{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T23:04:59Z","timestamp":1790809499790,"version":"4.1.0"},"reference-count":79,"publisher":"Springer Science and Business Media LLC","license":[{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"DOI":"10.1038\/s41586-026-11077-3","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T15:04:05Z","timestamp":1790780645000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Sugar-rich foods exacerbate antibiotic-induced microbiome disruption"],"prefix":"10.1038","author":[{"given":"Anqi","family":"Dai","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annamaria","family":"Ballweg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-5513-2375","authenticated-orcid":false,"given":"William","family":"Jogia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5825-2775","authenticated-orcid":false,"given":"Madhumitha","family":"Rangesa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7099-1143","authenticated-orcid":false,"given":"Peter A.","family":"Adintori","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mirae","family":"Baichoo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1612-5644","authenticated-orcid":false,"given":"Tyler","family":"Funnell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7888-1715","authenticated-orcid":false,"given":"Teng","family":"Fei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9035-2143","authenticated-orcid":false,"given":"Nicholas R.","family":"Waters","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abrielle","family":"Swartz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sukanya","family":"Sahu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-5837-8676","authenticated-orcid":false,"given":"Brianna","family":"Gipson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4629-0528","authenticated-orcid":false,"given":"Sandeep S.","family":"Raj","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4824-8844","authenticated-orcid":false,"given":"Eiko","family":"Hayase","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zoe","family":"Pierce","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1676-9837","authenticated-orcid":false,"given":"Kenton","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalie","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-2930-3754","authenticated-orcid":false,"given":"Justin","family":"Neuberger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam","family":"Warren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marina Burgos","family":"da Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1571-3893","authenticated-orcid":false,"given":"Oriana","family":"Miltiadous","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6396-2990","authenticated-orcid":false,"given":"Corrado","family":"Zuanelli Brambilla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marissa Lubin","family":"Buchan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatanisha K.","family":"Peets","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Gradissimo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4625-5119","authenticated-orcid":false,"given":"Luigi A.","family":"Amoretti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caichen","family":"Duan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenzhen","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fanny","family":"Matheis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9296-8112","authenticated-orcid":false,"given":"Alexis P.","family":"Sullivan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John B.","family":"Slingerland","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annelie G.","family":"Clurman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel G.","family":"Brereton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul A.","family":"Giardina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3790-3724","authenticated-orcid":false,"given":"Antonio L. C.","family":"Gomes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5998-4724","authenticated-orcid":false,"given":"Abigail J.","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Knights","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert