Dr. Thomas Sharpton, Associate Professor

sharpton Office 530 Nash Hall

Lab Website

Lab Members


Phone 541-737-8623
FAX 541-737-0496
Email thomas.sharpton@oregonstate.edu
Education Ph.D., University of California, Berkeley

 Research Interests:  Defining the Microbiome's Role in Health and Evolution

 Courses Taught: ST 599 Introduction to Quantitative Genomics; MB 499 The Human Microbiome; MB 436 The Human Microbiome; ST 591 Introduction to Quantitative Genomics; MB 668 Microbial Bioinformatics and Genome Evolution



Research Overview  

Our laboratory strives to resolve the molecular functions used by the gut microbiome to influence health with the long-term aim of applying this knowledge to develop disease diagnostics and therapeutics. To this end, we employ systems biology approaches that measure the complex milieu of microbiome features (e.g., taxa, genes) and statistically model these data to zero-in on those features linked to health as well as the exogeneous factors (e.g., dietary nutrients, environmental toxicants, infectious agents) that influence them. We also seek to use this knowledge to advance our understanding of vertebrate evolution and ecology. Our work often involves the innovation of new methodology and research tools.

We value interdisciplinary collaborations, commercial partnerships, and open science practices. As part of our effort to empower microbiome research, we develop open-source software and offer training workshops in microbiome data analytics.

Our work is generously supported by the National Institutes of Health, the National Science Foundation, and the United States Drug Administration.

Microbiome Core Facility  

The Sharpton Lab manages the Microbiome Core Facility at OSU, which provides services centered on the generation and analysis of microbiome data, especially 16S rRNA gene sequence and metagenomic data. This BSL-2 facility specializes in the analysis of animal-associated microbiomes, including human stool, saliva, and tissue biopsies. The core implements best practices in data generation and analysis that are guided by the Human Microbiome Project and Earth Microbiome Project consortiums. Services include community-wide DNA extraction, library preparation, DNA sequencing (in collaboration with the Center for Genome Research and Biocomputing at OSU), and custom bioinformatic analyses. The core has to date processed 1000s of samples spanning human, mice, and zebrafish associated microbiomes.


Pub Med                                  Google Scholar

Kundu, P., Stagaman, K., Kasschau, K., Holden, S., Shulzhenko, N., Sharpton, T.J. and Raber, J.   2022.  Fecal implants from AppNL-G-F and AppNL-G-FE4 donor mice sufficient to induce behavioral phenotypes in germ-free mice.  Front. Behav. Neurosci., https://doi.org/10.3389/fnbeh.2022.791128

David, M.M., Tataru, C., Pope, Q., Baker, L.J., English, M.K., Epstein, H.E., Kent, M., Sieler, Jr., M.J., Mueller, R.S., Sharpton, T.J., Tomas, F., Vega Thurber, R., and Fern, X.Z.,   2022.  Revealing general patterns of microbiomes that transcend systems:  Potential and challenges of deep transfer learning.  Computational Biol.  DOI:  https://doi.org/10.1128/msystems.01058-21.

Mirzayi, C., Renson, A., Zohra, F., Elsafoury, S., Geistlinger, L., Kasselman, L.J. et al.,   2021.   Reporting guidelines for human microbiome research: the STORMS checklist  Nature Med. 27(11):1885-1892.

Watson, K.M., Gardner, I.H., Anand, S., Siemens, K.N., Sharpton, T.J., Kasschau, K., Dewey, E.N., Martindale, R., Gaulke, C.A., and Tsikitis, V.L.  2021.  Colonic Microbial Abundances Predict Adenoma Formers  Annals of Surgery, Oct. 22.

Wong, C.P., Magnusson, K.R., Sharpton, T.J. and Ho, E.  2021.  Effects of zinc status on age-related T cell dysfunction and chronic inflammation.  Biometals.  34(2):291-301.

