{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T20:44:40Z","timestamp":1792183480930,"version":"4.4.0"},"reference-count":82,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T00:00:00Z","timestamp":1778630400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T00:00:00Z","timestamp":1784851200000},"content-version":"vor","delay-in-days":72,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"Government of Canada through Genome Canada and the Ontario Genomics Institute","award":["OGI-149"],"award-info":[{"award-number":["OGI-149"]}]},{"DOI":"10.13039\/501100000192","name":"Ontario Ministry of Economic Development and Innovation","doi-asserted-by":"publisher","award":["project number 13440"],"award-info":[{"award-number":["project number 13440"]}],"id":[{"id":"10.13039\/501100000192","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100019889","name":"Weston Family Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100019889","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["npj Biofilms Microbiomes"],"DOI":"10.1038\/s41522-026-01003-w","type":"journal-article","created":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T11:14:30Z","timestamp":1778670870000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Individual variability shapes ex vivo responses to resistant starch in inflammatory bowel disease derived microbiomes"],"prefix":"10.1038","volume":"12","author":[{"given":"Peter","family":"Dobranowski","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haonan","family":"Duan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Butcher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janice","family":"Mayne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Figeys","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David R.","family":"Mack","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alain","family":"Stintzi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,5,13]]},"reference":[{"key":"1003_CR1","doi-asserted-by":"publisher","first-page":"1450","DOI":"10.1093\/advances\/nmac075","volume":"13","author":"SM Gibbons","year":"2022","unstructured":"Gibbons, S. M. et al. Perspective: leveraging the gut microbiota to predict personalized responses to dietary, prebiotic, and probiotic interventions. Adv. Nutr. 13, 1450\u20131461 (2022).","journal-title":"Adv. Nutr."},{"key":"1003_CR2","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1016\/j.copbio.2019.10.008","volume":"61","author":"P DeMartino","year":"2020","unstructured":"DeMartino, P. & Cockburn, D. W. Resistant starch: impact on the gut microbiome and health. Curr. Opin. Biotechnol. 61, 66\u201371 (2020).","journal-title":"Curr. Opin. Biotechnol."},{"key":"1003_CR3","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1016\/j.nutres.2020.02.009","volume":"77","author":"ZA Bendiks","year":"2020","unstructured":"Bendiks, Z. A., Knudsen, K. E. B., Keenan, M. J. & Marco, M. L. Conserved and variable responses of the gut microbiome to resistant starch type 2. Nutr. Res. 77, 12\u201328 (2020).","journal-title":"Nutr. Res."},{"key":"1003_CR4","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-020-00806-z","volume":"8","author":"L Li","year":"2020","unstructured":"Li, L. et al. RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs. Microbiome 8, 33 (2020).","journal-title":"Microbiome"},{"key":"1003_CR5","doi-asserted-by":"publisher","first-page":"3833","DOI":"10.1016\/j.csbj.2020.10.042","volume":"18","author":"L Li","year":"2020","unstructured":"Li, L. et al. A functional ecological network based on metaproteomics responses of individual gut microbiomes to resistant starches. Comput. Struct. Biotechnol. J. 18, 3833\u20133842 (2020).","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"1003_CR6","doi-asserted-by":"publisher","first-page":"640253","DOI":"10.3389\/fmicb.2021.640253","volume":"12","author":"J Teichmann","year":"2021","unstructured":"Teichmann, J. & Cockburn, D. W. In vitro fermentation reveals changes in butyrate production dependent on resistant starch source and microbiome composition. Front. Microbiol. 