{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,12]],"date-time":"2026-11-12T13:46:36Z","timestamp":1794491196098,"version":"4.9.1"},"reference-count":52,"publisher":"Springer Science and Business Media LLC","issue":"7","license":[{"start":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T00:00:00Z","timestamp":1782172800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T00:00:00Z","timestamp":1782172800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100000002","name":"U.S. Department of Health & Human Services | National Institutes of Health","doi-asserted-by":"publisher","award":["DP1DK113643"],"award-info":[{"award-number":["DP1DK113643"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"U.S. Department of Health & Human Services | National Institutes of Health","doi-asserted-by":"publisher","award":["F30DK139739"],"award-info":[{"award-number":["F30DK139739"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"U.S. Department of Health & Human Services | National Institutes of Health","doi-asserted-by":"publisher","award":["R01AI172144"],"award-info":[{"award-number":["R01AI172144"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Metab"],"DOI":"10.1038\/s42255-026-01550-8","type":"journal-article","created":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T09:22:34Z","timestamp":1782206554000},"page":"1528-1544","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Host metabolism can produce many indoles and phenols independently of the microbiome"],"prefix":"10.1038","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5870-6984","authenticated-orcid":false,"given":"Jenna E.","family":"AbuSalim","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kellen","family":"Olszewski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-3499-7755","authenticated-orcid":false,"given":"Salma","family":"Youssef","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah J.","family":"Mitchell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Craig J.","family":"Hunter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"Little","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashley","family":"Sidebottom","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob A.","family":"Boyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steve D.","family":"Knutson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laith Z.","family":"Samarah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3593-6995","authenticated-orcid":false,"given":"Michael R.","family":"MacArthur","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9704-6045","authenticated-orcid":false,"given":"Alessa L.","family":"Henneberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5129-7332","authenticated-orcid":false,"given":"Rolf-Peter","family":"Ryseck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5575-9821","authenticated-orcid":false,"given":"Christiane A.","family":"Opitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David W. C.","family":"MacMillan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed S.","family":"Donia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6755-9904","authenticated-orcid":false,"given":"Eric G.","family":"Pamer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabrina","family":"Imam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher J.","family":"Lehmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olatoyosi","family":"Odenike","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1247-4727","authenticated-orcid":false,"given":"Joshua D.","family":"Rabinowitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,23]]},"reference":[{"key":"1550_CR1","doi-asserted-by":"publisher","first-page":"9561613","DOI":"10.1155\/2021\/9561613","volume":"2021","author":"Y Wu","year":"2021","unstructured":"Wu, Y. et al. Cinnamic acid ameliorates nonalcoholic fatty liver disease by suppressing hepatic lipogenesis and promoting fatty acid oxidation. Evid. Based Complement. Alternat. Med. 2021, 9561613 (2021).","journal-title":"Evid. Based Complement. Alternat. Med."