R.","family":"Jenq","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kate A.","family":"Markey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5910-4571","authenticated-orcid":false,"given":"Miguel-Angel","family":"Perales","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1944-5053","authenticated-orcid":false,"given":"Sergio A.","family":"Giralt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0696-4401","authenticated-orcid":false,"given":"Marcel R. M.","family":"van den Brink","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6214-9367","authenticated-orcid":false,"given":"Jonas","family":"Schluter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4029-7625","authenticated-orcid":false,"given":"Jonathan U.","family":"Peled","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"key":"11077_CR1","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1038\/s41586-021-03663-4","volume":"595","author":"R Jumpertz von Schwartzenberg","year":"2021","unstructured":"Jumpertz von Schwartzenberg, R. et al. Caloric restriction disrupts the microbiota and colonization resistance. Nature 595, 272\u2013277 (2021).","journal-title":"Nature"},{"key":"11077_CR2","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1016\/j.cell.2014.03.011","volume":"157","author":"Y Belkaid","year":"2014","unstructured":"Belkaid, Y. & Hand, T. W. Role of the microbiota in immunity and inflammation. Cell 157, 121\u2013141 (2014).","journal-title":"Cell"},{"key":"11077_CR3","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1038\/s41564-017-0072-8","volume":"3","author":"PI Costea","year":"2018","unstructured":"Costea, P. I. et al. Enterotypes in the landscape of gut microbial community composition. Nat. Microbiol. 3, 8\u201316 (2018).","journal-title":"Nat. Microbiol."},{"key":"11077_CR4","doi-asserted-by":"publisher","first-page":"1126","DOI":"10.1016\/j.chom.2023.05.027","volume":"31","author":"J Schluter","year":"2023","unstructured":"Schluter, J. et al. The TaxUMAP atlas: efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia. Cell Host Microbe 31, 1126\u20131139 (2023).","journal-title":"Cell Host Microbe"},{"key":"11077_CR5","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1016\/j.immuni.2019.08.003","volume":"51","author":"Y Litvak","year":"2019","unstructured":"Litvak, Y. & B\u00e4umler, A. J. Microbiota-nourishing immunity: a guide to understanding our microbial self. Immunity 51, 214\u2013224 (2019).","journal-title":"Immunity"},{"key":"11077_CR6","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1016\/j.chom.2008.02.015","volume":"3","author":"PJ Turnbaugh","year":"2008","unstructured":"Turnbaugh, P. J., B\u00e4ckhed, F., Fulton, L. & Gordon, J. I. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3, 213\u2013223 (2008).","journal-title":"Cell Host Microbe"},{"key":"11077_CR7","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1038\/s41586-022-04567-7","volume":"604","author":"R Gacesa","year":"2022","unstructured":"Gacesa, R. et al. Environmental factors shaping the gut microbiome in a Dutch population. Nature 604, 732\u2013739 (2022).","journal-title":"Nature"},{"key":"11077_CR8","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1016\/j.chom.2019.05.005","volume":"25","author":"AJ Johnson","year":"2019","unstructured":"Johnson, A. J. et al. Daily sampling reveals personalized diet-microbiome associations in humans. Cell Host Microbe 25, 789\u2013802 (2019).","journal-title":"Cell Host Microbe"},{"key":"11077_CR9","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1126\/science.1208344","volume":"334","author":"GD Wu","year":"2011","unstructured":"Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105\u2013108 (2011).","journal-title":"Science"},{"key":"11077_CR10","doi-asserted-by":"publisher","first-page":"4137","DOI":"10.1016\/j.cell.2021.06.019","volume":"184","author":"HC Wastyk","year":"2021","unstructured":"Wastyk, H. C. et al. Gut-microbiota-targeted diets modulate human immune status. Cell 184, 4137\u20134153 (2021).","journal-title":"Cell"},{"key":"11077_CR11","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-33395-6","volume":"13","author":"L Bernard-Raichon","year":"2022","unstructured":"Bernard-Raichon, L. et al. Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia. Nat. Commun. 13, 5926 (2022).","journal-title":"Nat. Commun."},{"key":"11077_CR12","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1016\/j.chom.2020.12.012","volume":"29","author":"C Tanes","year":"2021","unstructured":"Tanes, C. et al. Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. Cell Host Microbe 29, 394\u2013407 (2021).","journal-title":"Cell Host Microbe"},{"key":"11077_CR13","doi-asserted-by":"publisher","first-page":"650","DOI":"10.1016\/j.chom.2019.10.011","volume":"26","author":"KM Ng","year":"2019","unstructured":"Ng, K. M. et al. Recovery of the gut microbiota after antibiotics depends on host diet, community context, and environmental reservoirs. Cell Host Microbe 26, 650\u2013665 (2019).","journal-title":"Cell Host Microbe"},{"key":"11077_CR14","doi-asserted-by":"publisher","first-page":"1441","DOI":"10.1016\/j.cell.2020.08.027","volume":"182","author":"T Tuganbaev","year":"2020","unstructured":"Tuganbaev, T. et al. Diet diurnally regulates small intestinal microbiome-epithelial-immune homeostasis and enteritis. Cell 182, 1441\u20131459 (2020).","journal-title":"Cell"},{"key":"11077_CR15","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2014-15-7-r89","volume":"15","author":"LA David","year":"2014","unstructured":"David, L. A. et al. Host lifestyle affects human microbiota on daily timescales. Genome Biol. 15, R89 (2014).","journal-title":"Genome Biol."},{"key":"11077_CR16","doi-asserted-by":"publisher","first-page":"1339","DOI":"10.1016\/j.cell.2016.10.043","volume":"167","author":"MS Desai","year":"2016","unstructured":"Desai, M. S. et al. A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell 167, 1339\u20131353 (2016).","journal-title":"Cell"},{"key":"11077_CR17","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3000322","volume":"1","author":"PJ Turnbaugh","year":"2009","unstructured":"Turnbaugh, P. J. et al. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci. Transl. Med. 1, 6ra14 (2009).","journal-title":"Sci. Transl. Med."},{"key":"11077_CR18","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-025-09854-7","author":"F Asnicar","year":"2025","unstructured":"Asnicar, F. et al. Gut micro-organisms associated with health, nutrition and dietary interventions. Nature https:\/\/doi.org\/10.1038\/s41586-025-09854-7 (2025).","journal-title":"Nature"},{"key":"11077_CR19","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1126\/science.aad3369","volume":"352","author":"A Zhernakova","year":"2016","unstructured":"Zhernakova, A. et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 352, 565\u2013569 (2016).","journal-title":"Science"},{"key":"11077_CR20","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1038\/nature25973","volume":"555","author":"D Rothschild","year":"2018","unstructured":"Rothschild, D. et al. Environment dominates over host genetics in shaping human gut microbiota. Nature 555, 210\u2013215 (2018).","journal-title":"Nature"},{"key":"11077_CR21","doi-asserted-by":"publisher","first-page":"802","DOI":"10.1126\/science.aan4834","volume":"357","author":"SA Smits","year":"2017","unstructured":"Smits, S. A. et al. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. Science 357, 802\u2013806 (2017).","journal-title":"Science"},{"key":"11077_CR22","doi-asserted-by":"publisher","first-page":"962","DOI":"10.1016\/j.cell.2018.10.029","volume":"175","author":"P Vangay","year":"2018","unstructured":"Vangay, P. et al. US immigration westernizes the human gut microbiome. Cell 175, 962\u2013972 (2018).","journal-title":"Cell"},{"key":"11077_CR23","doi-asserted-by":"publisher","first-page":"e76632","DOI":"10.1371\/journal.pone.0076632","volume":"8","author":"E Archer","year":"2013","unstructured":"Archer, E., Hand, G. A. & Blair, S. N. Validity of U.S. nutritional surveillance: National Health and Nutrition Examination Survey caloric energy intake data, 1971\u20132010. PLoS ONE 8, e76632 (2013).","journal-title":"PLoS ONE"},{"key":"11077_CR24","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/aje\/kwg092","volume":"158","author":"AF Subar","year":"2003","unstructured":"Subar, A. F. et al. Using intake biomarkers to evaluate the extent of dietary misreporting in a large sample of adults: the OPEN Study. Am. J. Epidemiol. 