Logan, I.E., Shuzhenko, N., Sharpton, T.J., Bobe, G., Liu, K., Nuss, S., Jones, M.L., Miranda, C.L., Vasquez-Perez, S., Pennington, J.M., Leonard, S.W., Choi, J., Wu, W., Gurung, M., Kim, J.P., Lowry, M.B., Morgun, A., Maier, C.S., Stevens, J.F., and Gombart, A.F.  2021.  Xanthohumol Requires the Intestinal Microbiota to Improve Glucose Metabolism in Diet-Induced Obese Mice.   Mol Nutr Food Res. 2021 Nov;65(21):e2100389.

Bouranis, J.A., Beaver, L.M., Choi, J., Wong, C.P., Jiang, D., Sharpton, T.J., Stevens, J.F., and Ho, E., 2021.  Composition of the Gut Microbiome Influences Production of Sulforaphane-Nitrile and Iberin-Nitrile from Glucosinolates in Broccoli Sprouts.  Nutrients 13(9).

Sharpton, T.J., Stagaman, K., Sieler, M.J., Arnold, H.K., and Davis, E.W.   2021.  Phylogenetic integration reveals the zebrafish core microbiome and its sensitivity to environmental exposures.  Toics 9(1):10.

Kent, M.L., Wall, E.S., Sichel, S., Watral, V., Stagaman, K., Sharpton, T.J. and Guilleman, K.  2021.  Pseudocapillaria tomentosa, Mycoplasma spp., and intestinal lesions in experimentally infected zebrafish Danio rerio.  bioRxiv

Rodrigues, R.R., Gurung, M., Li, Z., Garcia-Jaramillo, M., Greer, R., Gaulke, C., Bauchinger, F., You, H., Pederson, J.W., Vasquez-Perez, S., White, K.D., Frink, B., Philmus, B., Jump, D.B., Trinchieri, G., Berry, D., Sharpton, T.J., Dzutsev, A., Morgun, A.,and Shulzhenko, N.   2021. Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet-induced diabetes.  Nature Commun. 12(1). doi: 10.1038/s41467-020-20313-x

Nalven, S.G., Ward, C.P., Payet, J.P., Cory, R.M., Kling, G.W., Sharpton, T. J., Sullivan, C.M., and Crump, B.C.   2020.   Experimental metatranscriptomics reveals the costs and benefits of dissolved organic matter photo-alteration for freshwater microbes. Environ Microbiol. 22(8). doi: 10.1111/1462-2920.15121

Raber, J., Fuentes Anaya, A., Torres, E.R.S., Lee, J., Boutros, S., Grygoryev, D., Hammer, A., Kasschau, K.D., Sharpton, T.J., Turker, M.S., and Kronenberg, A.   2020.   Effects of Six Sequential Charged Particle Beams on Behavioral and Cognitive Performance in B6D2F1 Female and Male Mice. Frontiers in Physiol. 11. doi: 10.3389/fphys.2020.00959

Couch, C.E., Arnold, H.K., Crowhurst, R.S., Jolles, A.E., Sharpton, T.J., Witczak, M.F., Epps, C.W., and Beechler, B.R.   2020.  Bighorn sheep gut microbiomes associate with genetic and spatial structure across a metapopulation. Scientific Rpts. 10(1). doi: 10.1038/s41598-020-63401-0

Kashyap, A., Rhodes, A., Kronmiller, B., Berger, J., Champagne, A., Davis, E.W., Finnegan, M.V., Geniza, M., Hendrix, D.A., Lohr, C.V., Petro, V.M., Sharpton, T.J., Wells, J., Epps, C.W., Jaiswal, P., Tyler, B.M., and Ramsey, S.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, I.E., Bobe, G., Miranda, C.L., Vasquez-Perez, S., Choi, J., Lowry, M.B., Sharpton, T.J., Morgun, A., Maier, C.S., Stevens, J.F., Shulzhenko, N., and Gombart, A.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, R.M., Sharpton, T. J., Murray, K.N., Kent, A.D., and Kent, M.L.   2020.   Retrospective analysis of the Zebrafish International Resource Center diagnostic data links Pseudocapillaria tomentosa to intestinal neoplasms in zebrafish Danio rerio (Hamilton 1822).  J of Fish Diseases. 43(11). doi: 10.1111/jfd.13233

