For most up to date publications, visit our google scholar page.
2025
  • Soumyadev Sarkar, Anna Kazarina, Paige M. Hansen, Kaitlyn Ward, Christopher Hargreaves, Nicholas Reese, Qinghong Ran, Willow Kessler, Ligia F.T. de Souza, Terry D. Loecke, Marcos V.M. Sarto, Charles W. Rice, Lydia H. Zeglin, Benjamin A. Sikes, Sonny T.M. Lee, Metabolism diversification of ammonia-oxidizing archaea and bacteria under different precipitation gradients and land legacies (2025). Applied Soil Ecology, Volume 206, 2025, 105831, ISSN 0929-1393, https://doi.org/10.1016/j.apsoil.2024.105831.
2024
  • Veerapandian Raja , Paudyal Anuja , Schneider Sarah M. , Lee Sonny T. M. , Vediyappan Govindsamy . A mouse model of immunosuppression facilitates oral Candida albicans biofilms, bacterial dysbiosis and dissemination of infection. (2024). Frontiers in Cellular and Infection Microbiology. VOLUME 14, DOI 10.3389/fcimb.2024.1467896, ISSN=2235-2988
  • Oguri N, Miyoshi J, Nishinarita Y, Wada H, Nemoto N, Hibi N, Kawamura N, Miyoshi S, Lee STM, Matsuura M, Osaki T, Hisamatsu T. Akkermansia muciniphila in the small intestine improves liver fibrosis in a murine liver cirrhosis model. NPJ Biofilms Microbiomes. (2024) Sep 16;10(1):81. doi: 10.1038/s41522-024-00564-y. PMID: 39285193; PMCID: PMC11405509.
2019 - 2023
  • Tanner G Richie, Leah Heeren, Abigail Kamke, Sophia Pogranichniy, Kourtney Rumback, Trey Summers, Hallie Wiechman, Qinghong Ran, Soumyadev Sarkar, Brandon Plattner, Lee STM. (2023). Limitation of sulfur-containing amino acid availability by specific bacterial populations during enhanced colitis in IBD mouse model. mSystems. (2023). doi: 10.1128/msystems.00703-23.
  • Jason W. Dallas, Anna Kazarina, Lee STM, Robin W. Warne; Cross-species gut microbiota transplantation predictably affects host heat tolerance. J Exp Biol (2023); jeb.246735. doi: https://doi.org/10.1242/jeb.246735
  • Brandi Feehan, Qinghong Ran, Victoria Dorman, Kourtney Rumback, Sophia Pogranichniy, Kaitlyn Ward, Robert Goodband, Megan Niederwerder, Sonny T M Lee. Novel Complete Methanogenic Pathways in Longitudinal Genomic Study of Monogastric Age-Associated Archaea. Animal Microbiome 5, 35 (2023). https://doi.org/10.1186/s42523-023-00256-6. 
  • Anna Kazarina, Soumyadev Sarkar, Shiva Thapa, Leah Heeren, Abigale Kamke, Kaitlyn Ward, Eli Hartung, Qinghong Ran, Matthew Galliart, Ari Jumpponen, Loretta Johnson, Sonny TM Lee. 2023. Home-field advantage affects the local adaptive interaction between Andropogon gerardii ecotypes and rhizobiome.  Microbiology Spectrum. e00208-23. (2023). doi: 10.1128/spectrum.00208-23.
  • Wada, H., Miyoshi, J., Kuronuma, S., Nishinarita, Y., Oguri, N., Hibi, N., Takeuchi, O., Akimoto, Y., Lee, STM., Matsuura, M., Kobayashi, T., Hibi, T., Hisamatsu, T.*  5-Aminosalicylic acid alters the gut microbiota and altered microbiota transmitted vertically to offspring have protective effects against colitis. Scientific Reports 13, 12241 (2023). https://doi.org/10.1038/s41598-023-39491-x.