158, 1\u201313 (2003).","journal-title":"Am. J. Epidemiol."},{"key":"11077_CR25","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1038\/bmt.2016.310","volume":"52","author":"A Baumgartner","year":"2017","unstructured":"Baumgartner, A. et al. Revisiting nutritional support for allogeneic hematologic stem cell transplantation\u2014a systematic review. Bone Marrow Transpl. 52, 506\u2013513 (2017).","journal-title":"Bone Marrow Transpl."},{"key":"11077_CR26","doi-asserted-by":"publisher","first-page":"822","DOI":"10.1056\/NEJMoa1900623","volume":"382","author":"JU Peled","year":"2020","unstructured":"Peled, J. U. et al. Microbiota as predictor of mortality in allogeneic hematopoietic-cell transplantation. N. Engl. J. Med. 382, 822\u2013834 (2020).","journal-title":"N. Engl. J. Med."},{"key":"11077_CR27","doi-asserted-by":"publisher","first-page":"1143","DOI":"10.1126\/science.aax3760","volume":"366","author":"CK Stein-Thoeringer","year":"2019","unstructured":"Stein-Thoeringer, C. K. et al. Lactose drives Enterococcus expansion to promote graft-versus-host disease. Science 366, 1143\u20131149 (2019).","journal-title":"Science"},{"key":"11077_CR28","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aaf2311","volume":"8","author":"Y Shono","year":"2016","unstructured":"Shono, Y. et al. Increased GVHD-related mortality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice. Sci. Transl. Med. 8, 339ra71 (2016).","journal-title":"Sci. Transl. Med."},{"key":"11077_CR29","doi-asserted-by":"publisher","first-page":"1373","DOI":"10.1016\/j.bbmt.2015.04.016","volume":"21","author":"RR Jenq","year":"2015","unstructured":"Jenq, R. R. et al. Intestinal blautia is associated with reduced death from graft-versus-host disease. Biol. Blood Marrow Transpl. 21, 1373\u20131383 (2015).","journal-title":"Biol. Blood Marrow Transpl."},{"key":"11077_CR30","doi-asserted-by":"publisher","unstructured":"Shouval, R. et al. Conditioning regimens are associated with distinct patterns of microbiota injury in allogeneic hematopoietic cell transplantation. Clin. Cancer Res. 29, 165\u2013173 https:\/\/doi.org\/10.1158\/1078-0432.CCR-22-1254 (2022).","DOI":"10.1158\/1078-0432.CCR-22-1254"},{"key":"11077_CR31","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1146\/annurev-publhealth-031816-044327","volume":"38","author":"P Craig","year":"2017","unstructured":"Craig, P., Katikireddi, S. V., Leyland, A. & Popham, F. Natural experiments: an overview of methods, approaches, and contributions to public health intervention research. Annu. Rev. Publ. Health 38, 39\u201356 (2017).","journal-title":"Annu. Rev. Publ. Health"},{"key":"11077_CR32","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1038\/s41586-020-2971-8","volume":"588","author":"J Schluter","year":"2020","unstructured":"Schluter, J. et al. The gut microbiota is associated with immune cell dynamics in humans. Nature 588, 303\u2013307 (2020).","journal-title":"Nature"},{"key":"11077_CR33","doi-asserted-by":"publisher","first-page":"640","DOI":"10.1016\/j.bbmt.2014.01.030","volume":"20","author":"E Holler","year":"2014","unstructured":"Holler, E. et al. Metagenomic analysis of the stool microbiome in patients receiving allogeneic stem cell transplantation: loss of diversity is associated with use of systemic antibiotics and more pronounced in gastrointestinal graft-versus-host disease. Biol. Blood Marrow Transpl. 20, 640\u2013645 (2014).","journal-title":"Biol. Blood Marrow Transpl."},{"key":"11077_CR34","unstructured":"Baumgartner, A. & Schuetz, P. in EBMT Handbook: Hematopoietic Stem Cell Transplantation and Cellular Therapies Ch. 24 (Springer, 2019)."},{"key":"11077_CR35","doi-asserted-by":"publisher","first-page":"1771","DOI":"10.1093\/cid\/ciz031","volume":"69","author":"GA Papanicolaou","year":"2019","unstructured":"Papanicolaou, G. A. et al. Bloodstream infection due to vancomycin-resistant Enterococcus is associated with increased mortality after hematopoietic cell transplantation for acute leukemia and myelodysplastic syndrome: a multicenter, retrospective cohort study. Clin. Infect. Dis. 69, 1771\u20131779 (2019).","journal-title":"Clin. Infect. Dis."