154632
  • Conley, Melissa N., Wong, Carmen P., Duyck, Kyle M., Hord, Norman, Ho, Emily, Sharpton, Thomas J. (2016) Aging and serum MCP-1 are associated with gut microbiome composition in a murine model.. PeerJ. 4. doi: 10.7717/peerj.1854
  • Kent, Michael L., Watral, Virginia G., Kirchoff, Nicole S., Spagnoli, Sean T., Sharpton, Thomas J. (2016) Effects of Subclinical Mycobacterium chelonae Infections on Fecundity and Embryo Survival in Zebrafish.. Zebrafish. 13 Suppl 1. doi: 10.1089/zeb.2015.1204
  • Quandt, C. Alisha, Kohler, Annegret, Hesse, Cedar N., Sharpton, Thomas J., Martin, Francis, Spatafora, Joseph W. (2015) Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome.. Environmental microbiology. 17(8). doi: 10.1111/1462-2920.12840
  • Nayfach, Stephen, Bradley, Patrick H., Wyman, Stacia K., Laurent, Timothy J., Williams, Alex, Eisen, Jonathan A., Pollard, Katherine S., Sharpton, Thomas J. (2015) Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes.. PLoS computational biology. 11(11). doi: 10.1371/journal.pcbi.1004573
  • O'Dwyer, James P., Kembel, Steven W., Sharpton, Thomas J. (2015) Backbones of evolutionary history test biodiversity theory for microbes.. Proceedings of the National Academy of Sciences of the United States of America. 112(27). doi: 10.1073/pnas.1419341112
  • Sharpton, Thomas J., Gaulke, Christopher A. (2015) Modeling the Context-Dependent Associations between the Gut Microbiome, Its Environment, and Host Health.. mBio. 6(5). doi: 10.1128/mBio.01367-15
  • Kent, M. L., Soderlund, K., Thomann, Estela, Schreck, C. B., Sharpton, T. J. (2014) Post-mortem sporulation of Ceratomyxa shasta (Myxozoa) after death in adult Chinook salmon.. The Journal of parasitology. 100(5). doi: 10.1645/13-490.1
  • Sharpton, Thomas J. (2014) An introduction to the analysis of shotgun metagenomic data.. Frontiers in plant science. 5. doi: 10.3389/fpls.2014.00209
  • Finucane, Mariel M., Sharpton, Thomas J., Laurent, Timothy J., Pollard, Katherine S. (2014) A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter.. PloS one. 9(1). doi: 10.1371/journal.pone.0084689
  • Kidd, Jeffrey M., Sharpton, Thomas J., Bobo, Dean, Norman, Paul J., Martin, Alicia R., Carpenter, Meredith L., Sikora, Martin, Gignoux, Christopher R., Nemat-Gorgani, Neda, Adams, Alexandra, Guadalupe, Moraima, Guo, Xiaosen, Feng, Qiang, Li, Yingrui, Liu, Xiao, Parham, Peter, Hoal, Eileen G., Feldman, Marcus W., Pollard, Katherine S., Wall, Jeffrey D., Bustamante, Carlos D., Henn, Brenna M. (2014) Exome capture from saliva produces high quality genomic and metagenomic data.. BMC genomics. 15. doi: 10.1186/1471-2164-15-262
  • Skewes-Cox, Peter, Sharpton, Thomas J., Pollard, Katherine S., DeRisi, Joseph L. (2014) Profile hidden Markov models for the detection of viruses within metagenomic sequence data.. PloS one. 9(8). doi: 10.1371/journal.pone.0105067
  • Ladau, Joshua, Sharpton, Thomas J., Finucane, Mariel M., Jospin, Guillaume, Kembel, Steven W., O'Dwyer, James, Koeppel, Alexander F., Green, Jessica L., Pollard, Katherine S. (2013) Global marine bacterial diversity peaks at high latitudes in winter.. The ISME journal. 7(9). doi: 10.1038/ismej.2013.37
  • Human Microbiome Project Consortium (2012) A framework for human microbiome research.. Nature. 486(7402). doi: 10.1038/nature11209
  • Wylie, Kristine M., Truty, Rebecca M., Sharpton, Thomas J., Mihindukulasuriya, Kathie A., Zhou, Yanjiao, Gao, Hongyu, Sodergren, Erica, Weinstock, George M., Pollard, Katherine S. (2012) Novel bacterial taxa in the human microbiome.. PloS one. 7(6). doi: 10.1371/journal.pone.0035294
  • Whiston, Emily, Zhang Wise, Hua, Sharpton, Thomas J., Jui, Ginger, Cole, Garry T., Taylor, John W. (2012) Comparative transcriptomics of the saprobic and parasitic growth phases in Coccidioides spp.. PloS one. 7(7). doi: 10.1371/journal.pone.0041034
  • Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome.. Nature. 486(7402). doi: 10.1038/nature11234
  • Sharpton, Thomas J., Jospin, Guillaume, Wu, Dongying, Langille, Morgan G. I., Pollard, Katherine S., Eisen, Jonathan A. (2012) Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource.. BMC bioinformatics. 13. doi: 10.1186/1471-2105-13-264
  • Sharpton, Thomas J., Riesenfeld, Samantha J., Kembel, Steven W., Ladau, Joshua, O'Dwyer, James P., Green, Jessica L., Eisen, Jonathan A., Pollard, Katherine S. (2011) PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.. PLoS computational biology. 7(1). doi: 10.1371/journal.pcbi.1001061
  • Neafsey, Daniel E., Barker, Bridget M., Sharpton, Thomas J., Stajich, Jason E., Park, Daniel J., Whiston, Emily, Hung, Chiung-Yu, McMahan, Cody, White, Jared, Sykes, Sean, Heiman, David, Young, Sarah, Zeng, Qiandong, Abouelleil, Amr, Aftuck, Lynne, Bessette, Daniel, Brown, Adam, FitzGerald, Michael, Lui, Annie, Macdonald, J. Pendexter, Priest, Margaret, Orbach, Marc J., Galgiani, John N., Kirkland, Theo N., Cole, Garry T., Birren, Bruce W., Henn, Matthew R., Taylor, John W., Rounsley, Steven D. (2010) Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control.. Genome research. 20(7). doi: 10.1101/gr.103911.109
  • Sharpton, Thomas J., Stajich, Jason E., Rounsley, Steven D., Gardner, Malcolm J., Wortman, Jennifer R., Jordar, Vinita S., Maiti, Rama, Kodira, Chinnappa D., Neafsey, Daniel E., Zeng, Qiandong, Hung, Chiung-Yu, McMahan, Cody, Muszewska, Anna, Grynberg, Marcin, Mandel, M. Alejandra, Kellner, Ellen M., Barker, Bridget M., Galgiani, John N., Orbach, Marc J., Kirkland, Theo N., Cole, Garry T., Henn, Matthew R., Birren, Bruce W., Taylor, John W. (2009) Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives.. Genome research. 19(10). doi: 10.1101/gr.087551.108
  • Sharpton, Thomas J., Neafsey, Daniel E., Galagan, James E., Taylor, John W. (2008) Mechanisms of intron gain and loss in Cryptococcus.. Genome biology. 9(1). doi: 10.1186/gb-2008-9-1-r24
  • Sharpton, Thomas J., Jhaveri, Arpan A. (2006) Leveraging the knowledge of our peers: online communities hold the promise to enhance scientific research.. PLoS biology. 4(6). doi: 10.1371/journal.pbio.0040199