Claire E Couch, PhD
Claire Couch is a molecular ecologist who studies fish disease, microbiomes, and gene expression to better understand how environmental factors affect fish health and behavior. The purpose of her research is to clarify the complex interactions of biological and physical factors that limit recovery of threatened fish populations. Prior to joining WFRC, Claire was faculty at Oregon State University.
Claire uses a variety of laboratory, field-based, and analytical approaches to study the details of how environmental changes affect fish populations. Currently, her research focuses on how dams, reservoirs, and rearing conditions alter fish disease and physiology, and the potential consequences for population recovery. Claire has also conducted research on the health of hatchery fish, and how different rearing methods affect fish microbiomes and gene expression. She works closely with Tribal, State, and Federal partners to identify management-relevant research questions, and she partners with Universities to develop cutting-edge research methods to address these questions.
Professional Experience
2024-Present – Biologist, U.S. Geological Survey, Western Fisheries Research Center, Columbia River Research Laboratory, Cook, WA
2023-2024 – Assistant Professor (Senior Research), Oregon State University, Corvallis, OR
2022-2023 – Research Associate and Instructor, Oregon State University, Corvallis, OR
2020-2022 – Postdoctoral Scholar, Oregon State University, Corvallis, OR
2015-2020 – PhD Student
Education and Certifications
PhD. 2020. Integrative Biology, Oregon State University, Corvallis, OR
BS. 2013. Biology, University of Portland, Portland, OR
Science and Products
Unique diet and Philonema sp. infections in reservoir-rearing juvenile Chinook Salmon
ObjectiveDams and reservoirs can alter juvenile growth and survival of migratory salmonids through several physical and biological mechanisms. Juvenile Chinook Salmon Oncorhynchus tshawytscha that are produced upstream of large hydropower dams may have associated passage mortality, but the reservoirs created by these dams can support rapid growth. Characterizing the biotic drivers of...
Authors
Marina S. Larson, Anindo Choudhury, Ethan N. Gardner, Peter Konstantinidis, Christina Amy Murphy, Michael L. Kent, James Peterson, Claire E Couch
Gut microbiome composition associates with corticosteroid treatment, morbidity, and senescence in Chinook salmon (Oncorhynchus tshawytscha)
Pacific salmon experience prolonged elevation in corticosteroid hormones during important life history events including migration, reproduction, and senescence. These periods of elevated corticosteroids correspond with changes to immunity and energy metabolism; therefore, fish may be particularly vulnerable to mortality at these times. Recent studies found that stress-induced cortisol...
Authors
Claire E Couch, William T. Neal, Crystal L. Herron, Michael L. Kent, Carl Schreck, James Peterson
Effects of supplemental feeding on the fecal bacterial communities of Rocky Mountain elk in the Greater Yellowstone Ecosystem
Supplemental feeding of wildlife is a common practice often undertaken for recreational or management purposes, but it may have unintended consequences for animal health. Understanding cryptic effects of diet supplementation on the gut microbiomes of wild mammals is important to inform conservation and management strategies. Multiple laboratory studies have demonstrated the importance of...
Authors
Claire E Couch, Benjamin L. Wise, Brandon M. Scurlock, Jared D. Rogerson, Rebecca K. Fuda, Eric K. Cole, Kimberly E Szcodronski, Adam Sepulveda, Patrick R. Hutchins, Paul C. Cross
Non-USGS Publications**
Polley, Tamsen & Couch, Claire & Leong, Connor & Peterson, James & Weiss, Louis & Takvorian, Peter & Kent, Michael. (2025). Laboratory transmission of Adult Salmon Enteritis and associated pathogens in juvenile Chinook Salmon (Oncorhynchus tshawytscha). 10.1101/2025.04.07.647091.
Carey, K. C., Kent, M., Schreck, C. B., Couch, C. E., Whitman, L., & Peterson, J. T. (2024). Influence of stream temperature and human disturbance on prespawn mortality of Chinook Salmon in the Willamette River basin. North American Journal of Fisheries Management, 44(5), 1147-1164.
Mani, A., Henn, C., Couch, C., Patel, S., Lieke, T., Chan, J. T., ... & Salinas, I. (2024). A brain microbiome in salmonids at homeostasis. Science Advances, 10(38), eado0277.
Schuster, C. J., Murray, K. N., Sanders, J. L., Couch, C. E., & Kent, M. L. (2024). Review of Pseudoloma neurophilia (Microsporidia): A common neural parasite of laboratory zebrafish (Danio rerio). Journal of Eukaryotic Microbiology, 71(5), e13040.
