Microbiota

Displaying 1 - 40 of 40CSV
Opron, K., Begley, L. A., Erb-Downward, J. R., Li, G., Alexis, N. E., Barjaktarevic, I., Barr, R. G., Bleecker, E. R., Boucher, R., Bowler, R. P., Christenson, S. A., Comellas, A. P., Criner, G., Cooper, C. B., Couper, D., Galban, C. J., Han, M. K., Hastie, A., Hatt, C., … Woodruff, P. G. (2024). Loss of Airway Phylogenetic Diversity Is Associated with Clinical and Pathobiological Markers of Disease Development in Chronic Obstructive Pulmonary Disease. American Journal of Respiratory and Critical Care Medicine, 210(2), 186–200. https://doi.org/10.1164/rccm.202303-0489oc
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Straub, T. J., Lombardo, M.-J., Bryant, J. A., Diao, L., Lodise, T. P., Freedberg, D. E., Wortman, J. R., Litcofsky, K. D., Hasson, B. R., McGovern, B. H., Ford, C. B., & Henn, M. R. (2023). Impact of a Purified Microbiome Therapeutic on Abundance of Antimicrobial Resistance Genes in Patients With Recurrent Clostridioides difficile Infection. Clinical Infectious Diseases, 78(4), 833–841. https://doi.org/10.1093/cid/ciad636
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Solfisburg, Q. S., Baldini, F., Baldwin-Hunter, B., Austin, G. I., Lee, H. H., Park, H., Freedberg, D. E., Lightdale, C. J., Korem, T., & Abrams, J. A. (2023). The Salivary Microbiome and Predicted Metabolite Production Are Associated with Barrett’s Esophagus and High-Grade Dysplasia or Adenocarcinoma. Cancer Epidemiology, Biomarkers & Prevention, 33(3), 371–380. https://doi.org/10.1158/1055-9965.epi-23-0652
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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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Burris, H. H., Yang, N., Riis, V., Valeri, L., South, E. C., Ravel, J., & Elovitz, M. A. (2024). The role of neighborhood deprivation in the cervicovaginal microbiota. American Journal of Obstetrics & Gynecology MFM, 6(3), 101291. https://doi.org/10.1016/j.ajogmf.2024.101291
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Xu, H., Wang, T., Miao, Y., Qian, M., Yang, Y., & Wang, S. (2024). MK-BMC: a Multi-Kernel framework with Boosted distance metrics for Microbiome data for Classification. Bioinformatics, 40(1). https://doi.org/10.1093/bioinformatics/btad757
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Golob, J. L., Oskotsky, T. T., Tang, A. S., Roldan, A., Chung, V., Ha, C. W. Y., Wong, R. J., Flynn, K. J., Parraga-Leo, A., Wibrand, C., Minot, S. S., Oskotsky, B., Andreoletti, G., Kosti, I., Bletz, J., Nelson, A., Gao, J., Wei, Z., Chen, G., … Sirota, M. (2024). Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research. Cell Reports Medicine, 5(1), 101350. https://doi.org/10.1016/j.xcrm.2023.101350
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Yong, G. J. M., Porsche, C. E., Sitarik, A. R., Fujimura, K. E., McCauley, K., Nguyen, D. T., Levin, A. M., Woodcroft, K. J., Ownby, D. R., Rundle, A. G., Johnson, C. C., Cassidy-Bushrow, A., & Lynch, S. V. (2023). Precocious infant fecal microbiome promotes enterocyte barrier dysfuction, altered neuroendocrine signaling and associates with increased childhood obesity risk. Gut Microbes, 16(1). https://doi.org/10.1080/19490976.2023.2290661
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Rachmühl, C., Lacroix, C., Giorgetti, A., Stoffel, N. U., Zimmermann, M. B., Brittenham, G. M., & Geirnaert, A. (2023). Validation of a batch cultivation protocol for fecal microbiota of Kenyan infants. BMC Microbiology, 23(1). https://doi.org/10.1186/s12866-023-02915-9
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Kim, J. M., Yoo, S.-Y., An, J.-S., Woo, J. J., Cho, Y.-D., Park, H. E., & Karm, M.-H. (2023). Effect of a multichannel oral irrigator on periodontal health and the oral microbiome. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-38894-0
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Liang, X., Zhang, Z., Wang, H., Lu, X., Li, W., Lu, H., Roy, A., Shen, X., Irwin, D. M., & Shen, Y. (2023). Early-life prophylactic antibiotic treatment disturbs the stability of the gut microbiota and increases susceptibility to H9N2 AIV in chicks. Microbiome, 11(1). https://doi.org/10.1186/s40168-023-01609-8
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Columbia Affiliation
Liao, J., Shenhav, L., Urban, J. A., Serrano, M., Zhu, B., Buck, G. A., & Korem, T. (2023). Microdiversity of the vaginal microbiome is associated with preterm birth. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-40719-7
