Diversity and Function of Gut Microbiome

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Park, H., Lynch, E., Tillman, A., Lewis, K., Jin, Z., Uhlemann, A.-C., Abrams, J. A., & Freedberg, D. E. (2025). A phase 2 randomized, placebo-controlled trial of inulin for the prevention of gut pathogen colonization and infection among patients admitted to the intensive care unit for sepsis. Critical Care, 29(1). https://doi.org/10.1186/s13054-024-05232-3
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Jakaria Al-Mujahidy, Sk. Md., Kryukov, K., Ikeo, K., Saito, K., Uddin, Md. E., & Ibn Sina, A. A. (2024). Functional genomic analysis of the isolated potential probiotic Lactobacillus delbrueckii subsp. indicus TY-11 and its comparison with other Lactobacillus delbrueckii strains. Microbiology Spectrum, 12(7). https://doi.org/10.1128/spectrum.03470-23
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Pannkuk, E. L., Shuryak, I., Kot, A., Yun-Tien Lin, L., Li, H.-H., & Fornace, A. J. (2024). Host microbiome depletion attenuates biofluid metabolite responses following radiation exposure. PLOS ONE, 19(5), e0300883. https://doi.org/10.1371/journal.pone.0300883
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Sepich-Poore, G. D., McDonald, D., Kopylova, E., Guccione, C., Zhu, Q., Austin, G., Carpenter, C., Fraraccio, S., Wandro, S., Kosciolek, T., Janssen, S., Metcalf, J. L., Song, S. J., Kanbar, J., Miller-Montgomery, S., Heaton, R., Mckay, R., Patel, S. P., Swafford, A. D., … Knight, R. (2024). Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene, 43(15), 1127–1148. https://doi.org/10.1038/s41388-024-02974-w
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Reuter, M. A., Tucker, M., Marfori, Z., Shishani, R., Bustamante, J. M., Moreno, R., Goodson, M. L., Ehrlich, A., Taha, A. Y., Lein, P. J., Joshi, N., Brito, I., Durbin-Johnson, B., Nandakumar, R., & Cummings, B. P. (2024). Dietary resistant starch supplementation increases gut luminal deoxycholic acid abundance in mice. Gut Microbes, 16(1). https://doi.org/10.1080/19490976.2024.2315632
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Mullish, B. H., Michael, D. R., Dabcheva, M., Webberley, T. S., Coates, N., John, D. A., Wang, D., Luo, Y., Plummer, S. F., & Marchesi, J. R. (2024). A double‐blind, randomized, placebo‐controlled study assessing the impact of probiotic supplementation on the symptoms of irritable bowel syndrome in females. Neurogastroenterology & Motility, 36(4). Portico. https://doi.org/10.1111/nmo.14751
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Columbia Affiliation
Okolo, O., Honzel, E., Britton, W. R., Yu, V. X., Flashner, S., Martin, C., Nakagawa, H., & Parikh, A. S. (2023). Experimental Modeling of Host–Bacterial Interactions in Head and Neck Squamous Cell Carcinoma. Cancers, 15(24), 5810. https://doi.org/10.3390/cancers15245810
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Gupta, Y., Ernst, A. L., Vorobyev, A., Beltsiou, F., Zillikens, D., Bieber, K., Sanna-Cherchi, S., Christiano, A. M., Sadik, C. D., Ludwig, R. J., & Sezin, T. (2023). Impact of diet and host genetics on the murine intestinal mycobiome. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-36479-z
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Van, N. T., Zhang, K., Wigmore, R. M., Kennedy, A. I., DaSilva, C. R., Huang, J., Ambelil, M., Villagomez, J. H., O’Connor, G. J., Longman, R. S., Cao, M., Snook, A. E., Platten, M., Kasenty, G., Sigal, L. J., Prendergast, G. C., & Kim, S. V. (2023). Dietary L-Tryptophan consumption determines the number of colonic regulatory T cells and susceptibility to colitis via GPR15. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-43211-4