},{"key":"1550_CR2","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1038\/s41575-019-0258-z","volume":"17","author":"A Lavelle","year":"2020","unstructured":"Lavelle, A. & Sokol, H. Gut microbiota-derived metabolites as key actors in inflammatory bowel disease. Nat. Rev. Gastroenterol. Hepatol. 17, 223\u2013237 (2020).","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"1550_CR3","doi-asserted-by":"publisher","first-page":"716","DOI":"10.1016\/j.chom.2018.05.003","volume":"23","author":"A Agus","year":"2018","unstructured":"Agus, A., Planchais, J. & Sokol, H. Gut microbiota regulation of tryptophan metabolism in health and disease. Cell Host Microbe 23, 716\u2013724 (2018).","journal-title":"Cell Host Microbe"},{"key":"1550_CR4","doi-asserted-by":"publisher","first-page":"1183","DOI":"10.1016\/j.ajpath.2018.01.011","volume":"188","author":"EE Alexeev","year":"2018","unstructured":"Alexeev, E. E. et al. Microbiota-derived indole metabolites promote human and murine intestinal homeostasis through regulation of interleukin-10 receptor. Am. J. Pathol. 188, 1183\u20131194 (2018).","journal-title":"Am. J. Pathol."},{"key":"1550_CR5","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09735-4","volume":"10","author":"K Kikuchi","year":"2019","unstructured":"Kikuchi, K. et al. Gut microbiome-derived phenyl sulfate contributes to albuminuria in diabetic kidney disease. Nat. Commun. 10, 1835 (2019).","journal-title":"Nat. Commun."},{"key":"1550_CR6","doi-asserted-by":"publisher","first-page":"2813","DOI":"10.1093\/ndt\/14.12.2813","volume":"14","author":"R Vanholder","year":"1999","unstructured":"Vanholder, R., De Smet, R. & Lesaffer, G. P-Cresol: a toxin revealing many neglected but relevant aspects of uraemic toxicity. Nephrol. Dial. Transplant. 14, 2813\u20132815 (1999).","journal-title":"Nephrol. Dial. Transplant."},{"key":"1550_CR7","doi-asserted-by":"publisher","first-page":"2377576","DOI":"10.1080\/19490976.2024.2377576","volume":"16","author":"M Li","year":"2024","unstructured":"Li, M. et al. Gut microbiota metabolite indole-3-acetic acid maintains intestinal epithelial homeostasis through mucin sulfation. Gut Microbes 16, 2377576 (2024).","journal-title":"Gut Microbes"},{"key":"1550_CR8","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-68412-9","volume":"14","author":"C Dimopoulou","year":"2024","unstructured":"Dimopoulou, C. et al. Potential of using an engineered indole lactic acid producing Escherichia coli Nissle 1917 in a murine model of colitis. Sci. Rep. 14, 17542 (2024).","journal-title":"Sci. Rep."},{"key":"1550_CR9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s12276-019-0304-5","volume":"51","author":"ZH Zhao","year":"2019","unstructured":"Zhao, Z. H. et al. Indole-3-propionic acid inhibits gut dysbiosis and endotoxin leakage to attenuate steatohepatitis in rats. Exp. Mol. Med. 51, 1\u201314 (2019).","journal-title":"Exp. Mol. Med."},{"key":"1550_CR10","doi-asserted-by":"publisher","first-page":"4369","DOI":"10.1007\/s13197-014-1488-2","volume":"52","author":"K Mnafgui","year":"2015","unstructured":"Mnafgui, K. et al. Anti-obesity and cardioprotective effects of cinnamic acid in high fat diet-induced obese rats. J. Food Sci. Technol. 52, 4369\u20134377 (2015).","journal-title":"J. Food Sci. Technol."},{"key":"1550_CR11","doi-asserted-by":"publisher","first-page":"fiy125","DOI":"10.1093\/femsec\/fiy125","volume":"94","author":"Y Saito","year":"2018","unstructured":"Saito, Y., Sato, T., Nomoto, K. & Tsuji, H. Identification of phenol- and p-cresol-producing intestinal bacteria by using media supplemented with tyrosine and its metabolites. FEMS Microbiol. Ecol. 94, fiy125 (2018).","journal-title":"FEMS Microbiol. Ecol."