12, 640253 (2021).","journal-title":"Front. Microbiol."},{"key":"1003_CR7","doi-asserted-by":"publisher","first-page":"1926842","DOI":"10.1080\/19490976.2021.1926842","volume":"13","author":"PA Dobranowski","year":"2021","unstructured":"Dobranowski, P. A. & Stintzi, A. Resistant starch, microbiome, and precision modulation. Gut Microbes 13, 1926842 (2021).","journal-title":"Gut Microbes"},{"key":"1003_CR8","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.tim.2019.09.004","volume":"28","author":"FM Cerqueira","year":"2020","unstructured":"Cerqueira, F. M., Photenhauer, A. L., Pollet, R. M., Brown, H. A. & Koropatkin, N. M. Starch digestion by gut bacteria: crowdsourcing for carbs. Trends Microbiol 28, 95\u2013108 (2020).","journal-title":"Trends Microbiol"},{"key":"1003_CR9","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1016\/j.chom.2020.01.006","volume":"27","author":"EC Deehan","year":"2020","unstructured":"Deehan, E. C. et al. Precision microbiome modulation with discrete dietary fiber structures directs short-chain fatty acid production. Cell Host Microbe 27, 389\u2013404.e6 (2020).","journal-title":"Cell Host Microbe"},{"key":"1003_CR10","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-016-0178-x","volume":"4","author":"A Venkataraman","year":"2016","unstructured":"Venkataraman, A. et al. Variable responses of human microbiomes to dietary supplementation with resistant starch. Microbiome 4, 33 (2016).","journal-title":"Microbiome"},{"key":"1003_CR11","doi-asserted-by":"publisher","first-page":"13728","DOI":"10.1021\/acs.jafc.9b04410","volume":"67","author":"S Wang","year":"2019","unstructured":"Wang, S. et al. Chemical cross-linking controls in vitro fecal fermentation rate of high-amylose maize starches and regulates gut microbiota composition. J. Agric. Food Chem. 67, 13728\u201313736 (2019).","journal-title":"J. Agric. Food Chem."},{"key":"1003_CR12","doi-asserted-by":"publisher","first-page":"3593","DOI":"10.1128\/AEM.72.5.3593-3599.2006","volume":"72","author":"A Belenguer","year":"2006","unstructured":"Belenguer, A. et al. Two routes of metabolic cross-feeding between Bifidobacterium adolescentis and butyrate-producing anaerobes from the human gut. Appl. Environ. Microbiol. 72, 3593\u20133599 (2006).","journal-title":"Appl. Environ. Microbiol."},{"key":"1003_CR13","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1016\/j.chom.2019.03.001","volume":"25","author":"AC Poole","year":"2019","unstructured":"Poole, A. C. et al. Human salivary amylase gene copy number impacts oral and gut microbiomes. Cell Host Microbe 25, 553\u2013564.e7 (2019).","journal-title":"Cell Host Microbe"},{"key":"1003_CR14","doi-asserted-by":"publisher","first-page":"e03145","DOI":"10.1016\/j.heliyon.2019.e03145","volume":"6","author":"G Giuberti","year":"2020","unstructured":"Giuberti, G. & Gallo, A. In vitro evaluation of fermentation characteristics of type 3 resistant starch. Heliyon 6, e03145 (2020).","journal-title":"Heliyon"},{"key":"1003_CR15","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1111\/j.1574-6941.2008.00527.x","volume":"66","author":"GCJ Abell","year":"2008","unstructured":"Abell, G. C. J., Cooke, C. M., Bennett, C. N., Conlon, M. A. & McOrist, A. L. Phylotypes related to Ruminococcus bromii are abundant in the large bowel of humans and increase in response to a diet high in resistant starch. FEMS Microbiol. Ecol. 66, 505\u2013515 (2008).","journal-title":"FEMS Microbiol. Ecol."},{"key":"1003_CR16","first-page":"797","volume":"37","author":"MJ Alfa","year":"2018","unstructured":"Alfa, M. J. et al. A randomized trial to determine the impact of a digestion resistant starch composition on the gut microbiome in older and mid-age adults. Clin. Nutr. Edinb. Scotl. 