Tsuchida, D. Y., Gentzkow, M. F., Spaan, R. S., Burco, J., Couch, C. E., Spaan, J. M., ... & Beechler, B. R. (2024). Bighorn Sheep (Ovis canadensis) with Higher Whole Blood Selenium Levels Have Improved Survival and Altered Immune Responses. The Journal of Wildlife Diseases, 60(3), 721-726.
Larson, M. S., Choudhury, A., Gardner, E. N., Konstantinidis, P., Murphy, C. A., Kent, M. L., ... & Couch, C. E. (2024). Unique diet and Philonema sp. infections in reservoir‐rearing juvenile Chinook Salmon. Transactions of the American Fisheries Society, 153(3), 312-325.
Couch, C., Sanders, J., Sweitzer, D., Deignan, K., Cohen, L., Broughton, H., ... & Beechler, B. (2022). The relationship between dietary trophic level, parasites and the microbiome of Pacific walrus (Odobenus rosmarus divergens). Proceedings of the Royal Society B, 289(1972), 20220079.
Laliberte, C., Devan-Song, A., Burco, J. D., Couch, C. E., Gentzkow, M. F., Spaan, R. S., ... & Beechler, B. R. (2023). A simple biochemical plasma test as an indicator of maternal energy balance predicts offspring survival in bighorn sheep. Frontiers in Ecology and Evolution, 11, 1106635.
Couch, C. E., Neal, W. T., Herron, C. L., Kent, M. L., Schreck, C. B., & Peterson, J. T. (2023). Gut microbiome composition associates with corticosteroid treatment, morbidity, and senescence in Chinook salmon (Oncorhynchus tshawytscha). Scientific Reports, 13(1), 2567.
Couch, C. E., Peterson, J. T., & Heimowitz, P. (2023). Evaluating the institutional and ecological effects of invasive species prevention policy: a case study from the US Fish and Wildlife Service. Management of Biological Invasions, 14(2), 269-288.
Couch, C. E., Colvin, M. E., Chitwood, R. L., Peterson, J. T., & Schreck, C. B. (2022). Scope of the cortisol stress response in Chinook salmon during maturation. Fisheries Research, 254, 106416.
Schuster, C. J., Sanders, J. L., Couch, C., & Kent, M. L. (2022). Recent advances with fish microsporidia. In Microsporidia: Current Advances in Biology (pp. 285-317). Cham: Springer International Publishing.
Yarborough, E., Glidden, C., Coon, C., Couch, C., Sisson, D., Johns, J., ... & Beechler, B. (2022). Exploring the use of the erythrocyte sedimentation rate as an inflammatory marker for free-ranging wildlife: a case study in african buffalo (syncerus caffer). The Journal of Wildlife Diseases, 58(2), 298-308.
Couch, C. E., Kent, M. L., Weiss, L. M., Takvorian, P. M., Nervino, S., Cummins, L., & Sanders, J. L. (2022). Enterocytozoon schreckii n. sp. infects the enterocytes of adult chinook salmon (Oncorhynchus tshawytscha) and may be a sentinel of immunosenescence. Msphere, 7(1), e00908-21.
Couch, C. E., & Epps, C. W. (2022). Host, microbiome, and complex space: applying population and landscape genetic approaches to gut microbiome research in wild populations. Journal of Heredity, 113(3), 221-234.
Rothenberg, S. E., Sweitzer, D. N., Rackerby, B. R., Couch, C. E., Cohen, L. A., Broughton, H. M., ... & Beechler, B. R. (2021). Fecal methylmercury correlates with gut microbiota taxa in Pacific walruses (Odobenus rosmarus divergens). Frontiers in Microbiology, 12, 648685.
Couch, C. E., Stagaman, K., Spaan, R. S., Combrink, H. J., Sharpton, T. J., Beechler, B. R., & Jolles, A. E. (2021). Diet and gut microbiome enterotype are associated at the population level in African buffalo. Nature communications, 12(1), 2267.
Yang, C., Kari, L., Lei, L., Carlson, J. H., Ma, L., Couch, C. E., ... & Caldwell, H. D. (2020). Chlamydia trachomatis plasmid gene protein 3 is essential for the establishment of persistent infection and associated immunopathology. MBio, 11(4), 10-1128.
Couch, C. E., Arnold, H. K., Crowhurst, R. S., Jolles, A. E., Sharpton, T. J., Witczak, M. F., ... & Beechler, B. R. (2020). Bighorn sheep gut microbiomes associate with genetic and spatial structure across a metapopulation. Scientific reports, 10(1), 6582.