  • Watson, A., Füssel, J., Veseli, I., Zaal DeLongchamp, J., Silva, M., Trigodet, F., Lolans, K., Shaiber, A., Fogarty, E., Runde, J., Quince, C., Yu, M., Söylev, A., Morrison, H., Lee, STM, Kao, D., Rubin, D., Jabri, B., Louie, T.,  Eren, AM.* Metabolic independence drives gut microbial colonization and resilience in health and disease. Genome Biology (2023). 24:78. https://doi.org/10.1186/s13059-023-02924-x
  • Morrison AG, Sarkar S, Umar S, Lee STM, Thomas SM. The Contribution of the Human Oral Microbiome to Oral Disease: A Review. Microorganisms. 2023 Jan 26;11(2):318. doi: 10.3390/microorganisms11020318. PMID: 36838283; PMCID: PMC9962706.
  • Bender MJ, McPherson AC, Phelps CM, Pandey SP, Laughlin CR, Shapira JH, Medina Sanchez L, Rana M, Richie TG, Mims TS, Gocher-Demske AM, Cervantes-Barragan L, Mullett SJ, Gelhaus SL, Bruno TC, Cannon N, McCulloch JA, Vignali DAA, Hinterleitner R, Joglekar AV, Pierre JF, Lee STM, Davar D, Zarour HM, Meisel M. Dietary tryptophan metabolite released by intratumoral Lactobacillus reuteri facilitates immune checkpoint inhibitor treatment. Cell. 2023 Apr 27;186(9):1846-1862.e26. doi: 10.1016/j.cell.2023.03.011. Epub 2023 Apr 6. PMID: 37028428; PMCID: PMC10148916.
  • Sarkar S, Kamke A, Ward K, Rudick AK, Baer SG, Ran Q, Feehan B, Thapa S, Anderson L. Galliart M, Jumpponen A, Johnson L, Sonny T.M. Lee. Bacterial but Not Fungal Rhizosphere Community Composition Differ among Perennial Grass Ecotypes under Abiotic Environmental Stress. Microbiol Spectr. (2022) Apr 20; PubMed PMID: 35442065.
  • Attard, T.M., Septer, S., Lawson, C.E. Attard, M.I., Lee, S.T.M., Umar, S. Microbiome insights into pediatric familial adenomatous polyposis. Orphanet J Rare Dis 17, 416 (2022). https://doi.org/10.1186/s13023-022-02569-
  • Hannah Irene Dea, Abigail Urban, Anna Kazarina, Gregory Houseman, Samantha G Thomas, Terry Loecke, Mitchell J Greer, Thomas Gene Platt, Sonny Lee, Ari Jumpponen. Precipitation, not land use, primarily determines the composition of both plant and phyllosphere fungal communities. 2022. Frontiers in Fungal Biology, section Fungi-Plant Interactions
  • Proctor A, Parvinroo S, Richie T, Jia X, Lee S.T.M., Karp PD, Paley S, Kostic AD, Pierre JF, Wannemuehler MJ, Phillips GJ. Resources to Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model to Study Microbiome Function. mSystems. 2022 Oct 26;7(5):e0029322. doi: 10.1128/msystems.00293-22. Epub 2022 Aug 15. PMID: 35968975; PMCID: PMC9600240.
  • Brandi Feehan, Qinghong Ran, Victoria Dorman, Kourtney Rumback, Sophia Pogranichniy, Kaitlyn Ward, Robert Goodband, Megan C Niederwerder, Katie Lynn Summers, Sonny T.M. Lee. Stability and volatility shape the gut bacteriome and mycobiome dynamics in a pig model. 2022. Scientific Reports volume 12, Article number: 15080. https://doi.org/10.1038/s41598-022-19093-9
  • Sarkar S, Kamke A, Ward K, Rudick A, Baer S, Ran Q, Feehan B, Thapa S, Anderson L, Galliart M, Jumpponen A, Johnson L, Sonny T.M. Lee. Bacterial but Not Fungal Rhizosphere Community Composition Differ among Perennial Grass Ecotypes under Abiotic Environmental Stress. Microbiology Spectrum. DOI:https://doi.org/10.1128/spectrum.02391-21. 
  • Soumyadev Sarkar, Kaitlyn Ward, Abigail Kamke, Qinghong Ran, Brandi Feehan, Tanner Richie, Sonny T.M. Lee. Simple state communities to study microbial interactions: examples and future direction. Frontiers in Microbiology. (2022). Front. Microbiol., 27 January 2022 | https://doi.org/10.3389/fmicb.2022.801864
  • Suchetana Gupta, Ditipriya Mallick, Kumarjeet Banerjee, Shrimon Mukherjee, Soumyadev Sarkar, Sonny T.M. Lee, Partha Basuchowdhuri, Siddhartha S Jana. D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. (2022) Computational and Structural Biotechnology Journal, Volume 20, 2022, Pages 766-778, ISSN 2001-0370, https://doi.org/10.1016/j.csbj.2022.01.017. 