37, 797\u2013807 (2018).","journal-title":"Clin. Nutr. Edinb. Scotl."},{"key":"1003_CR17","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1017\/S0007114520003943","volume":"126","author":"D So","year":"2021","unstructured":"So, D. et al. Screening dietary fibres for fermentation characteristics and metabolic profiles using a rapid in vitro approach: implications for irritable bowel syndrome. Br. J. Nutr. 126, 208\u2013218 (2021).","journal-title":"Br. J. Nutr."},{"key":"1003_CR18","doi-asserted-by":"publisher","first-page":"883","DOI":"10.3945\/jn.110.128504","volume":"141","author":"AL McOrist","year":"2011","unstructured":"McOrist, A. L. et al. Fecal butyrate levels vary widely among individuals but are usually increased by a diet high in resistant starch. J. Nutr. 141, 883\u2013889 (2011).","journal-title":"J. Nutr."},{"key":"1003_CR19","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1079\/BJN19960177","volume":"75","author":"JH Cummings","year":"1996","unstructured":"Cummings, J. H., Beatty, E. R., Kingman, S. M., Bingham, S. A. & Englyst, H. N. Digestion and physiological properties of resistant starch in the human large bowel. Br. J. Nutr. 75, 733\u2013747 (1996).","journal-title":"Br. J. Nutr."},{"key":"1003_CR20","doi-asserted-by":"publisher","DOI":"10.1016\/j.clnu.2022.10.024","author":"K Hodgkinson","year":"2022","unstructured":"Hodgkinson, K. et al. Butyrate\u2019s role in human health and the current progress towards its clinical application to treat gastrointestinal disease. Clin. Nutr. https:\/\/doi.org\/10.1016\/j.clnu.2022.10.024 (2022).","journal-title":"Clin. Nutr."},{"key":"1003_CR21","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1038\/s41564-018-0306-4","volume":"4","author":"EA Franzosa","year":"2019","unstructured":"Franzosa, E. A. et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat. Microbiol. 4, 293\u2013305 (2019).","journal-title":"Nat. Microbiol."},{"key":"1003_CR22","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1038\/s41586-023-06906-8","volume":"626","author":"EC Gentry","year":"2024","unstructured":"Gentry, E. C. et al. Reverse metabolomics for the discovery of chemical structures from humans. Nature 626, 419\u2013426 (2024).","journal-title":"Nature"},{"key":"1003_CR23","doi-asserted-by":"publisher","first-page":"1472","DOI":"10.1136\/gutjnl-2022-328048","volume":"72","author":"A Vich Vila","year":"2023","unstructured":"Vich Vila, A. et al. Faecal metabolome and its determinants in inflammatory bowel disease. Gut 72, 1472\u20131485 (2023).","journal-title":"Gut"},{"key":"1003_CR24","doi-asserted-by":"publisher","first-page":"670","DOI":"10.1053\/j.gastro.2023.05.032","volume":"165","author":"JA Raygoza Garay","year":"2023","unstructured":"Raygoza Garay, J. A. et al. Gut microbiome composition is associated with future onset of crohn\u2019s disease in healthy first-degree relatives. Gastroenterology 165, 670\u2013681 (2023).","journal-title":"Gastroenterology"},{"key":"1003_CR25","doi-asserted-by":"publisher","first-page":"E3204","DOI":"10.3390\/nu12103204","volume":"12","author":"GR Healey","year":"2020","unstructured":"Healey, G. R., Celiberto, L. S., Lee, S. M. & Jacobson, K. Fiber and prebiotic interventions in pediatric inflammatory bowel disease: What role does the gut microbiome play? Nutrients 12, E3204 (2020).","journal-title":"Nutrients"},{"key":"1003_CR26","doi-asserted-by":"publisher","first-page":"372","DOI":"10.1186\/s12876-020-01516-4","volume":"20","author":"J Montroy","year":"2020","unstructured":"Montroy, J. et al. The effects of resistant starches on inflammatory bowel disease in preclinical and clinical settings: a systematic review and meta-analysis. BMC Gastroenterol. 20, 372 (2020).","journal-title":"BMC Gastroenterol."},{"key":"1003_CR27","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-022-01307-x","volume":"10","author":"ZC Holmes","year":"2022","unstructured":"Holmes, Z. C. et al. Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake. Microbiome 10, 114 (2022).","journal-title":"Microbiome"},{"key":"1003_CR28","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01028-21","volume":"12","author":"TM Cantu-Jungles","year":"2021","unstructured":"Cantu-Jungles, T. M. et al. Dietary fiber hierarchical specificity: the missing link for predictable and strong shifts in gut bacterial communities. mBio 12, e0102821 (2021).","journal-title":"mBio"},{"key":"1003_CR29","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":"1003_CR30","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-12087-8","volume":"10","author":"L Li","year":"2019","unstructured":"Li, L. et al. An in vitro model maintaining taxon-specific functional activities of the gut microbiome. Nat. Commun. 10, 4146 (2019).","journal-title":"Nat. Commun."},{"key":"1003_CR31","doi-asserted-by":"publisher","unstructured":"Jiang, P., Wu, S., Luo, Q., Zhao, X. & Chen, W.-H. Metagenomic analysis of common intestinal diseases reveals relationships among microbial signatures and powers multidisease diagnostic models. mSystems 6, https:\/\/doi.org\/10.1128\/msystems.00112-21 (2021).","DOI":"10.1128\/msystems.00112-21"},{"key":"1003_CR32","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1093\/ibd\/izac194","volume":"29","author":"LIH Abdel-Rahman","year":"2023","unstructured":"Abdel-Rahman, L. I. H. & Morgan, X. C. Searching for a consensus among inflammatory bowel disease studies: a systematic meta-analysis. Inflamm. Bowel Dis. 29, 125\u2013139 (2023).","journal-title":"Inflamm. Bowel Dis."},{"key":"1003_CR33","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1002\/ueg2.12485","volume":"12","author":"MV Vestergaard","year":"2024","unstructured":"Vestergaard, M. V. et al. Gut microbiota signatures in inflammatory bowel disease. U. Eur. Gastroenterol. J. 12, 22\u201333 (2024).","journal-title":"U. Eur. Gastroenterol. J."},{"key":"1003_CR34","doi-asserted-by":"publisher","first-page":"863","DOI":"10.1016\/j.chom.2022.05.003","volume":"30","author":"L Guthrie","year":"2022","unstructured":"Guthrie, L. et al. Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes. Cell Host Microbe 30, 863\u2013874.e4 (2022).","journal-title":"Cell Host Microbe"},{"key":"1003_CR35","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":"1003_CR36","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.e5 (2019).","journal-title":"Cell Host Microbe"},{"key":"1003_CR37","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-017-0375-2","volume":"5","author":"K Cheng","year":"2017","unstructured":"Cheng, K. et al. MetaLab: an automated pipeline for metaproteomic data analysis. Microbiome 5, 157 (2017).","journal-title":"Microbiome"},{"key":"1003_CR38","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-11819-z","volume":"12","author":"JS Glover","year":"2022","unstructured":"Glover, J. S., Ticer, T. D. & Engevik, M. A. Characterizing the mucin-degrading capacity of the human gut microbiota. Sci. Rep. 12, 8456 (2022).","journal-title":"Sci. Rep."},{"key":"1003_CR39","doi-asserted-by":"publisher","first-page":"2924","DOI":"10.3390\/nu13092924","volume":"13","author":"AD Romero Marcia","year":"2021","unstructured":"Romero Marcia, A. D., Yao, T., Chen, M.-H., Oles, R. E. & Lindemann, S. R. Fine carbohydrate structure of dietary resistant glucans governs the structure and function of human gut microbiota. Nutrients 13, 2924 (2021).","journal-title":"Nutrients"},{"key":"1003_CR40","doi-asserted-by":"publisher","first-page":"3838","DOI":"10.1016\/j.jmb.2014.07.028","volume":"426","author":"BR Hamaker","year":"2014","unstructured":"Hamaker, B. R. & Tuncil, Y. E. A perspective on the complexity of dietary fiber structures and their potential effect on the gut microbiota. J. Mol. Biol. 426, 3838\u20133850 (2014).","journal-title":"J. Mol. Biol."