Couch, C. E., Movius, M. A., Jolles, A. E., Gorman, M. E., Rigas, J. D., & Beechler, B. R. (2017). Serum biochemistry panels in African buffalo: Defining reference intervals and assessing variability across season, age and sex. PLoS One, 12(5), e0176830.
Yang, C., Kari, L., Sturdevant, G. L., Song, L., Patton, M. J., Couch, C. E., ... & Caldwell, H. D. (2017). Chlamydia trachomatis ChxR is a transcriptional regulator of virulence factors that function in in vivo host–pathogen interactions. Pathogens and Disease, 75(3), ftx035.
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
Science and Products
Unique diet and Philonema sp. infections in reservoir-rearing juvenile Chinook Salmon
ObjectiveDams and reservoirs can alter juvenile growth and survival of migratory salmonids through several physical and biological mechanisms. Juvenile Chinook Salmon Oncorhynchus tshawytscha that are produced upstream of large hydropower dams may have associated passage mortality, but the reservoirs created by these dams can support rapid growth. Characterizing the biotic drivers of...
Authors
Marina S. Larson, Anindo Choudhury, Ethan N. Gardner, Peter Konstantinidis, Christina Amy Murphy, Michael L. Kent, James Peterson, Claire E Couch
Gut microbiome composition associates with corticosteroid treatment, morbidity, and senescence in Chinook salmon (Oncorhynchus tshawytscha)
Pacific salmon experience prolonged elevation in corticosteroid hormones during important life history events including migration, reproduction, and senescence. These periods of elevated corticosteroids correspond with changes to immunity and energy metabolism; therefore, fish may be particularly vulnerable to mortality at these times. Recent studies found that stress-induced cortisol...
Authors
Claire E Couch, William T. Neal, Crystal L. Herron, Michael L. Kent, Carl Schreck, James Peterson
Effects of supplemental feeding on the fecal bacterial communities of Rocky Mountain elk in the Greater Yellowstone Ecosystem
Supplemental feeding of wildlife is a common practice often undertaken for recreational or management purposes, but it may have unintended consequences for animal health. Understanding cryptic effects of diet supplementation on the gut microbiomes of wild mammals is important to inform conservation and management strategies. Multiple laboratory studies have demonstrated the importance of...
Authors
Claire E Couch, Benjamin L. Wise, Brandon M. Scurlock, Jared D. Rogerson, Rebecca K. Fuda, Eric K. Cole, Kimberly E Szcodronski, Adam Sepulveda, Patrick R. Hutchins, Paul C. Cross
Non-USGS Publications**
Polley, Tamsen & Couch, Claire & Leong, Connor & Peterson, James & Weiss, Louis & Takvorian, Peter & Kent, Michael. (2025). Laboratory transmission of Adult Salmon Enteritis and associated pathogens in juvenile Chinook Salmon (Oncorhynchus tshawytscha). 10.1101/2025.04.07.647091.
Carey, K. C., Kent, M., Schreck, C. B., Couch, C. E., Whitman, L., & Peterson, J. T. (2024). Influence of stream temperature and human disturbance on prespawn mortality of Chinook Salmon in the Willamette River basin. North American Journal of Fisheries Management, 44(5), 1147-1164.
Mani, A., Henn, C., Couch, C., Patel, S., Lieke, T., Chan, J. T., ... & Salinas, I. (2024). A brain microbiome in salmonids at homeostasis. Science Advances, 10(38), eado0277.
Schuster, C. J., Murray, K. N., Sanders, J. L., Couch, C. E., & Kent, M. L. (2024). Review of Pseudoloma neurophilia (Microsporidia): A common neural parasite of laboratory zebrafish (Danio rerio). Journal of Eukaryotic Microbiology, 71(5), e13040.
Tsuchida, D. Y., Gentzkow, M. F., Spaan, R. S., Burco, J., Couch, C. E., Spaan, J. M., ... & Beechler, B. R. (2024). Bighorn Sheep (Ovis canadensis) with Higher Whole Blood Selenium Levels Have Improved Survival and Altered Immune Responses. The Journal of Wildlife Diseases, 60(3), 721-726.
Larson, M. S., Choudhury, A., Gardner, E. N., Konstantinidis, P., Murphy, C. A., Kent, M. L., ... & Couch, C. E. (2024). Unique diet and Philonema sp. infections in reservoir‐rearing juvenile Chinook Salmon. Transactions of the American Fisheries Society, 153(3), 312-325.