},{"key":"11077_CR36","doi-asserted-by":"publisher","first-page":"1243","DOI":"10.1016\/j.cmet.2017.05.002","volume":"25","author":"T Korem","year":"2017","unstructured":"Korem, T. et al. Bread affects clinical parameters and induces gut microbiome-associated personal glycemic responses. Cell Metab. 25, 1243\u20131253 (2017).","journal-title":"Cell Metab."},{"key":"11077_CR37","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1016\/j.jcmgh.2020.09.008","volume":"11","author":"DC Montrose","year":"2021","unstructured":"Montrose, D. C. et al. Dietary fructose alters the composition, localization, and metabolism of gut microbiota in association with worsening colitis. Cell. Mol. Gastroenterol. Hepatol. 11, 525\u2013550 (2021).","journal-title":"Cell. Mol. Gastroenterol. Hepatol."},{"key":"11077_CR38","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aay6218","volume":"12","author":"S Khan","year":"2020","unstructured":"Khan, S. et al. Dietary simple sugars alter microbial ecology in the gut and promote colitis in mice. Sci. Transl. Med. 12, eaay6218 (2020).","journal-title":"Sci. Transl. Med."},{"key":"11077_CR39","doi-asserted-by":"publisher","first-page":"3501","DOI":"10.1016\/j.cell.2022.08.005","volume":"185","author":"Y Kawano","year":"2022","unstructured":"Kawano, Y. et al. Microbiota imbalance induced by dietary sugar disrupts immune-mediated protection from metabolic syndrome. Cell 185, 3501\u20133519 (2022).","journal-title":"Cell"},{"key":"11077_CR40","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-48749-2","volume":"9","author":"M Laffin","year":"2019","unstructured":"Laffin, M. et al. A high-sugar diet rapidly enhances susceptibility to colitis via depletion of luminal short-chain fatty acids in mice. Sci. Rep. 9, 12294 (2019).","journal-title":"Sci. Rep."},{"key":"11077_CR41","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-35380-5","volume":"13","author":"S Isaac","year":"2022","unstructured":"Isaac, S. et al. Microbiome-mediated fructose depletion restricts murine gut colonization by vancomycin-resistant Enterococcus. Nat. Commun. 13, 7718 (2022).","journal-title":"Nat. Commun."},{"key":"11077_CR42","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-78998-5","volume":"10","author":"M-A Kim","year":"2020","unstructured":"Kim, M.-A., Rosa, V. & Min, K.-S. Characterization of Enterococcus faecalis in different culture conditions. Sci. Rep. 10, 21867 (2020).","journal-title":"Sci. Rep."},{"key":"11077_CR43","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1038\/nature12503","volume":"502","author":"KM Ng","year":"2013","unstructured":"Ng, K. M. et al. Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature 502, 96\u201399 (2013).","journal-title":"Nature"},{"key":"11077_CR44","doi-asserted-by":"publisher","DOI":"10.1126\/science.adj3502","volume":"382","author":"F Spragge","year":"2023","unstructured":"Spragge, F. et al. Microbiome diversity protects against pathogens by nutrient blocking. Science 382, eadj3502 (2023).","journal-title":"Science"},{"key":"11077_CR45","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1038\/nature18597","volume":"534","author":"F Faber","year":"2016","unstructured":"Faber, F. et al. Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion. Nature 534, 697\u2013699 (2016).","journal-title":"Nature"},{"key":"11077_CR46","unstructured":"USDA Food and Nutrient Database for Dietary Studies 2015-2016 (US Department of Agriculture, Agricultural Research Service, 2018)."},{"key":"11077_CR47","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/0006-3207(92)91201-3","volume":"61","author":"DP Faith","year":"1992","unstructured":"Faith, D. P. Conservation evaluation and phylogenetic diversity. Biol. Conserv. 61, 1\u201310 (1992).","journal-title":"Biol. Conserv."},{"key":"11077_CR48","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","volume":"37","author":"E Bolyen","year":"2019","unstructured":"Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852\u2013857 (2019).","journal-title":"Nat. Biotechnol."