Stagaman, K., Sharpton, T.J., and Guillemin, K.   2020.   Zebrafish microbiome studies make waves.   Lab Animal. 49(7). doi: 10.1038/s41684-020-0573-\

Flannery, J.E., Stagaman, K., Burns, A.R., Hickey, R.J., Roos, L.E., Giuliano, R.J. Fisher, P.A., and Sharpton, T.J.  2020.  Gut Feelings Begin in Childhood:  The Gut Metagenome Correlates with Early Environment, Caregiving and BehaviormBio 11(1). doi: 10.1128/mBio.02780-19

Sharpton, T.J., Combrink, L., Arnold, H.K., Gaulke, C.A., and Kent, M.   2020.   Harnessing the gut microbiome in the fight against anthelminthic drug resistance.  Current Opinion in Microbiol. 53:26. 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 Intl J of Animal Biosci. 14(4). doi: 10.1017/S1751731119002453

Zhang, Y., Bobe, G., Revel, J.S., Rodrigues, R.R., Sharpton, T.J., Fantacone, M.L., Raslan, K., Miranda, C.L., Lowry, M.B., Blakemore, P.R., Morgun, A., Shulzhenko, N., Maier, C.S., Stevens, J.F., and Gombart, A.F.   2020.   Improvements in Metabolic Syndrome by Xanthohumol Derivatives Are Linked to Altered Gut Microbiota and Bile Acid MetabolismMolec Nutr and Food Res. 64(1). doi: 10.1002/mnfr.201900789

Mendez, R.L., Miranda, C., Armour, C.R., Sharpton, T.J., Stevens, J.F., and Kwon, J.Y.   2020.  Supplementation with Sea Vegetables Palmaria mollis and Undaria pinnatifida Exerts Metabolic Benefits in Diet-Induced Obesity in Mice.  Current Develop in Nutr. 4(5). doi: 10.1093/cdn/nzaa072

Jiang, D., Armour, C.R., Hu, C., Mei, M., Tian, C., Sharpton, T.J., and Jiang, Y.  2019.  Microbiome multi-omics network analysis:  Statistical considerations, limitations, and opportunities.  Front Genet.  10:995.  Doi: 10.3389/fgene.2019.00995.

Kent, M.L., Watral, V., Gaulke, C.A., and Sharpton, T.J.  2019.  Further evaluation of the efficacy of emamectin benzoate for treating Pseudocapillaria tomentosa (Dujardin 1843) in zebrafish Danio rerio (Hamilton 1822).  J. Fish Dis. doi:10.1111/jfd.13057.

Li, Y., Jin, W., Sharpton, T.J., Mackie, R.I., Cann, I., Cheng, Y., and Zhu, W.  2019.  Combined genomic, transcriptomic, proteomic, and physiological characterization of the growth of Pecoramyces sp. F1 in monoculture and co-culture with a syntrophic methanogen.  Front. Microbiol.  doi:10.3389/fmicb.2019.00435.

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.

Burns, AR., Watral, V., Sichel, S. Spagnoli, S., Banse, A.V., Mittge, E., Sharpton, T.J., Guillemin, K., Kent, M.L. 2018. Transmission of a common gastrointestinal neoplasm in zebrafish by co-habituation. J Fish Dis.41:569-579.

Gaulke, C.A., Arnold, H.K., Humphreys, I.R., Kembel, S.W., O'Dwyer, J.P., and Sharpton, T.J.  2018.  Ecophylogenetics clarifies the evolutionary association between mammals and their gut microbiota.  MBio. 9:(5).

Torres, E.R.S., Akinyeke, T., Stagaman, K., Duvoisin, R.M., Meshul, C.K., Sharpton, T.J. and Raber, J.  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.  Front Behav. Neurosci. 12:140.

Sharpton, T.J.  2018.  Role of the gut microbiome in vertebrate evolution.  mSystems.  3(2).  PMID 29629413.

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.

