PUBLICATIONS

Ayayee, P., Custer, G., Clayton, J. B., Price, J., Ramer-Tait, A., & Larsen, T. Assessing gut microbial provisioning of essential amino acids to host in a mouse model with reconstituted gut microbiomes. Commun Biol 8, 1604 (2025). https://doi.org/10.1038/s42003-025-08966-0

Hernandez, J.B., Hayer, S.S., Alvarez, S., Fischer, A., Hassenstab, H.R., Cooper, K., Alsafwani, Z.W., Benson, A.K., Suhr Van Haute, M.J., Izard, J., Song, H., Clayton, J.B.(2025). Microbiome and metabolome association network analysis identifies Clostridium_sensu_stricto_1 as a stronger keystone genus candidate than Bifidobacterium in the gut of common marmosets. mSystems0:e00214-25. https://doi.org/10.1128/msystems.00214-25

Davison S., Mascellani Bergo A., Ward Z., Sackett A., Strykova A., Jaimes J.D., et al. Cardiometabolic disease risk in gorillas is associated with altered gut microbial metabolism. npj Biofilms Microbiomes. 2025 Feb 21;11(1):33. https://doi.org/10.1038/s41522-025-00664-3

Hayer, S. S., Conrin, M., French, J. A., Benson, A. K., Alvarez, S., Cooper, K., … Clayton, J. B. (2024). Antibiotic-induced gut dysbiosis elicits gut-brain axis relevant multi-omic signatures and behavioral and neuroendocrine changes in a nonhuman primate model. Gut Microbes, 16(1). https://doi.org/10.1080/19490976.2024.2305476

Corewyn, L. C., Kelaita, M. A., Nollman, J., Hagnauer, I., Blanco-Peña, K., Lessnau, R. G., Clayton, J. B., Shields-Cutler, R., & Stoos, K. B. (2023). Hematology and blood biochemistry in a declining population of mantled howler monkeys (Alouatta palliata palliata) at La Pacifica, Costa Rica. Journal of Medical Primatology, 52(6), 353-360. https://doi.org/10.1111/jmp.12669

Hayer, S. S., Hwang, S., & Clayton, J. B. (2023). Antibiotic-induced gut dysbiosis and cognitive, emotional, and behavioral changes in rodents: A systematic review and meta-analysis. Frontiers in Neuroscience, 17, 1237177. https://doi.org/10.3389/fnins.2023.1237177

Cooper, K., Clarke, M., & Clayton, J. B. (2023). Informatics for your Gut: at the Interface of Nutrition, the Microbiome, and Technology. Yearbook of Medical Informatics, 32(01), 089–098. https://doi.org/10.1055/s-0043-1768723

Greene, L. K., McKenney, E. A., Gasper, W., Wrampelmeier, C., Hayer, S., Ehmke, E. E., & Clayton, J. B. (2023). Gut site and gut morphology predict microbiome structure and function in ecologically diverse lemurs. Microbial Ecology, 85(4), 1608–1619. https://doi.org/10.1007/s00248-022-02034-4

De Campos, L. J., Seleem, M. A., Feng, J., De Oliveira, K. M. P., De Andrade Dos Santos, J. V., Hayer, S., Clayton, J. B., Kathi, S., Fisher, D. J., Ouellette, S. P., & Conda-Sheridan, M. (2023). Design, biological Evaluation, and Computer-Aided analysis of dihydrothiazepines as selective antichlamydial agents. Journal of Medicinal Chemistry, 66(3), 2116–2142. https://doi.org/10.1021/acs.jmedchem.2c01894

Wills, M. O., R., R., Brunmeier, E., Weissenborn, M., Murphy, T., Knights, D., Johnson, T. J., & Clayton, J. B. (2022). Host Species and Captivity Distinguish the Microbiome Compositions of a Diverse Zoo-Resident Non-Human Primate Population. Diversity, 14(9), 715. https://doi.org/10.3390/d14090715

Sharma, A. K., Davison, S., Pafco, B., Clayton, J. B., Rothman, J. M., McLennan, M. R., Cibot, M., Fuh, T., Vodicka, R., Robinson, C. J., Petrzelkova, K., & Gomez, A. (2022). The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors. Npj Biofilms and Microbiomes, 8(1), 1-11. https://doi.org/10.1038/s41522-022-00274-3

Amato, K. R., Clayton, J. B., & Hale, V. L. (2022). 7 Colobine Gut Microbiota. The Colobines: Natural History, Behaviour and Ecological Diversity, 89, 78. https://books.google.com/books?id=3XJdEAAAQBAJ&pg=PA78

Eschweiler, K., Clayton, J. B., Moresco, A., McKenney, E. A., Minter, L. J., J., M., Gasper, W., Hayer, S. S., Zhu, L., & Cooper, K. (2021). Host Identity and Geographic Location Significantly Affect Gastrointestinal Microbial Richness and Diversity in Western Lowland Gorillas (Gorilla gorilla gorilla) under Human Care. Animals, 11(12), 3399. https://doi.org/10.3390/ani11123399