},{"key":"1003_CR41","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1038\/s41579-021-00604-w","volume":"20","author":"R Debray","year":"2022","unstructured":"Debray, R. et al. Priority effects in microbiome assembly. Nat. Rev. Microbiol. 20, 109\u2013121 (2022).","journal-title":"Nat. Rev. Microbiol."},{"key":"1003_CR42","doi-asserted-by":"publisher","unstructured":"Baxter, N. T. et al. Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers. mBio 10, https:\/\/doi.org\/10.1128\/mbio.02566-18 (2019).","DOI":"10.1128\/mbio.02566-18"},{"key":"1003_CR43","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0015046","volume":"5","author":"I Mart\u00ednez","year":"2010","unstructured":"Mart\u00ednez, I., Kim, J., Duffy, P. R., Schlegel, V. L. & Walter, J. Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLOS ONE 5, e15046 (2010).","journal-title":"PLOS ONE"},{"key":"1003_CR44","doi-asserted-by":"publisher","first-page":"e01343","DOI":"10.1128\/mBio.01343-17","volume":"8","author":"TV Maier","year":"2017","unstructured":"Maier, T. V. et al. Impact of dietary resistant starch on the human gut microbiome, metaproteome, and metabolome. mBio 8, e01343\u201317 (2017).","journal-title":"mBio"},{"key":"1003_CR45","doi-asserted-by":"publisher","first-page":"e01562","DOI":"10.1128\/AEM.01562-18","volume":"84","author":"M Vital","year":"2018","unstructured":"Vital, M. et al. Metagenomic insights into the degradation of resistant starch by human gut microbiota. Appl. Environ. Microbiol. 84, e01562\u201318 (2018).","journal-title":"Appl. Environ. Microbiol."},{"key":"1003_CR46","doi-asserted-by":"publisher","unstructured":"Blecksmith, S. E., Oliver, A., Alkan, Z. & Lemay, D. G. Gut microbiome genes involved in plant and mucin breakdown correlate with diet and gastrointestinal inflammation in healthy United States adults. J. Nutr. https:\/\/doi.org\/10.1016\/j.tjnut.2025.08.027 (2025).","DOI":"10.1016\/j.tjnut.2025.08.027"},{"key":"1003_CR47","doi-asserted-by":"publisher","first-page":"2420","DOI":"10.1038\/ajg.2010.281","volume":"105","author":"CW Png","year":"2010","unstructured":"Png, C. W. et al. Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria. Am. J. Gastroenterol. 105, 2420\u20132428 (2010).","journal-title":"Am. J. Gastroenterol."},{"key":"1003_CR48","doi-asserted-by":"publisher","first-page":"13882","DOI":"10.1021\/acs.jafc.2c04641","volume":"70","author":"X Si","year":"2022","unstructured":"Si, X. et al. -Ketoglutarate restores intestinal barrier function through promoting intestinal stem cells-mediated epithelial regeneration in colitis. J. Agric. Food Chem. 70, 13882\u201313892 (2022).","journal-title":"J. Agric. Food Chem."},{"key":"1003_CR49","doi-asserted-by":"publisher","first-page":"2000936","DOI":"10.1002\/mnfr.202000936","volume":"65","author":"Q Tian","year":"2021","unstructured":"Tian, Q. et al. Dietary alpha-ketoglutarate promotes epithelial metabolic transition and protects against DSS-induced colitis. Mol. Nutr. Food Res. 65, 2000936 (2021).","journal-title":"Mol. Nutr. Food Res."},{"key":"1003_CR50","doi-asserted-by":"publisher","first-page":"61","DOI":"10.3109\/00365513.2012.734859","volume":"73","author":"S Uraz","year":"2013","unstructured":"Uraz, S., Tahan, G., Aytekin, H. & Tahan, V. N-acetylcysteine expresses powerful anti-inflammatory and antioxidant activities resulting in complete improvement of acetic acid-induced colitis in rats. Scand. J. Clin. Lab. Invest. 73, 61\u201366 (2013).","journal-title":"Scand. J. Clin. Lab. Invest."},{"key":"1003_CR51","doi-asserted-by":"publisher","first-page":"2851","DOI":"10.3748\/wjg.14.2851","volume":"14","author":"LG Guijarro","year":"2008","unstructured":"Guijarro, L. G. et al. N-acetyl-L-cysteine combined with mesalamine in the treatment of ulcerative colitis: Randomized, placebo-controlled pilot study. World J. Gastroenterol. 14, 2851\u20132857 (2008).","journal-title":"World J. Gastroenterol."