Cheng, Y., Wang, Y., Li, Y., Zhang, Y., Liu, T., Wang, Y., Sharpton, T.J., and Zhu, W. 2017.  Progressive colonization of bacteria and degradation of rice straw in the rumen by illumina sequencing.  Front Microbiol. 8:2165.

Wilson, A.K., Watral, V.G., Kent, M.L., Sharpton, T.J., and Gaulke, C.A.  2017.  Draft genome sequence of Pseudomonas sp. strain DrBHL1 (Phylum Proteobacteria).  Genome Announc. 5(39):PMID 28963227.

Sharpton, T., Lyalina, S., Luong, J., Pham, J., Deal, E.M., Armour, C., Gaulke, C., Sanjabi, S., and Pollard, K.S.  2017.  Development of inflammatory bowel disease is linked to a longitudinal restructuring of the gut metagenome in mice. newmSystems. 2(5). pii: e00036-17. doi: 10.1128/mSystems.00036-17.

Wilson, A.K., Watral, V.G., Kent, M.L., Sharpton, T.J., and Gaulke, C.A.  2017. Draft genome sequence of Pseudomonas sp. strain DrBHI1 (Phylum Proteobacteria).  Genome Announc. Sep 28;5(39).  PMID: 29023774

Foster, Z.S., Sharpton, T.J., and Grünwald, N.J.  2017.  Metacoder: An R package for visualization and manipulation of community taxonomic diversity data.  PLoS Comput Biol. 13(2):e1005404. doi: 10.1371/journal.pcbi.1005404.

Conley, M.N., Wong, C.P., Duyck, K.M., Hord, N., Ho, E., and Sharpton, T.J.  2016.  Aging and serum MCP-1 are associated with gut microbiome composition in a murine model.  PeerJ. PMID 27069796.

Gaulke, C.A., Barton, C.L., Proffitt, S., Tanguay, R.L., and Sharpton, T.J.  2016.  Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish.  PLoS One.  PMID  27191725

Kent, M.L., Watral, V.G., Kirchoff, N.S., Spagnoli, S.T., and Sharpton, T.J.  2016.  Effects of subclinical Mycobacterium chelonae infections on fecundity and embryo survival in zebrafish.  Zebrafish PMID 27031171.

Nayfach, S., Bradley, P.H., Wyman, S.K., Laurent, T.J., Williams, A., Eisen, J.A., Pollard, K.S., and Sharpton, T.J.  2015.  Automated and accurate estimation of gene family abundance from shotgun metagenomes.  PLoS Comput. Biol. 11(11)e1004573.

Sharpton, T.J. and Gaulke, C.A.  2015.  Modeling the context-dependent associations between the gut microbiome, its environment, and host health.  MBio.  6(5):e01367-15. doi:10.1128.

O'Dwyer J.P., Kembel, S.W. and Sharpton, T.J.  2015.  Backbones of evolutionary history test biodiversity theory for microbes.  Proc. Natl. Acad. Sci., 112(27):8356-61.

Quandt, C.A., Kohler, A., Hesse, C.N., Sharpton, T.J., Martin, F. and Spatafora, J.W.  2015.  Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome.  Environ. Microbiol. 17(8):2952-68.

Skewes-Cox, P., Sharpton, T.J., Ruby, J.G., Pollard, K.S., and DeRisi, J.L.  2014.  Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PLOS ONE. 9(8):e105067.

Sharpton, T.J.  2014.  An introduction to the analysis of shotgun metagenomic data.  Frontiers in Plant Genetics and Genomics. 16(5):209.

Kent, M.L., Soderlund, K., Thomann, E., Schreck, C.B., and Sharpton, T.J.  2014.  Post-mortem sporulation of Ceratomyxa shasta (myxozoa) after death in adult chinook salmon.  J. Parisitol.  PMID: 24725089.