Muehlbauer, A. L., Richards, A. L., Alazizi, A., Burns, M. B., Gomez, A., Clayton, J. B., Petrzelkova, K., Cascardo, C., Resztak, J., Wen, X., Pique-Regi, R., Luca, F., & Blekhman, R. (2021, November 23). Interspecies variation in hominid gut microbiota controls host gene regulation. Cell Reports. https://doi.org/10.1016/j.celrep.2021.110057

Guevara, E. E., Greene, L. K., Blanco, M. B., Farmer, C., Ranaivonasy, J., Ratsirarson, J., Mahefarisoa, K. L., Rajaonarivelo, T., Rakotondrainibe, H. H., Junge, R. E., Williams, C. V., Rambeloson, E., Rasoanaivo, H. A., Rahalinarivo, V., Andrianandrianina, L. H., Clayton, J. B., Rothman, R. S., Lawler, R. R., Bradley, B. J., . . . Yoder, A. D. (2021). Molecular Adaptation to Folivory and the Conservation Implications for Madagascar’s Lemurs. Frontiers in Ecology and Evolution, 9, 736741. https://doi.org/10.3389/fevo.2021.736741

Johnstone, K. F., Wei, Y., Bittner-Eddy, P. D., Vreeman, G. W., Stone, I. A., Clayton, J. B., Reilly, C. S., Walbon, T. B., Wright, E. N., Hoops, S. L., Boyle, W. S., Costalonga, M., & Herzberg, M. C. (2021). Calprotectin (S100A8/A9) is an innate immune effector in experimental periodontitis. Infection and Immunity, 89(10). https://doi.org/10.1128/iai.00122-21

Joseph, N., Clayton, J. B., Hoops, S. L., Linhardt, C. A., Mohd Hashim, A., Mohd Yusof, B. N., Kumar, S., & Amin Nordin, S. (2020). Alteration of the Gut Microbiome in Normal and Overweight School Children from Selangor with Lactobacillus Fermented Milk Administration. Evolutionary Bioinformatics. https://doi.org/10.1177/1176934320965943

Hayer, S. S., Lim, S., Hong, S., Elnekave, E., Johnson, T., Rovira, A., Vannucci, F., Clayton, J. B., Perez, A., & Alvarez, J. (2020). Genetic Determinants of Resistance to Extended-Spectrum Cephalosporin and Fluoroquinolone in Escherichia coli Isolated from Diseased Pigs in the United States. MSphere, 5(5). https://doi.org/10.1128/msphere.00990-20

Sidiropoulos, D. N., Al-Ghalith, G. A., Shields-Cutler, R. R., Ward, T. L., Johnson, A. J., Vangay, P., Knights, D., Kashyap, P. C., Xian, Y., Ramer-Tait, A. E., & Clayton, J. B. (2020). Wild primate microbiomes prevent weight gain in germ-free mice. Animal Microbiome, 2(1). https://doi.org/10.1186/s42523-020-00033-9

Zhu, L., Clayton, J. B., Van Haute, M. J. S., Yang, Q., Hassenstab, H. R., Mustoe, A. C., Knights, D., Benson, A. K., & French, J. A. (2020). Sex Bias in Gut Microbiome Transmission in Newly Paired Marmosets (Callithrix jacchus). MSystems, 5(2). https://doi.org/10.1128/msystems.00910-19

Ward, T. L., Weber, B. P., Mendoza, K. M., Danzeisen, J. L., Llop, K., Lang, K., Clayton, J. B., Grace, E., Brannon, J., Radovic, I., Beauclaire, M., Heisel, T. J., Knights, D., Cardona, C., Kogut, M., Johnson, C., Noll, S. L., Arsenault, R., Reed, K. M., & Johnson, T. J. (2019). Antibiotics and Host-Tailored probiotics similarly modulate effects on the developing avian microbiome, mycobiome, and host gene expression. MBio, 10(5). https://doi.org/10.1128/mbio.02171-19

Clayton, J. B., Shields-Cutler, R. R., Hoops, S. L., Al-Ghalith, G. A., M. Sha, J. C., Johnson, T. J., & Knights, D. (2019). Bacterial community structure and function distinguish gut sites in captive red-shanked doucs (Pygathrix nemaeus). American Journal of Primatology, 81(10-11), e22977. https://doi.org/10.1002/ajp.22977

Greene, L. K., Clayton, J. B., Rothman, R. S., Semel, B. P., Semel, M. A., Gillespie, T. R., Wright, P. C., & Drea, C. M. (2019). Local habitat, not phylogenetic relatedness, predicts gut microbiota better within folivorous than frugivorous lemur lineages. Biology Letters, 15(6), 20190028. https://doi.org/10.1098/rsbl.2019.0028