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Chung, C. J., Hermes, B. M., Gupta, Y., Ibrahim, S., Belheouane, M., & Baines, J. F. (2023). Genome-wide mapping of gene-microbe interactions in the murine lung microbiota based on quantitative microbial profiling. Animal Microbiome, 5(1). https://doi.org/10.1186/s42523-023-00250-y
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Nobel, Y. R., Park, H., Koerner, A., Tillman, A. M., Seeram, D., Moallem, D. H., Annavajhala, M. K., Gomez-Simmonds, A., Verna, E. C., & Uhlemann, A.-C. (2023). S1499 Gut Microbiota as a Biomarker of Hepatocellular Carcinoma in Patients With Cirrhosis. American Journal of Gastroenterology, 118(10S), S1136–S1137. https://doi.org/10.14309/01.ajg.0000955636.85132.22
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Irajizad, E., Kenney, A., Tang, T., Vykoukal, J., Wu, R., Murage, E., Dennison, J. B., Sans, M., Long, J. P., Loftus, M., Chabot, J. A., Kluger, M. D., Kastrinos, F., Brais, L., Babic, A., Jajoo, K., Lee, L. S., Clancy, T. E., Ng, K., … Fahrmann, J. F. (2023). A blood-based metabolomic signature predictive of risk for pancreatic cancer. Cell Reports Medicine, 4(9), 101194. https://doi.org/10.1016/j.xcrm.2023.101194
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Saeed, A., Ali, H., Yasmin, A., Baig, M., Ullah, A., Kazmi, A., Ahmed, M. A., Albadrani, G. M., El-Demerdash, F. M., Bibi, M., Abdel-Daim, M. M., Ali, I., & Hussain, S. (2023). Unveiling the Antibiotic Susceptibility and Antimicrobial Potential of Bacteria from Human Breast Milk of Pakistani Women: An Exploratory Study. BioMed Research International, 2023(1). Portico. https://doi.org/10.1155/2023/6399699
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Becerra, C. Y., Wells, R. K., Kunihiro, B. P., Lee, R. H., Umeda, L., Allan, N. P., Rubas, N. C., McCracken, T. A., Nunokawa, C. K. L., Lee, M.-H., Pidlaoan, F. G. S., Phankitnirondorn, K., Dye, C. K., Yamamoto, B. Y., Peres, R., Juarez, R., & Maunakea, A. K. (2023). Examining the immunoepigenetic-gut microbiome axis in the context of self-esteem among Native Hawaiians and other Pacific Islanders. Frontiers in Genetics, 14. https://doi.org/10.3389/fgene.2023.1125217
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Shin, A. E., Tesfagiorgis, Y., Larsen, F., Derouet, M., Zeng, P. Y. F., Good, H. J., Zhang, L., Rubinstein, M. R., Han, Y. W., Kerfoot, S. M., Nichols, A. C., Hayakawa, Y., Howlett, C. J., Wang, T. C., & Asfaha, S. (2023). F4/80+Ly6Chigh Macrophages Lead to Cell Plasticity and Cancer Initiation in Colitis. Gastroenterology, 164(4), 593-609.e13. https://doi.org/10.1053/j.gastro.2023.01.002
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Rankin, L. C., Kaiser, K. A., de los Santos-Alexis, K., Park, H., Uhlemann, A.-C., Gray, D. H. D., & Arpaia, N. (2023). Dietary tryptophan deficiency promotes gut RORγt+ Treg cells at the expense of Gata3+ Treg cells and alters commensal microbiota metabolism. Cell Reports, 42(3), 112135. https://doi.org/10.1016/j.celrep.2023.112135
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Galeano Niño, J. L., Wu, H., LaCourse, K. D., Kempchinsky, A. G., Baryiames, A., Barber, B., Futran, N., Houlton, J., Sather, C., Sicinska, E., Taylor, A., Minot, S. S., Johnston, C. D., & Bullman, S. (2022). Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer. Nature, 611(7937), 810–817. https://doi.org/10.1038/s41586-022-05435-0