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Austin, G. I., Park, H., Meydan, Y., Seeram, D., Sezin, T., Lou, Y. C., Firek, B. A., Morowitz, M. J., Banfield, J. F., Christiano, A. M., Pe’er, I., Uhlemann, A.-C., Shenhav, L., & Korem, T. (2023). Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data. Nature Biotechnology, 41(12), 1820–1828. https://doi.org/10.1038/s41587-023-01696-w
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Huang, Z., Li, Y., Park, H., Ho, M., Bhardwaj, K., Sugimura, N., Lee, H. W., Meng, H., Ebert, M. P., Chao, K., Burgermeister, E., Bhatt, A. P., Shetty, S. A., Li, K., Wen, W., & Zuo, T. (2023). Unveiling and harnessing the human gut microbiome in the rising burden of non-communicable diseases during urbanization. Gut Microbes, 15(1). https://doi.org/10.1080/19490976.2023.2237645
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Bertucci Zoccali, M., Moallem, D. H., Park, H., Uhlemann, A., Church, J. M., & Kiran, R. P. (2023). Role of Microbiome in the Outcomes Following Surgical Repair of Perianal Fistula: Prospective Cohort Study Design and Preliminary Results. World Journal of Surgery, 47(12), 3373–3379. Portico. https://doi.org/10.1007/s00268-023-07212-0
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Khan, I., Wu, S., Hudson, A., Hughes, C., Stryjniak, G., Westblade, L. F., Satlin, M. J., Tedrow, N., Uhlemann, A.-C., Kraft, C., Dadhania, D. M., Silberzweig, J., De Vlaminck, I., Li, C., Srivatana, V., & Lee, J. R. (2023). A Distinct Nasal Microbiota Signature in Peritoneal Dialysis Patients. Kidney360, 4(10), 1419–1429. https://doi.org/10.34067/kid.0000000000000249
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Balasubramanian, I., Bandyopadhyay, S., Flores, J., Bianchi‐Smak, J., Lin, X., Liu, H., Sun, S., Golovchenko, N. B., Liu, Y., Wang, D., Patel, R., Joseph, I., Suntornsaratoon, P., Vargas, J., Green, P. H., Bhagat, G., Lagana, S. M., Ying, W., Zhang, Y., … Gao, N. (2023). Infection and inflammation stimulate expansion of a CD74+ Paneth cell subset to regulate disease progression. The EMBO Journal, 42(21). Portico. https://doi.org/10.15252/embj.2023113975
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Kuhn, L., Wang, T., Li, F., Strehlau, R., Tobin, N. H., Violari, A., Brooker, S., Patel, F., Liberty, A., Shiau, S., Arpadi, S. M., Wadhwa, S., Yin, M. T., Wang, S., Tiemessen, C. T., & Aldrovandi, G. M. (2023). Microbiota in the oral cavity of school-age children with HIV who started antiretroviral therapy at young ages in South Africa. AIDS, 37(10), 1583–1591. https://doi.org/10.1097/qad.0000000000003599
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Yuzefpolskaya, M., Bohn, B., Ladanyi, A., Khoruts, A., Colombo, P. C., & Demmer, R. T. (2023). Oral and gut microbiome alterations in heart failure: Epidemiology, pathogenesis and response to advanced heart failure therapies. The Journal of Heart and Lung Transplantation, 42(3), 291–300. https://doi.org/10.1016/j.healun.2022.12.009
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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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Dixon, M., Dunlop, A. L., Corwin, E. J., & Kramer, M. R. (2023). Joint effects of individual socioeconomic status and residential neighborhood context on vaginal microbiome composition. Frontiers in Public Health, 11. https://doi.org/10.3389/fpubh.2023.1029741
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Columbia Affiliation
Dang, J. T., Mocanu, V., Park, H., Laffin, M., Hotte, N., Karmali, S., Birch, D. W., & Madsen, K. L. (2022). Roux-en-Y gastric bypass and sleeve gastrectomy induce substantial and persistent changes in microbial communities and metabolic pathways. Gut Microbes, 14(1). https://doi.org/10.1080/19490976.2022.2050636
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Campana, A. M., Laue, H. E., Shen, Y., Shrubsole, M. J., & Baccarelli, A. A. (2022). Assessing the role of the gut microbiome at the interface between environmental chemical exposures and human health: Current knowledge and challenges. Environmental Pollution, 315, 120380. https://doi.org/10.1016/j.envpol.2022.120380
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Al-Marzooq, F., Al Kawas, S., Rahman, B., Shearston, J. A., Saad, H., Benzina, D., & Weitzman, M. (2022). Supragingival microbiome alternations as a consequence of smoking different tobacco types and its relation to dental caries. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-06907-z