},{"key":"1003_CR52","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1093\/ibd\/izad185","volume":"30","author":"JP Jacobs","year":"2024","unstructured":"Jacobs, J. P. et al. Microbial and metabolite signatures of stress reactivity in ulcerative colitis patients in clinical remission predict clinical flare risk. Inflamm. Bowel Dis. 30, 336\u2013346 (2024).","journal-title":"Inflamm. Bowel Dis."},{"key":"1003_CR53","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1016\/j.chom.2023.12.013","volume":"32","author":"M Schirmer","year":"2024","unstructured":"Schirmer, M. et al. Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course. Cell Host Microbe 32, 209\u2013226.e7 (2024).","journal-title":"Cell Host Microbe"},{"key":"1003_CR54","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-42788-0","volume":"14","author":"L Ning","year":"2023","unstructured":"Ning, L. et al. Microbiome and metabolome features in inflammatory bowel disease via multi-omics integration analyses across cohorts. Nat. Commun. 14, 7135 (2023).","journal-title":"Nat. Commun."},{"key":"1003_CR55","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-60233-2","volume":"16","author":"J Taubenheim","year":"2025","unstructured":"Taubenheim, J. et al. Metabolic modeling reveals a multi-level deregulation of host-microbiome metabolic networks in IBD. Nat. Commun. 16, 5120 (2025).","journal-title":"Nat. Commun."},{"key":"1003_CR56","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1016\/j.jcmgh.2022.10.014","volume":"15","author":"KL Flannigan","year":"2023","unstructured":"Flannigan, K. L. et al. The pregnane X receptor and indole-3-propionic acid shape the intestinal mesenchyme to restrain inflammation and fibrosis. Cell. Mol. Gastroenterol. Hepatol. 15, 765\u2013795 (2023).","journal-title":"Cell. Mol. Gastroenterol. Hepatol."},{"key":"1003_CR57","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2025.2467235","volume":"17","author":"H Gao","year":"2025","unstructured":"Gao, H. et al. Microbiota-derived IPA alleviates intestinal mucosal inflammation through upregulating Th1\/Th17 cell apoptosis in inflammatory bowel disease. Gut Microbes 17, 2467235 (2025).","journal-title":"Gut Microbes"},{"key":"1003_CR58","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.1053\/j.gastro.2019.07.025","volume":"157","author":"K Aden","year":"2019","unstructured":"Aden, K. et al. Metabolic functions of gut microbes associate with efficacy of tumor necrosis factor antagonists in patients with inflammatory bowel diseases. Gastroenterology 157, 1279\u20131292.e11 (2019).","journal-title":"Gastroenterology"},{"key":"1003_CR59","doi-asserted-by":"publisher","first-page":"848","DOI":"10.1016\/j.chom.2022.03.036","volume":"30","author":"SM Lancaster","year":"2022","unstructured":"Lancaster, S. M. et al. Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans. Cell Host Microbe 30, 848\u2013862.e7 (2022).","journal-title":"Cell Host Microbe"},{"key":"1003_CR60","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-023-01724-6","volume":"12","author":"E Bonazzi","year":"2024","unstructured":"Bonazzi, E. et al. Individualized microbiotas dictate the impact of dietary fiber on colitis sensitivity. Microbiome 12, 5 (2024).","journal-title":"Microbiome"},{"key":"1003_CR61","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1093\/ajcn\/nqab402","volume":"115","author":"M Sobh","year":"2022","unstructured":"Sobh, M. et al. Tolerability and SCFA production after resistant starch supplementation in humans: a systematic review of randomized controlled studies. Am. J. Clin. Nutr. 115, 608\u2013618 (2022).","journal-title":"Am. J. Clin. Nutr."