},{"key":"11077_CR49","doi-asserted-by":"publisher","first-page":"2705","DOI":"10.1016\/j.cell.2023.05.007","volume":"186","author":"CL Nguyen","year":"2023","unstructured":"Nguyen, C. L. et al. High-resolution analyses of associations between medications, microbiome, and mortality in cancer patients. Cell 186, 2705\u20132718 (2023).","journal-title":"Cell"},{"key":"11077_CR50","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581\u2013583 (2016).","journal-title":"Nat. Methods"},{"key":"11077_CR51","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403\u2013410 (1990).","journal-title":"J. Mol. Biol."},{"key":"11077_CR52","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/nmeth.f.303","volume":"7","author":"JG Caporaso","year":"2010","unstructured":"Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335\u2013336 (2010).","journal-title":"Nat. Methods"},{"key":"11077_CR53","unstructured":"Oksanen, J. et al. vegan: community ecology package (2022)."},{"key":"11077_CR54","doi-asserted-by":"publisher","first-page":"e1009442","DOI":"10.1371\/journal.pcbi.1009442","volume":"17","author":"H Mallick","year":"2021","unstructured":"Mallick, H. et al. Multivariable association discovery in population-scale meta-omics studies. PLoS Comput. Biol. 17, e1009442 (2021).","journal-title":"PLoS Comput. Biol."},{"key":"11077_CR55","volume":"6","author":"SJ Bush","year":"2020","unstructured":"Bush, S. J., Connor, T. R., Peto, T. E. A., Crook, D. W. & Walker, A. S. Evaluation of methods for detecting human reads in microbial sequencing datasets. Microb. Genom. 6, mgen000393 (2020).","journal-title":"Microb. Genom."},{"key":"11077_CR56","doi-asserted-by":"publisher","first-page":"1633","DOI":"10.1038\/s41587-023-01688-w","volume":"41","author":"A Blanco-M\u00edguez","year":"2023","unstructured":"Blanco-M\u00edguez, A. et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat. Biotechnol. 41, 1633\u20131644 (2023).","journal-title":"Nat. Biotechnol."},{"key":"11077_CR57","doi-asserted-by":"publisher","first-page":"776","DOI":"10.1126\/science.aau5812","volume":"362","author":"CL Gentile","year":"2018","unstructured":"Gentile, C. L. & Weir, T. L. The gut microbiota at the intersection of diet and human health. Science 362, 776\u2013780 (2018).","journal-title":"Science"},{"key":"11077_CR58","doi-asserted-by":"publisher","first-page":"1174","DOI":"10.1182\/blood-2014-02-554725","volume":"124","author":"Y Taur","year":"2014","unstructured":"Taur, Y. et al. The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation. Blood 124, 1174\u20131182 (2014).","journal-title":"Blood"},{"key":"11077_CR59","doi-asserted-by":"publisher","first-page":"778","DOI":"10.1016\/j.bbmt.2019.12.722","volume":"26","author":"A Rashidi","year":"2020","unstructured":"Rashidi, A. et al. Levaquin gets a pass. Biol. Blood Marrow Transpl. 26, 778\u2013781 (2020).","journal-title":"Biol. Blood Marrow Transpl."},{"key":"11077_CR60","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1016\/j.jinf.2014.06.004","volume":"69","author":"SK Seo","year":"2014","unstructured":"Seo, S. K. et al. Impact of peri-transplant vancomycin and fluoroquinolone administration on rates of bacteremia in allogeneic hematopoietic stem cell transplant (HSCT) recipients: a 12-year single institution study. J. Infect. 69, 341\u2013351 (2014).","journal-title":"J. Infect."},{"key":"11077_CR61","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1093\/jac\/14.suppl_D.43","volume":"14","author":"RC Moellering Jr.","year":"1984","unstructured":"Moellering, R. C. Jr. Pharmacokinetics of vancomycin. J. Antimicrob. Chemother. 14, 43\u201352 (1984).","journal-title":"J. Antimicrob. Chemother."},{"key":"11077_CR62","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aap9489","volume":"10","author":"Y Taur","year":"2018","unstructured":"Taur, Y. et al. Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant. Sci. Transl. Med. 10, eaap9489 (2018).","journal-title":"Sci. Transl. Med."