},{"key":"1550_CR12","doi-asserted-by":"publisher","first-page":"648","DOI":"10.1038\/nature24661","volume":"551","author":"D Dodd","year":"2017","unstructured":"Dodd, D. et al. A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature 551, 648\u2013652 (2017).","journal-title":"Nature"},{"key":"1550_CR13","doi-asserted-by":"publisher","first-page":"372","DOI":"10.1016\/j.immuni.2013.08.003","volume":"39","author":"T Zelante","year":"2013","unstructured":"Zelante, T. et al. Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity 39, 372\u2013385 (2013).","journal-title":"Immunity"},{"key":"1550_CR14","doi-asserted-by":"publisher","first-page":"598","DOI":"10.1038\/nm.4102","volume":"22","author":"B Lamas","year":"2016","unstructured":"Lamas, B. et al. CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nat. Med. 22, 598\u2013605 (2016).","journal-title":"Nat. Med."},{"key":"1550_CR15","doi-asserted-by":"publisher","first-page":"5512","DOI":"10.1021\/pr2007945","volume":"10","author":"X Zheng","year":"2011","unstructured":"Zheng, X. et al. The footprints of gut microbial-mammalian co-metabolism. J. Proteome Res. 10, 5512\u20135522 (2011).","journal-title":"J. Proteome Res."},{"key":"1550_CR16","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1038\/s41591-020-01183-8","volume":"27","author":"F Asnicar","year":"2021","unstructured":"Asnicar, F. et al. Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nat. Med. 27, 321\u2013332 (2021).","journal-title":"Nat. Med."},{"key":"1550_CR17","doi-asserted-by":"publisher","first-page":"1927","DOI":"10.1016\/j.chom.2024.10.008","volume":"32","author":"J Wu","year":"2024","unstructured":"Wu, J. et al. Microbiota-induced alteration of kynurenine metabolism in macrophages drives formation of creeping fat in Crohn\u2019s disease. Cell Host Microbe 32, 1927\u20131943.e9 (2024).","journal-title":"Cell Host Microbe"},{"key":"1550_CR18","doi-asserted-by":"publisher","first-page":"592","DOI":"10.1016\/j.cmet.2020.01.012","volume":"31","author":"TI Krisko","year":"2020","unstructured":"Krisko, T. I. et al. Dissociation of adaptive thermogenesis from glucose homeostasis in microbiome-deficient mice. Cell Metab. 31, 592\u2013604.e9 (2020).","journal-title":"Cell Metab."},{"key":"1550_CR19","doi-asserted-by":"publisher","first-page":"1252","DOI":"10.1016\/j.cell.2020.07.038","volume":"182","author":"A Sadik","year":"2020","unstructured":"Sadik, A. et al. IL4I1 is a metabolic immune checkpoint that activates the AHR and promotes tumor progression. Cell 182, 1252\u20131270.e34 (2020).","journal-title":"Cell"},{"key":"1550_CR20","doi-asserted-by":"publisher","first-page":"10678","DOI":"10.1021\/acs.jafc.0c03735","volume":"68","author":"X Zhang","year":"2020","unstructured":"Zhang, X. et al. Endogenous indole pyruvate pathway for tryptophan metabolism mediated by IL4I1. J. Agric. Food Chem. 68, 10678\u201310684 (2020).","journal-title":"J. Agric. Food Chem."},{"key":"1550_CR21","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1182\/blood-2006-07-036210","volume":"110","author":"ML Boulland","year":"2007","unstructured":"Boulland, M. L. et al. Human IL4I1 is a secreted L-phenylalanine oxidase expressed by mature dendritic cells that inhibits T-lymphocyte proliferation. Blood 110, 220\u2013227 (2007).","journal-title":"Blood"},{"key":"1550_CR22","doi-asserted-by":"publisher","first-page":"117864692311825","DOI":"10.1177\/11786469231182510","volume":"16","author":"EW Morgan","year":"2023","unstructured":"Morgan, E. W. et al. Contribution of circulating host and microbial tryptophan metabolites toward Ah receptor activation. Int. J. Tryptophan Res. 16, 11786469231182510 (2023).","journal-title":"Int. J. Tryptophan Res."