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Marotz, C., Molinsky, R., Martino, C., Bohn, B., Roy, S., Rosenbaum, M., Desvarieux, M., Yuzefpolskaya, M., Paster, B. J., Jacobs, D. R., Colombo, P. C., Papapanou, P. N., Knight, R., & Demmer, R. T. (2022). Early microbial markers of periodontal and cardiometabolic diseases in ORIGINS. Npj Biofilms and Microbiomes, 8(1). https://doi.org/10.1038/s41522-022-00289-w
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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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Kawano, Y., Edwards, M., Huang, Y., Bilate, A. M., Araujo, L. P., Tanoue, T., Atarashi, K., Ladinsky, M. S., Reiner, S. L., Wang, H. H., Mucida, D., Honda, K., & Ivanov, I. I. (2022). Microbiota imbalance induced by dietary sugar disrupts immune-mediated protection from metabolic syndrome. Cell, 185(19), 3501-3519.e20. https://doi.org/10.1016/j.cell.2022.08.005
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Chang, C.-C. J., Somohano, K., Zemsky, C., Uhlemann, A.-C., Liebmann, J., Cioffi, G. A., Al-Aswad, L. A., Lynch, S. V., & Winn, B. J. (2022). Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome. Investigative Opthalmology & Visual Science, 63(9), 32. https://doi.org/10.1167/iovs.63.9.32
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Madapoosi, S. S., Cruickshank-Quinn, C., Opron, K., Erb-Downward, J. R., Begley, L. A., Li, G., Barjaktarevic, I., Barr, R. G., Comellas, A. P., Couper, D. J., Cooper, C. B., Freeman, C. M., Han, M. K., Kaner, R. J., Labaki, W., Martinez, F. J., Ortega, V. E., Peters, S. P., Paine, R., … Wise, R. A. (2022). Lung Microbiota and Metabolites Collectively Associate with Clinical Outcomes in Milder Stage Chronic Obstructive Pulmonary Disease. American Journal of Respiratory and Critical Care Medicine, 206(4), 427–439. https://doi.org/10.1164/rccm.202110-2241oc
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McCauley, K. E., Flynn, K., Calatroni, A., DiMassa, V., LaMere, B., Fadrosh, D. W., Lynch, K. V., Gill, M. A., Pongracic, J. A., Khurana Hershey, G. K., Kercsmar, C. M., Liu, A. H., Johnson, C. C., Kim, H., Kattan, M., O’Connor, G. T., Bacharier, L. B., Teach, S. J., Gergen, P. J., … Lynch, S. V. (2022). Seasonal airway microbiome and transcriptome interactions promote childhood asthma exacerbations. Journal of Allergy and Clinical Immunology, 150(1), 204–213. https://doi.org/10.1016/j.jaci.2022.01.020
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Yang, I., Claussen, H., Arthur, R. A., Hertzberg, V. S., Geurs, N., Corwin, E. J., & Dunlop, A. L. (2022). Subgingival Microbiome in Pregnancy and a Potential Relationship to Early Term Birth. Frontiers in Cellular and Infection Microbiology, 12. https://doi.org/10.3389/fcimb.2022.873683
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Columbia Affiliation
Goh, C. E., Bohn, B., Marotz, C., Molinsky, R., Roy, S., Paster, B. J., Chen, C., Rosenbaum, M., Yuzefpolskaya, M., Colombo, P. C., Desvarieux, M., Papapanou, P. N., Jacobs, D. R., Knight, R., & Demmer, R. T. (2022). Nitrite Generating and Depleting Capacity of the Oral Microbiome and Cardiometabolic Risk: Results from ORIGINS. Journal of the American Heart Association, 11(10). https://doi.org/10.1161/jaha.121.023038
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Bain, C. C., Louwe, P. A., Steers, N. J., Bravo‐Blas, A., Hegarty, L. M., Pridans, C., Milling, S. W. F., MacDonald, A. S., Rückerl, D., & Jenkins, S. J. (2022). CD11c identifies microbiota and EGR2‐dependent MHCII+ serous cavity macrophages with sexually dimorphic fate in mice. European Journal of Immunology, 52(8), 1243–1257. Portico. https://doi.org/10.1002/eji.202149756
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Lam, S., Bai, X., Shkoporov, A. N., Park, H., Wu, X., Lan, P., & Zuo, T. (2022). Roles of the gut virome and mycobiome in faecal microbiota transplantation. The Lancet Gastroenterology & Hepatology, 7(5), 472–484. https://doi.org/10.1016/s2468-1253(21)00303-4
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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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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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