Kidd, J.M., Sharpton, T.J., Bobo, D., Norman, P.J., Martin, A.R., Carpenter, M.L., Sikora, M.,Gignoux, C.R., Nemat-Gorgani, N., Adams, A., Guadalupe, M., Guo, X., Feng, Q., Li, Y., Liu, X., Parham, P., Hoal, E.G. Feldman, M.W., Pollard, K.S., Wall, J.D., Bustamante, C.D. and Henn, B.M.  2014.  Exome capture from saliva produces high quality genomic and metagenomic data.   BMC Genomics 4(15):262.

Finucane, M.M., Sharpton, T.J., Laurent, T.J., Pollard, K.S.  A taxonomic signature of obesity in the microbiome?  Getting to the guts of the matter.  2014.  PLOS ONE.  8;9(1):e84689.

Ladau, J., Sharpton, T.J., Jospin, G., Kembel, S.W., O'Dwyer, J.P., Koeppel, A., Green, J.L., and Pollard, K.S.  2013.  Global marine bacterial diversity peaks at high latitudes in winter. Intl. Soc. of Microbial Ecology J., March 1, DOI:10.1038/ismej.2013.37. PMC Journal, in process.

Wylie, K.M., Truty, R.M., Sharpton, T.J., Mihindukulasuriya, K.A., Zhou, Y., Gao, H., Sodergren, E., Weinstock, G.M., Pollard, K.S. and Pollard, K.S.  2012.  Novel bacterial taxa in the human microbiome. PLoS ONE, 7(6):e3529.  PMCID:PMC3374617.

The Human Microbiome Project Consortium.  2012.  A framework for human microbiome research. Nature, 486:215-221.  PMCID:PMC3377744.

The Human Microbiome Project Consortium.  2012.  Structure, function and diversity of the human microbiome in an adult reference population.  Nature, 486:207-214.  PMCID:PMC3564958.

Sharpton, T.J., Jospin, G., Wu, D., Langille, M., Pollard, K.S. and Eisen, J.A.  2012.  Sifting through genomes with iterative-sequence clustering produces a large, phylogentically diverse protein-family resource.  BMC Bioinformatics, 13:264.

Whiston, E., Wise, H.-Z., Jui, G., Sharpton, T.J., Cole, G.T., Tayor, J.W.  2012.  Comparative transcriptomics of the saprobic and parasitic growth phases in Coccidioides spp.  PLoS One, 7:e41034.

Sharpton, T.J., Riesenfed, S.J., Kembel, S.W., Ladau, J., O’Dwyer, J.P., Green, J.L., Eisen, J.A. and Pollard, K.S.  2011.  PhylOTU:  A high-throughput procedure quantified microbial community diversity and resolves novel taxa from metagenomic data.  PLoS Comput. Biol. , 7(1):e1001061. Doi:10.1371/ Journal.pcbi1001061.

Neafsey, D.E., Barker, B.M., Sharpton, T.J. Stajich, J.E., Park, D. et al. 2010.  Population genomic sequencing of Coccidiodes fungi reveals recent hybridization and transposon control.  Genome Research 20:938-946.

Sharpton, T.J., Stajich, J.E., Rounsley, S.D., Gardner, M.J., Wortman, J.R., Jordar, V.S., Maiti, R., Kodira, C.D., Neafsey, D.E., Zeng, Q., Hung, C., McMahan, C., Muszewska, A., Grynberg, M., Mandel, A., Kellner, E.M., Barker, B.M., Galgiani, J.N., Orbach, M.J., Kirkland, T.N., Cole, G.T., Henn, M.R., Birren, B.W. and Taylor, J.W.  2009.  Comparative genomic analyses of the human fungal pathogens Cocciodioides and their relatives.  Genome Research, 19(10):1722-1731.

Sharpton, T.J., Neafsey, D.E., Galagan, J.E. and Taylor, J.W.  2008.  Mechanisms of intron gain and loss in Cryptococcus.  2008.  Genome Biology, 9:R24; doi:10.1186/gb-2008-9-1-r24.

Sharpton, T.J. and Jhaveri, A.J.  2006.  Leveraging the knowledge of our peers:  Online communities hold the promise to enhance scientific research.  PLOS Biology, 4(6):904-905.