},{"key":"11077_CR63","doi-asserted-by":"publisher","first-page":"1523","DOI":"10.1016\/j.chom.2023.08.004","volume":"31","author":"JE Button","year":"2023","unstructured":"Button, J. E. et al. Precision modulation of dysbiotic adult microbiomes with a human-milk-derived synbiotic reshapes gut microbial composition and metabolites. Cell Host Microbe 31, 1523\u20131538 (2023).","journal-title":"Cell Host Microbe"},{"key":"11077_CR64","unstructured":"van den Boogaart, K. G., Tolosana-Delgado, R. & Bren, M. compositions: compositional data analysis. (2023)."},{"key":"11077_CR65","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v100.i05","volume":"100","author":"P-C B\u00fcrkner","year":"2021","unstructured":"B\u00fcrkner, P.-C. Bayesian item response modeling in R with brms and Stan. J. Stat. Softw. 100, 1\u201354 (2021).","journal-title":"J. Stat. Softw."},{"key":"11077_CR66","doi-asserted-by":"publisher","first-page":"395","DOI":"10.32614\/RJ-2018-017","volume":"10","author":"P-C B\u00fcrkner","year":"2018","unstructured":"B\u00fcrkner, P.-C. Advanced Bayesian multilevel modeling with the r Package brms. R J. 10, 395 (2018).","journal-title":"R J."},{"key":"11077_CR67","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v080.i01","volume":"80","author":"P-C B\u00fcrkner","year":"2017","unstructured":"B\u00fcrkner, P.-C. brms: an R package for Bayesian multilevel models using Stan. J. Stat. Softw. 80, 1\u201328 (2017).","journal-title":"J. Stat. Softw."},{"key":"11077_CR68","unstructured":"Stan Development Team. RStan: the R interface to Stan https:\/\/mc-stan.org\/ (2022)."},{"key":"11077_CR69","doi-asserted-by":"publisher","unstructured":"McElreath, R. Statistical Rethinking: A Bayesian Course with Examples in R and STAN https:\/\/doi.org\/10.1201\/9780429029608 (Chapman and Hall\/CRC, 2020).","DOI":"10.1201\/9780429029608"},{"key":"11077_CR70","doi-asserted-by":"publisher","unstructured":"Gelman, A., Hill, J. & Vehtari, A. Regression and Other Stories https:\/\/doi.org\/10.1017\/9781139161879 (Cambridge Aspire, 2020).","DOI":"10.1017\/9781139161879"},{"key":"11077_CR71","doi-asserted-by":"crossref","unstructured":"Wickham, H. Ggplot2: elegant graphics for data analysis (Springer, 2016).","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"11077_CR72","unstructured":"Kay, M. tidybayes: tidy data and geoms for Bayesian models (2022)."},{"key":"11077_CR73","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","volume":"16","author":"P Rice","year":"2000","unstructured":"Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16, 276\u2013277 (2000).","journal-title":"Trends Genet."},{"key":"11077_CR74","doi-asserted-by":"publisher","first-page":"e191","DOI":"10.1002\/imt2.191","volume":"3","author":"W Shen","year":"2024","unstructured":"Shen, W., Sipos, B. & Zhao, L. SeqKit2: a Swiss army knife for sequence and alignment processing. iMeta 3, e191 (2024).","journal-title":"iMeta"},{"key":"11077_CR75","doi-asserted-by":"publisher","first-page":"e2584","DOI":"10.7717\/peerj.2584","volume":"4","author":"T Rognes","year":"2016","unstructured":"Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mah\u00e9, F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).","journal-title":"PeerJ"},{"key":"11077_CR76","doi-asserted-by":"publisher","first-page":"1118","DOI":"10.1111\/biom.13366","volume":"77","author":"KR Hart","year":"2021","unstructured":"Hart, K. R., Fei, T. & Hanfelt, J. J. Scalable and robust latent trajectory class analysis using artificial likelihood. Biometrics 77, 1118\u20131128 (2021).","journal-title":"Biometrics"},{"key":"11077_CR77","first-page":"1","volume":"15","author":"S H\u00f8jsgaard","year":"2006","unstructured":"H\u00f8jsgaard, S., Halekoh, U. & Yan, J. The R package Geepack for generalized estimating equations. J. Stat. Softw. 15, 1\u201311 (2006).","journal-title":"J. Stat. Softw."