},{"key":"1550_CR23","doi-asserted-by":"publisher","first-page":"822","DOI":"10.1016\/j.cell.2018.03.055","volume":"173","author":"C Jang","year":"2018","unstructured":"Jang, C., Chen, L. & Rabinowitz, J. D. Metabolomics and isotope tracing. Cell 173, 822\u2013837 (2018).","journal-title":"Cell"},{"key":"1550_CR24","doi-asserted-by":"publisher","first-page":"3441","DOI":"10.1016\/j.cell.2022.07.020","volume":"185","author":"X Zeng","year":"2022","unstructured":"Zeng, X. et al. Gut bacterial nutrient preferences quantified in vivo. Cell 185, 3441\u20133456.e19 (2022).","journal-title":"Cell"},{"key":"1550_CR25","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1016\/j.tifs.2022.02.004","volume":"121","author":"M Demarco","year":"2022","unstructured":"Demarco, M. et al. Digestibility, bioaccessibility and bioactivity of compounds from algae. Trends Food Sci. Technol. 121, 114\u2013128 (2022).","journal-title":"Trends Food Sci. Technol."},{"key":"1550_CR26","doi-asserted-by":"publisher","first-page":"115553","DOI":"10.1016\/j.taap.2021.115553","volume":"425","author":"Y Rong","year":"2021","unstructured":"Rong, Y. & Kiang, T. K. L. Characterization of human sulfotransferases catalyzing the formation of p-cresol sulfate and identification of mefenamic acid as a potent metabolism inhibitor and potential therapeutic agent for detoxification. Toxicol. Appl. Pharmacol. 425, 115553 (2021).","journal-title":"Toxicol. Appl. Pharmacol."},{"key":"1550_CR27","doi-asserted-by":"publisher","first-page":"6702","DOI":"10.1021\/acs.jafc.4c12596","volume":"73","author":"I Tsiara","year":"2025","unstructured":"Tsiara, I. et al. Characterizing the sulfated and glucuronidated (poly)phenol metabolome for dietary biomarker discovery. J. Agric. Food Chem. 73, 6702\u20136710 (2025).","journal-title":"J. Agric. Food Chem."},{"key":"1550_CR28","doi-asserted-by":"publisher","first-page":"101798","DOI":"10.1016\/j.xcrm.2024.101798","volume":"5","author":"X Qian","year":"2024","unstructured":"Qian, X. et al. Bifidobacteria with indole-3-lactic acid-producing capacity exhibit psychobiotic potential via reducing neuroinflammation. Cell Rep. Med. 5, 101798 (2024).","journal-title":"Cell Rep. Med."},{"key":"1550_CR29","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","volume":"569","author":"J Lloyd-Price","year":"2019","unstructured":"Lloyd-Price, J. et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569, 655\u2013662 (2019).","journal-title":"Nature"},{"key":"1550_CR30","doi-asserted-by":"publisher","first-page":"1800","DOI":"10.1038\/s42003-025-09207-0","volume":"8","author":"G Mallaret","year":"2025","unstructured":"Mallaret, G. et al. The autism-linked gut microbial metabolite p-cresol inhibits host catecholamine biosynthesizing enzymes to elicit social deficits. Commun. Biol. 8, 1800 (2025).","journal-title":"Commun. Biol."},{"key":"1550_CR31","doi-asserted-by":"publisher","first-page":"85","DOI":"10.2215\/CJN.02570607","volume":"3","author":"NM Pham","year":"2008","unstructured":"Pham, N. M., Recht, N. S., Hostetter, T. H. & Meyer, T. W. Removal of the protein-bound solutes indican and p-cresol sulfate by peritoneal dialysis. Clin. J. Am. Soc. Nephrol. 3, 85\u201390 (2008).","journal-title":"Clin. J. Am. Soc. Nephrol."},{"key":"1550_CR32","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.2215\/CJN.00160116","volume":"11","author":"R Poesen","year":"2016","unstructured":"Poesen, R., de Loor, H., Kuypers, D., Augustijns, P. & Meijers, B. Metabolism, protein binding, and renal clearance of microbiota-derived p-cresol in patients with CKD. Clin. J. Am. Soc. Nephrol. 11, 1136\u20131144 (2016).","journal-title":"Clin. J. Am. Soc. Nephrol."