Couch, C., Sanders, J., Sweitzer, D., Deignan, K., Cohen, L., Broughton, H., ... & Beechler, B. (2022). The relationship between dietary trophic level, parasites and the microbiome of Pacific walrus (Odobenus rosmarus divergens). Proceedings of the Royal Society B, 289(1972), 20220079.
Laliberte, C., Devan-Song, A., Burco, J. D., Couch, C. E., Gentzkow, M. F., Spaan, R. S., ... & Beechler, B. R. (2023). A simple biochemical plasma test as an indicator of maternal energy balance predicts offspring survival in bighorn sheep. Frontiers in Ecology and Evolution, 11, 1106635.
Couch, C. E., Neal, W. T., Herron, C. L., Kent, M. L., Schreck, C. B., & Peterson, J. T. (2023). Gut microbiome composition associates with corticosteroid treatment, morbidity, and senescence in Chinook salmon (Oncorhynchus tshawytscha). Scientific Reports, 13(1), 2567.
Couch, C. E., Peterson, J. T., & Heimowitz, P. (2023). Evaluating the institutional and ecological effects of invasive species prevention policy: a case study from the US Fish and Wildlife Service. Management of Biological Invasions, 14(2), 269-288.
Couch, C. E., Colvin, M. E., Chitwood, R. L., Peterson, J. T., & Schreck, C. B. (2022). Scope of the cortisol stress response in Chinook salmon during maturation. Fisheries Research, 254, 106416.
Schuster, C. J., Sanders, J. L., Couch, C., & Kent, M. L. (2022). Recent advances with fish microsporidia. In Microsporidia: Current Advances in Biology (pp. 285-317). Cham: Springer International Publishing.
Yarborough, E., Glidden, C., Coon, C., Couch, C., Sisson, D., Johns, J., ... & Beechler, B. (2022). Exploring the use of the erythrocyte sedimentation rate as an inflammatory marker for free-ranging wildlife: a case study in african buffalo (syncerus caffer). The Journal of Wildlife Diseases, 58(2), 298-308.
Couch, C. E., Kent, M. L., Weiss, L. M., Takvorian, P. M., Nervino, S., Cummins, L., & Sanders, J. L. (2022). Enterocytozoon schreckii n. sp. infects the enterocytes of adult chinook salmon (Oncorhynchus tshawytscha) and may be a sentinel of immunosenescence. Msphere, 7(1), e00908-21.
Couch, C. E., & Epps, C. W. (2022). Host, microbiome, and complex space: applying population and landscape genetic approaches to gut microbiome research in wild populations. Journal of Heredity, 113(3), 221-234.
Rothenberg, S. E., Sweitzer, D. N., Rackerby, B. R., Couch, C. E., Cohen, L. A., Broughton, H. M., ... & Beechler, B. R. (2021). Fecal methylmercury correlates with gut microbiota taxa in Pacific walruses (Odobenus rosmarus divergens). Frontiers in Microbiology, 12, 648685.
Couch, C. E., Stagaman, K., Spaan, R. S., Combrink, H. J., Sharpton, T. J., Beechler, B. R., & Jolles, A. E. (2021). Diet and gut microbiome enterotype are associated at the population level in African buffalo. Nature communications, 12(1), 2267.
Yang, C., Kari, L., Lei, L., Carlson, J. H., Ma, L., Couch, C. E., ... & Caldwell, H. D. (2020). Chlamydia trachomatis plasmid gene protein 3 is essential for the establishment of persistent infection and associated immunopathology. MBio, 11(4), 10-1128.
Couch, C. E., Arnold, H. K., Crowhurst, R. S., Jolles, A. E., Sharpton, T. J., Witczak, M. F., ... & Beechler, B. R. (2020). Bighorn sheep gut microbiomes associate with genetic and spatial structure across a metapopulation. Scientific reports, 10(1), 6582.
Couch, C. E., Movius, M. A., Jolles, A. E., Gorman, M. E., Rigas, J. D., & Beechler, B. R. (2017). Serum biochemistry panels in African buffalo: Defining reference intervals and assessing variability across season, age and sex. PLoS One, 12(5), e0176830.
Yang, C., Kari, L., Sturdevant, G. L., Song, L., Patton, M. J., Couch, C. E., ... & Caldwell, H. D. (2017). Chlamydia trachomatis ChxR is a transcriptional regulator of virulence factors that function in in vivo host–pathogen interactions. Pathogens and Disease, 75(3), ftx035.
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.