},{"key":"11077_CR78","doi-asserted-by":"publisher","unstructured":"Dai, A. Supplementary data for \u2018Sugar-rich foods exacerbate antibiotic-induced microbiome disruption\u2019. Zenodo https:\/\/doi.org\/10.5281\/ZENODO.14538105 (2026).","DOI":"10.5281\/ZENODO.14538105"},{"key":"11077_CR79","doi-asserted-by":"publisher","unstructured":"Dai, A. Nutrition_microbiome_reproducibility: reproduction of the public figures of \u2018Sugar-rich foods exacerbate antibiotic-induced microbiome disruption\u2019. Zenodo https:\/\/doi.org\/10.5281\/ZENODO.21290618 (2026).","DOI":"10.5281\/ZENODO.21290618"}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41586-026-11077-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-026-11077-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-026-11077-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T22:52:44Z","timestamp":1790808764000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41586-026-11077-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,30]]},"references-count":79,"alternative-id":["11077"],"URL":"https:\/\/doi.org\/10.1038\/s41586-026-11077-3","relation":{},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,30]]},"assertion":[{"value":"4 March 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 August 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 September 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"J.S. has filed intellectual property applications related to the microbiome (reference numbers US2025\/0064882A1, PCT\/US2025\/023826), serves on an advisory board and holds equity of Jona Health, and is cofounder of Postbiotics Plus Research. J.U.P. reports research funding, intellectual property fees and travel reimbursement from Seres Therapeutics, and consulting fees from DaVolterra, CSL Behring, Crestone, MaaT Pharma and Canaccord Genuity and RA Capital; he serves on an advisory board of and holds equity in Postbiotics Plus Research; he serves on an advisory board of and holds equity in Prodigy Biosciences; he has filed intellectual property applications related to the microbiome (reference numbers 62\/843,849, 62\/977,908 and 15\/756,845). Memorial Sloan Kettering Cancer Center (MSK) has financial interests relative to Seres Therapeutics. K.A.M. reports previous consulting for Incucyte and Crestone; she serves on an advisory board of and holds equity in Postbiotics Plus Research. M.R.M.v.d.B. has received research support and stock options from Seres Therapeutics and stock options from Notch Therapeutics, Pluto Therapeutics and TymoFox; he has received royalties from Wolters Kluwer; he has consulted, received honorarium from or participated in advisory boards for Seres Therapeutics, Vor Biopharma, WindMIL Therapeutics, Rheos Medicines, Merck, Magenta Therapeutics, Frazier Healthcare Partners, Nektar Therapeutics, Notch Therapeutics, Forty Seven, Priothera, Ceramedix, Lygenesis, Pluto Therapeutics, GlaskoSmithKline, Da Volterra, Garuda, Thymofox, smarNovartis (spouse), Synthekine (spouse), Beigene (spouse), Kite (spouse), MustangBio (spouse) and Cellectar (spouse); he has IP licensing with Seres Therapeutics and Juno Therapeutics; he holds a fiduciary role on the Foundation Board of the non-profit organization DKMS; and he is the chairman of the scientific advisory board for Smart Immune. M.-A.P. reports honoraria from Arog Pharmaceuticals, Bristol-Myers Squibb, Cartesian, Celgene, Incyte, Kite\/Gilead, Merck, Miltenyi Biotec, Novartis, Omeros, OrcaBio, Ossium Health, Pierre Fabre, Sanofi and Takeda; he serves on data and safety monitoring boards for Cidara Therapeutics\/ Mundipharma and Sellas Life Sciences; he has ownership interests in Omeros and OrcaBio; he has received institutional research support for clinical trials from Allogene, Genmab, Incyte, Kite\/Gilead, Miltenyi Biotec, Novartis and Tr1x. R.R.J. reports patent royalties and stock options from Seres Therapeutics, and consulting fees from MaaT Pharma and Nestle; he serves on the scientific advisory board of Postbiotics Plus Research. S.A.G. reports research funding from Amgen, Johnson & Johnson, Takeda, Celgene, Actinuum, Sanofi, Miltenyi, Kite, EUSA and Incyte; he serves on advisory boards at Amgen, Bristol-Myers Squibb, Actinuum, Celgene, Johnson & Johnson, Miltenyi, Takeda, Novartis, EUSA Omeros, Sanofi, Kite and Spectrum Pharma. A.L.C.G. reports stock\/shares from Seres Therapeutics and equity ownership at Xbiome. M.L.B. reports employment and equity ownership at Savor Health. The other authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}]}}