},{"key":"1003_CR62","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2023.2274127","volume":"15","author":"J Tan","year":"2023","unstructured":"Tan, J. et al. Functional profiling of gut microbial and immune responses toward different types of dietary fiber: a step toward personalized dietary interventions. Gut Microbes 15, 2274127 (2023).","journal-title":"Gut Microbes"},{"key":"1003_CR63","doi-asserted-by":"publisher","first-page":"116271","DOI":"10.1016\/j.foodres.2025.116271","volume":"209","author":"T van Deuren","year":"2025","unstructured":"van Deuren, T. et al. Specific dietary fibers steer toward distal colonic saccharolytic fermentation using the microbiota of individuals with overweight\/obesity. Food Res. Int. 209, 116271 (2025).","journal-title":"Food Res. Int."},{"key":"1003_CR64","doi-asserted-by":"publisher","DOI":"10.1016\/j.cyto.2025.156990","volume":"193","author":"CV Hall","year":"2025","unstructured":"Hall, C. V. et al. Characterising high-resolution dynamics of inflammatory and SCFA responses to food consumption in healthy men: a pilot biomarker discovery study. Cytokine 193, 156990 (2025).","journal-title":"Cytokine"},{"key":"1003_CR65","doi-asserted-by":"publisher","first-page":"795","DOI":"10.1097\/MPG.0000000000000239","volume":"58","author":"A Levine","year":"2014","unstructured":"Levine, A. et al. ESPGHAN revised porto criteria for the diagnosis of inflammatory bowel disease in children and adolescents. J. Pediatr. Gastroenterol. Nutr. 58, 795\u2013806 (2014).","journal-title":"J. Pediatr. Gastroenterol. Nutr."},{"key":"1003_CR66","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1002\/ibd.21649","volume":"18","author":"D Turner","year":"2012","unstructured":"Turner, D. et al. Mathematical weighting of the pediatric Crohn\u2019s disease activity index (PCDAI) and comparison with its other short versions. Inflamm. Bowel Dis. 18, 55\u201362 (2012).","journal-title":"Inflamm. Bowel Dis."},{"key":"1003_CR67","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1053\/j.gastro.2007.05.029","volume":"133","author":"D Turner","year":"2007","unstructured":"Turner, D. et al. Development, Validation, and Evaluation of a Pediatric Ulcerative Colitis Activity Index: A Prospective Multicenter Study. Gastroenterology 133, 423\u2013432 (2007).","journal-title":"Gastroenterology"},{"key":"1003_CR68","doi-asserted-by":"publisher","first-page":"26","DOI":"10.20517\/mrr.2023.57","volume":"3","author":"L Li","year":"2024","unstructured":"Li, L. et al. RapidAIM 2.0: a high-throughput assay to study functional response of human gut microbiome to xenobiotics. Microbiome Res. Rep. 3, 26 (2024).","journal-title":"Microbiome Res. Rep."},{"key":"1003_CR69","first-page":"677","volume":"68","author":"L Prosky","year":"1985","unstructured":"Prosky, L. et al. Determination of total dietary fiber in foods and food products: collaborative study. J. Assoc. Anal. Chem. 68, 677\u2013679 (1985).","journal-title":"J. Assoc. Anal. Chem."},{"key":"1003_CR70","doi-asserted-by":"publisher","first-page":"1103","DOI":"10.1093\/jaoac\/85.5.1103","volume":"85","author":"BV McCleary","year":"2002","unstructured":"McCleary, B. V., McNally, M. & Rossiter, P. Measurement of resistant starch by enzymatic digestion in starch and selected plant materials: collaborative study. J. AOAC Int. 85, 1103\u20131111 (2002).","journal-title":"J. AOAC Int."},{"key":"1003_CR71","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2022.2035658","volume":"14","author":"X Zhang","year":"2022","unstructured":"Zhang, X. et al. Evaluating live microbiota biobanking using an ex vivo microbiome assay and metaproteomics. Gut Microbes 14, 2035658 (2022).","journal-title":"Gut Microbes"},{"key":"1003_CR72","doi-asserted-by":"publisher","first-page":"1734","DOI":"10.3390\/v13091734","volume":"13","author":"J Mayne","year":"2021","unstructured":"Mayne, J. et al. Examining the effects of an anti-salmonella bacteriophage preparation, BAFASAL\u00ae, on ex-vivo human gut microbiome composition and function using a multi-omics approach. Viruses 13, 1734 (2021).","journal-title":"Viruses"},{"key":"1003_CR73","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1016\/j.bbi.2023.03.009","volume":"110","author":"E Murray","year":"2023","unstructured":"Murray, E. et al. Effects of pair-housing pubertal and adult male and female mice on LPS-induced age-dependent immune responses: a potential role for the gut microbiota. Brain. Behav. Immun. 