  • Justin Chau, Meeta Yadav, Ben Liu, Muhammad Furqan, Qun Dai, Shailesh Shahi, Arnav Gupta, Keri Nace Mercer, Evan Eastman, Taher Abu Hejleh, Carlos Chan, George J Weiner, Catherine Cherwin, Sonny T.M. Lee, Cuncong Zhong, Ashutosh Mangalam, Jun Zhang. (2021) Prospective correlation between the patient microbiome with response to and development of immune-mediated adverse effects to immunotherapy in lung cancer. BMC Cancer 21,1, 1-14. 
  • Jun Miyoshi, Sawako Miyoshi, Tom O Delmont, Candace Cham, Sonny T.M. Lee, Aki Sakatani, Karen Yang, Yue Shan, 
    Evan Kiefl, Mahmoud Yousef, Sean Crosson, Mitchell Sogin, Dionysios A Antonopoulos, A Murat Eren, Vanessa Leone, Eugene B Chang. (2021) Early-Life Microbial Restitution Reduces Colitis Risk Promoted by Antibiotic-Induced Gut Dysbiosis in Interleukin 10–/– Mice. Gastroenterology https://doi.org/10.1053/j.gastro.2021.05.054
  • Alon Shaiber, Amy D Willis, Tom O Delmont, Simon Roux, Lin-Xing Chen, Abigail C Schmid, Mahmoud Yousef, Andrea R Watson, Karen Lolans, Ozcan C Esen, Sonny T.M. Lee, Nora Downey, Hilary G Morrison, Floyd Dewhirst, Jessica L Mark Welch, A. Murat Eren. (2020) Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome. Genome Biol 21, 292. https://doi.org/10.1186/s13059-020-02195-w
  • Jun Miyoshi, Sonny T.M. Lee, Megan Kennedy, Mora Puertolas, Mary Frith, Jason C. Koval, Sawako Miyoshi, Dionysios A. Antonopoulos, Vanessa Leone, Eugene B. Chang. (2020). Metagenomic alterations in gut microbiota precede and predict onset of colitis in the IL10 gene-deficient murine model. Cellular and Molecular Gastroenterology and Hepatology https://doi.org/10.1016/j.jcmgh.2020.08.008
  • Sonny TM Lee, Jiun-Yan Ding, Pei-Wen Chiang, Mike Dyall-Smith, Sen-Lin Tang. (2020). Insights into gene regulation of the halovirus His2 infecting Haloarcula hispanica. MicrobiologyOpen. ​DOI: 10.1002/mbo3.1016.
  • Jun Miyoshi,  Vanessa Leone,  Sawako Miyoshi,  Lee Sonny T.M.,  Aki Sakatani, A Murat Eren, Eugene Chang. (2019) Peripartum antibiotic exposure induces persistence gut dysbiosis, impairs the development of immune tolerance, and increases risk for inflammatory bowel disease in genetically susceptible offspring. Gastroenterology 156(3):S101. DOI:10.1053/j.gastro.2019.01.235
​
Preprints
  • Eubacterium rectale detoxification mechanism increases resilience of the gut environment. Tanner G Richie, Hallie Wiechman, Carson Ingold, Leah Heeren, Abigail Kamke, Sophia Pogranichniy, Kourtney Monk, Trey Summers, Qinghong Ran, Soumyadev Sarkar, Brandon L Plattner, Ashley M Sidebottom, Eugene Chang, Sonny TM Lee. (2024). bioRxiv. doi: https://doi.org/10.1101/2024.05.09.593360
  • Brandi Feehan, Qinghong Ran, Kourtney Monk, T. G. Nagaraja, M. D. Tokach, Raghavendra G. Amachawadi, Sonny T M Lee. High proportions of single-nucleotide variations associated with multidrug resistance in swine gut microbial populations. (2022). bioRxiv 2022.12.03.518979; doi: https://doi.org/10.1101/2022.12.03.518979

​