Clayton, J. B., Danzeisen, J. L., Johnson, T. J., Trent, A. M., Hayer, S. S., Murphy, T., Wuenschmann, A., Elder, M., Shen, Z., Mannion, A., Bryant, E., Knights, D., & Fox, J. G. (2019). Characterization of Campylobacter jejuni, Campylobacter upsaliensis, and a novel Campylobacter sp. In a captive non-human primate zoological collection. Journal of Medical Primatology, 48(2), 114-122. https://doi.org/10.1111/jmp.12393

Cabana, F., Clayton, J. B., Nekaris, K. A., Wirdateti, W., Knights, D., & Seedorf, H. (2019). Nutrient-based diet modifications impact on the gut microbiome of the Javan slow loris (Nycticebus javanicus). Scientific Reports, 9(1), 1-11. https://doi.org/10.1038/s41598-019-40911-0

Clayton, J. B., A., G., Long, H. T., Tuan, B. V., Cabana, F., Huang, H., Vangay, P., Ward, T., Minh, V. V., Tam, N. A., Dat, N. T., Travis, D. A., Murtaugh, M. P., Covert, H., Glander, K. E., Nadler, T., Toddes, B., Sha, J. C., Singer, R., . . . Johnson, T. J. (2018). Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model. Scientific Reports, 8(1), 1-16. https://doi.org/10.1038/s41598-018-29277-x

Clayton, J. B., Gomez, A., Amato, K., Knights, D., Travis, D. A., Blekhman, R., Knight, R., Leigh, S., Stumpf, R., Wolf, T., Glander, K. E., Cabana, F., & Johnson, T. J. (2018). The gut microbiome of nonhuman primates: Lessons in ecology and evolution. American Journal of Primatology, 80(6), e22867. https://doi.org/10.1002/ajp.22867

Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., A., J., Janssen, S., Kopylova, E., González, A., Morton, J. T., Mirarab, S., Zech Xu, Z., Jiang, L., Haroon, M. F., Clayton, J.B. . . . Knight, R. (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551(7681), 457-463. https://doi.org/10.1038/nature24621

Springer, A., Fichtel, C., Al-Ghalith, G. A., Koch, F., Amato, K. R., Clayton, J. B., Knights, D., & Kappeler, P. M. (2017). Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux's sifakas (Propithecus verreauxi). Ecology and Evolution, 7(15), 5732-5745. https://doi.org/10.1002/ece3.3148

Torres, S., Clayton, J. B., Danzeisen, J. L., Ward, T., Huang, H., Knights, D., & Johnson, T. J. (2017). Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time. PeerJ, 5, e3075. https://doi.org/10.7717/peerj.3075

Clayton, J. B., Vangay, P., Huang, H., Ward, T., Hillmann, B. M., A., G., Travis, D. A., Long, H. T., Tuan, B. V., Minh, V. V., Cabana, F., Nadler, T., Toddes, B., Murphy, T., Glander, K. E., Johnson, T. J., & Knights, D. (2016). Captivity humanizes the primate microbiome. Proceedings of the National Academy of Sciences, 113(37), 10376-10381. https://doi.org/10.1073/pnas.1521835113

Gohl, D. M., Vangay, P., Garbe, J., MacLean, A., Hauge, A., Becker, A., Gould, T. J., Clayton, J. B., Johnson, T. J., Hunter, R., Knights, D., & Beckman, K. B. (2016). Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies. Nature Biotechnology, 34(9), 942-949. https://doi.org/10.1038/nbt.3601

Amato, K. R., Metcalf, J. L., Song, S. J., Hale, V. L., Clayton, J.B., Ackermann, G., Humphrey, G., Niu, K., Cui, D., Zhao, H., Schrenzel, M. D., Tan, C. L., Knight, R., & Braun, J. (2016). Using the gut microbiota as a novel tool for examining colobine primate GI health. Global Ecology and Conservation, 7, 225-237. https://doi.org/10.1016/j.gecco.2016.06.004

Danzeisen, J.L., Clayton, J.B., Huang, H., Knights, D., McComb, B., Hayer, S.S., and Johnson, T.J. (2015) Temporal Relationships Exist Between Cecum, Ileum, and Litter Bacterial Microbiomes in a Commercial Turkey Flock, and Subtherapeutic Penicillin Treatment Impacts Ileum Bacterial Community Establishment. Front. Vet. Sci. 2:56. http://doi.org/10.3389/fvets.2015.00056.

Clayton, J. B., Danzeisen, J. L., Trent, A. M., Murphy, T., & Johnson, T. J. (2014). Longitudinal Characterization of Escherichia coli in Healthy Captive Non-Human Primates. Frontiers in Veterinary Science, 1, 119633. https://doi.org/10.3389/fvets.2014.00024

Clayton, J. B., & Glander, K. E. (2011). Dietary choices by four captive slender lorises (Loris tardigradus) when presented with various insect life stages. Zoo Biology, 30(2), 189-198. https://doi.org/10.1002/zoo.20346