110, 297\u2013309 (2023).","journal-title":"Brain. Behav. Immun."},{"key":"1003_CR74","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","volume":"17","author":"M Martin","year":"2011","unstructured":"Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10\u201312 (2011).","journal-title":"EMBnet. J."},{"key":"1003_CR75","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":"1003_CR76","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0605-2","volume":"6","author":"NM Davis","year":"2018","unstructured":"Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A. & Callahan, B. J. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome 6, 226 (2018).","journal-title":"Microbiome"},{"key":"1003_CR77","doi-asserted-by":"publisher","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":"1003_CR78","doi-asserted-by":"publisher","first-page":"D543","DOI":"10.1093\/nar\/gkab1038","volume":"50","author":"Y Perez-Riverol","year":"2022","unstructured":"Perez-Riverol, Y. et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res 50, D543\u2013D552 (2022).","journal-title":"Nucleic Acids Res"},{"key":"1003_CR79","doi-asserted-by":"publisher","first-page":"2524","DOI":"10.1093\/bioinformatics\/btu305","volume":"30","author":"M Choi","year":"2014","unstructured":"Choi, M. et al. MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics 30, 2524\u20132526 (2014).","journal-title":"Bioinformatics"},{"key":"1003_CR80","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1016\/j.aca.2014.11.015","volume":"854","author":"J Han","year":"2015","unstructured":"Han, J., Lin, K., Sequeira, C. & Borchers, C. H. An isotope-labeled chemical derivatization method for the quantitation of short-chain fatty acids in human feces by liquid chromatography-tandem mass spectrometry. Anal. Chim. Acta 854, 86\u201394 (2015).","journal-title":"Anal. Chim. Acta"},{"key":"1003_CR81","doi-asserted-by":"publisher","first-page":"14.11.1","DOI":"10.1002\/0471250953.bi1411s37","volume":"37","author":"MF Clasquin","year":"2012","unstructured":"Clasquin, M. F., Melamud, E. & Rabinowitz, J. D. LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine. Curr. Protoc. Bioinform. 37, 14.11.1\u201314.11.23 (2012).","journal-title":"Curr. Protoc. Bioinform."},{"key":"1003_CR82","doi-asserted-by":"publisher","first-page":"9818","DOI":"10.1021\/ac1021166","volume":"82","author":"E Melamud","year":"2010","unstructured":"Melamud, E., Vastag, L. & Rabinowitz, J. D. Metabolomic analysis and visualization engine for LC\u2212MS data. Anal. Chem. 82, 9818\u20139826 (2010).","journal-title":"Anal. Chem."}],"container-title":["npj Biofilms and Microbiomes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41522-026-01003-w","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41522-026-01003-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41522-026-01003-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T03:16:09Z","timestamp":1785122169000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41522-026-01003-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,13]]},"references-count":82,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["1003"],"URL":"https:\/\/doi.org\/10.1038\/s41522-026-01003-w","relation":{},"ISSN":["2055-5008"],"issn-type":[{"value":"2055-5008","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,13]]},"assertion":[{"value":"11 December 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 April 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 May 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"D.F., D.R.M., and A.S. are co-founders of Medbiome Inc. J.M. serves as a consultant for Medbiome Inc. All other authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}],"article-number":"142"}}