},{"key":"1550_CR33","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1097\/01.EE9.0000608184.18665.30","volume":"3","author":"S Kong","year":"2019","unstructured":"Kong, S. & Hernandez-Ferrer, C. Assessment of plasma metabolomic biomarkers in various pediatric diseases. Environ. Epidemiol. 3, 213 (2019).","journal-title":"Environ. Epidemiol."},{"key":"1550_CR34","doi-asserted-by":"publisher","first-page":"D640","DOI":"10.1093\/nar\/gkad1045","volume":"52","author":"O Yurekten","year":"2024","unstructured":"Yurekten, O. et al. MetaboLights: open data repository for metabolomics. Nucleic Acids Res. 52, D640\u2013D646 (2024).","journal-title":"Nucleic Acids Res."},{"key":"1550_CR35","doi-asserted-by":"publisher","first-page":"6343","DOI":"10.3390\/ijms20246343","volume":"20","author":"X Cao","year":"2019","unstructured":"Cao, X. et al. The roles of auxin biosynthesis YUCCA gene family in plants. Int. J. Mol. Sci. 20, 6343 (2019).","journal-title":"Int. J. Mol. Sci."},{"key":"1550_CR36","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1111\/j.1574-6976.2007.00072.x","volume":"31","author":"S Spaepen","year":"2007","unstructured":"Spaepen, S., Vanderleyden, J. & Remans, R. Indole-3-acetic acid in microbial and microorganism\u2013plant signaling. FEMS Microbiol. Rev. 31, 425\u2013448 (2007).","journal-title":"FEMS Microbiol. Rev."},{"key":"1550_CR37","doi-asserted-by":"publisher","first-page":"2409209","DOI":"10.1080\/19490976.2024.2409209","volume":"16","author":"D Jia","year":"2024","unstructured":"Jia, D., Kuang, Z. & Wang, L. The role of microbial indole metabolites in tumor. Gut Microbes 16, 2409209 (2024).","journal-title":"Gut Microbes"},{"key":"1550_CR38","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1038\/s41421-024-00709-5","volume":"10","author":"H Li","year":"2024","unstructured":"Li, H. et al. Gut microbiota-derived indole-3-acetic acid suppresses high myopia progression by promoting type I collagen synthesis. Cell Discov. 10, 89 (2024).","journal-title":"Cell Discov."},{"key":"1550_CR39","doi-asserted-by":"publisher","first-page":"903526","DOI":"10.3389\/fimmu.2022.903526","volume":"13","author":"X Ye","year":"2022","unstructured":"Ye, X. et al. Dual role of indoles derived from intestinal microbiota on human health. Front. Immunol. 13, 903526 (2022).","journal-title":"Front. Immunol."},{"key":"1550_CR40","doi-asserted-by":"publisher","first-page":"1964","DOI":"10.1038\/s41564-024-01737-3","volume":"9","author":"AK Sinha","year":"2024","unstructured":"Sinha, A. K. et al. Dietary fibre directs microbial tryptophan metabolism via metabolic interactions in the gut microbiota. Nat. Microbiol. 9, 1964\u20131978 (2024).","journal-title":"Nat. Microbiol."},{"key":"1550_CR41","doi-asserted-by":"publisher","first-page":"e202400583","DOI":"10.1002\/mnfr.202400583","volume":"69","author":"P Zhu","year":"2025","unstructured":"Zhu, P. et al. Exploring the fecal metabolome in infants with cow\u2019s milk allergy: the distinct impacts of cow\u2019s milk protein tolerance acquisition and of synbiotic supplementation. Mol. Nutr. Food Res. 69, e202400583 (2025).","journal-title":"Mol. Nutr. Food Res."},{"key":"1550_CR42","doi-asserted-by":"crossref","unstructured":"D'Alessandro, A. (ed.) High-Throughput Metabolomics: Methods and Protocols (Humana Press, 2019).","DOI":"10.1007\/978-1-4939-9236-2"},{"key":"1550_CR43","doi-asserted-by":"publisher","first-page":"5940","DOI":"10.1021\/acs.analchem.7b00396","volume":"89","author":"X Su","year":"2017","unstructured":"Su, X., Lu, W. & Rabinowitz, J. D. Metabolite spectral accuracy on orbitraps. Anal. Chem. 89, 5940\u20135948 (2017).","journal-title":"Anal. Chem."},{"key":"1550_CR44","doi-asserted-by":"publisher","first-page":"D593","DOI":"10.1093\/nar\/gku1201","volume":"43","author":"SF Stoddard","year":"2015","unstructured":"Stoddard, S. F., Smith, B. J., Hein, R., Roller, B. R. K. & Schmidt, T. M. rrnDB: Improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. Nucleic Acids Res. 43, D593\u2013D598 (2015).","journal-title":"Nucleic Acids Res."