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Qiu, A., Wang, L., Dei Zotti, F., Hudson, K. E., Hod, E. A., & La Carpia, F. (2022). Iron Overload and Iron-Induced Microbiome Changes May Affect Lymphoid Levels Post Bone Marrow Transplant and Graft-Versus-Host Disease Survival in Mice. Blood, 140(Supplement 1), 2465–2466. https://doi.org/10.1182/blood-2022-167300
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Gomez-Simmonds, A., Annavajhala, M. K., Nunez, M. P., Macesic, N., Park, H., & Uhlemann, A.-C. (2022). Intestinal Dysbiosis and Risk of Posttransplant Clostridioides difficile Infection in a Longitudinal Cohort of Liver Transplant Recipients. MSphere, 7(5). https://doi.org/10.1128/msphere.00361-22
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Fei, Y., Zhang, S., Han, S., Qiu, B., Lu, Y., Huang, W., Li, F., Chen, D., Berglund, B., Xiao, H., Li, L., & Yao, M. (2022). The Role of Dihydroresveratrol in Enhancing the Synergistic Effect of Ligilactobacillus salivarius Li01 and Resveratrol in Ameliorating Colitis in Mice. Research, 2022. https://doi.org/10.34133/2022/9863845
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Yao, M., Fei, Y., Zhang, S., Qiu, B., Zhu, L., Li, F., Berglund, B., Xiao, H., & Li, L. (2022). Gut Microbiota Composition in Relation to the Metabolism of Oral Administrated Resveratrol. Nutrients, 14(5), 1013. https://doi.org/10.3390/nu14051013
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LaMonte, M. J., Gordon, J. H., Diaz‐Moreno, P., Andrews, C. A., Shimbo, D., Hovey, K. M., Buck, M. J., & Wactawski‐Wende, J. (2022). Oral Microbiome Is Associated With Incident Hypertension Among Postmenopausal Women. Journal of the American Heart Association, 11(6). https://doi.org/10.1161/jaha.121.021930
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Bansal, R., Park, H., Taborda, C. C., Gordillo, C., Mapara, M. Y., Assal, A., Uhlemann, A.-C., & Reshef, R. (2022). Antibiotic Exposure, Not Alloreactivity, Is the Major Driver of Microbiome Changes in Hematopoietic Cell Transplantation. Transplantation and Cellular Therapy, 28(3), 135–144. https://doi.org/10.1016/j.jtct.2021.12.015
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Joseph, T. A., Chlenski, P., Litman, A., Korem, T., & Pe’er, I. (2022). Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates. Genome Research, 32(3), 558–568. https://doi.org/10.1101/gr.275533.121
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Bagheri, M., Wang, C., Shi, M., Manouchehri, A., Murray, K. T., Murphy, M. B., Shaffer, C. M., Singh, K., Davis, L. K., Jarvik, G. P., Stanaway, I. B., Hebbring, S., Reilly, M. P., Gerszten, R. E., Wang, T. J., Mosley, J. D., & Ferguson, J. F. (2021). The genetic architecture of plasma kynurenine includes cardiometabolic disease mechanisms associated with the SH2B3 gene. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-95154-9
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Kim, J., Lee, M., Baldwin-Hunter, B., Solfisburg, Q. S., Lightdale, C. J., Korem, T., Hur, C., & Abrams, J. A. (2021). Minimal Associations between Short-Term Dietary Intake and Salivary Microbiome Composition. Microorganisms, 9(8), 1739. https://doi.org/10.3390/microorganisms9081739
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Campana, A. M., Wu, H., Shen, Y., Laue, H. E., Bloomquist, T., Posner, J., Takser, L., & Baccarelli, A. A. (2021). Association between mid-childhood gut microbiome and neurocognitive outcomes in GESTE, a Canadian cohort Study. ISEE Conference Abstracts, 2021(1). https://doi.org/10.1289/isee.2021.p-173
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