},{"key":"1550_CR45","doi-asserted-by":"publisher","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","volume":"44","author":"NA O\u2019Leary","year":"2016","unstructured":"O\u2019Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 44, D733\u2013D745 (2016).","journal-title":"Nucleic Acids Res."},{"key":"1550_CR46","doi-asserted-by":"publisher","first-page":"baaa062","DOI":"10.1093\/database\/baaa062","volume":"2020","author":"CL Schoch","year":"2020","unstructured":"Schoch, C. L. et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database 2020, baaa062 (2020).","journal-title":"Database"},{"key":"1550_CR47","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","volume":"8","author":"PJ McMurdie","year":"2013","unstructured":"McMurdie, P. J. & Holmes, S. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).","journal-title":"PLoS ONE"},{"key":"1550_CR48","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1038\/nmeth.3901","volume":"13","author":"S Tyanova","year":"2016","unstructured":"Tyanova, S. et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods 13, 731\u2013740 (2016).","journal-title":"Nat. Methods"},{"key":"1550_CR49","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114\u20132120 (2014).","journal-title":"Bioinformatics"},{"key":"1550_CR50","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":"1550_CR51","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","volume":"31","author":"D Li","year":"2015","unstructured":"Li, D., Liu, C. M., Luo, R., Sadakane, K. & Lam, T. W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674\u20131676 (2015).","journal-title":"Bioinformatics"},{"key":"1550_CR52","doi-asserted-by":"publisher","unstructured":"sulakhe-uc. uchicago-dfi-informatics\/Metabolite-and-gut-microbial-composition-in-AML-Patients: March 1, 2026. Zenodo https:\/\/doi.org\/10.5281\/zenodo.18829320 (2026).","DOI":"10.5281\/zenodo.18829320"}],"container-title":["Nature Metabolism"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42255-026-01550-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42255-026-01550-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42255-026-01550-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T10:51:31Z","timestamp":1784890291000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42255-026-01550-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,23]]},"references-count":52,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2026,7]]}},"alternative-id":["1550"],"URL":"https:\/\/doi.org\/10.1038\/s42255-026-01550-8","relation":{},"ISSN":["2522-5812"],"issn-type":[{"value":"2522-5812","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,23]]},"assertion":[{"value":"7 May 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 May 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 June 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"J.D.R. is a member of the Rutgers Cancer Institute of New Jersey (RCINJ) and the University of Pennsylvania Diabetes Research Center (U Penn DRC); a director of the U Penn DRC\u2013Princeton inter-institutional metabolomics core and RCINJ metabolomics core; an advisor and stockholder in Colorado Research Partners, Bantam Pharmaceuticals and Rafael Pharmaceuticals; a founder, director and stockholder of Farber Partners, Raze Therapeutics and Sofro Pharmaceuticals; a founder, advisor and stockholder in Marea Therapeutics; an advisor and stockholder in Empress Therapeutics (which investigates microbiome metabolites); and inventor of patents held by Princeton University. The remaining authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}]}}