{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,23]],"date-time":"2026-08-23T17:22:08Z","timestamp":1787505728126,"version":"build-2736575974"},"reference-count":56,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2025,6,19]],"date-time":"2025-06-19T00:00:00Z","timestamp":1750291200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,6,19]],"date-time":"2025-06-19T00:00:00Z","timestamp":1750291200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/501100003032","name":"Association Nationale de la Recherche et de la Technologie","doi-asserted-by":"publisher","award":["2021\/0931"],"award-info":[{"award-number":["2021\/0931"]}],"id":[{"id":"10.13039\/501100003032","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003032","name":"Association Nationale de la Recherche et de la Technologie","doi-asserted-by":"publisher","award":["2021\/0931"],"award-info":[{"award-number":["2021\/0931"]}],"id":[{"id":"10.13039\/501100003032","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006342","name":"Association Vaincre la Mucoviscidose","doi-asserted-by":"publisher","award":["RF20230503289"],"award-info":[{"award-number":["RF20230503289"]}],"id":[{"id":"10.13039\/501100006342","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ANR","award":["ANR-15-IDEX-02"],"award-info":[{"award-number":["ANR-15-IDEX-02"]}]},{"DOI":"10.13039\/100019979","name":"Fondation Universit\u00e9 Grenoble Alpes","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100019979","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Metabolomics"],"DOI":"10.1007\/s11306-025-02288-2","type":"journal-article","created":{"date-parts":[[2025,6,19]],"date-time":"2025-06-19T14:33:07Z","timestamp":1750343587000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Untargeted and semi-targeted metabolomics approach for profiling small intestinal and fecal metabolome using high-resolution mass spectrometry"],"prefix":"10.1007","volume":"21","author":[{"given":"Alexandre","family":"Tronel","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morgane","family":"Roger-Margueritat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline","family":"Plazy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Val\u00e9rie","family":"Cunin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ipsita","family":"Mohanty","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pieter C.","family":"Dorrestein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Soranzo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Audrey","family":"Le Gouellec","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,6,19]]},"reference":[{"issue":"6","key":"2288_CR1","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. (2018). Gut microbiota regulation of Tryptophan metabolism in health and disease. Cell Host & Microbe, 23(6), 716\u2013724. https:\/\/doi.org\/10.1016\/j.chom.2018.05.003","journal-title":"Cell Host & Microbe"},{"issue":"1","key":"2288_CR2","doi-asserted-by":"publisher","first-page":"2350173","DOI":"10.1080\/19490976.2024.2350173","volume":"16","author":"R An","year":"2024","unstructured":"An, R., Wilms, E., Gerritsen, J., Kim, H. K., P\u00e9rez, C. S., Besseling-van der Vaart, I., et al. (2024). Spatio-temporal dynamics of the human small intestinal Microbiome and its response to a synbiotic. Gut Microbes, 16(1), 2350173. https:\/\/doi.org\/10.1080\/19490976.2024.2350173","journal-title":"Gut Microbes"},{"issue":"5","key":"2288_CR3","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1007\/s11306-024-02155-6","volume":"20","author":"RD Beger","year":"2024","unstructured":"Beger, R. D., Goodacre, R., Jones, C. M., Lippa, K. A., Mayboroda, O. A., O\u2019Neill, D., et al. (2024). Analysis types and quantification methods applied in UHPLC-MS metabolomics research: A tutorial. Metabolomics, 20(5), 95. https:\/\/doi.org\/10.1007\/s11306-024-02155-6","journal-title":"Metabolomics"},{"issue":"4","key":"2288_CR4","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1016\/j.femsre.2004.09.003","volume":"29","author":"M Begley","year":"2005","unstructured":"Begley, M., Gahan, C. G. M., & Hill, C. (2005). The interaction between bacteria and bile. FEMS Microbiology Reviews, 29(4), 625\u2013651. https:\/\/doi.org\/10.1016\/j.femsre.2004.09.003","journal-title":"FEMS Microbiology Reviews"},{"issue":"1","key":"2288_CR5","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1186\/s40168-020-00875-0","volume":"8","author":"G Berg","year":"2020","unstructured":"Berg, G., Rybakova, D., Fischer, D., Cernava, T., Verg\u00e8s, M. C. C., Charles, T., et al. (2020). Microbiome definition re-visited: Old concepts and new challenges. Microbiome, 8(1), 103. https:\/\/doi.org\/10.1186\/s40168-020-00875-0","journal-title":"Microbiome"},{"issue":"5","key":"2288_CR6","doi-asserted-by":"publisher","first-page":"411","DOI":"10.3920\/BM2020.0057","volume":"11","author":"E Blaak","year":"2020","unstructured":"Blaak, E., Canfora, E., Theis, S., Frost, G., Groen, A., Mithieux, G., et al. (2020). Short chain fatty acids in human gut and metabolic health. Beneficial Microbes, 11(5), 411\u2013455. https:\/\/doi.org\/10.3920\/BM2020.0057","journal-title":"Beneficial Microbes"},{"issue":"6","key":"2288_CR7","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1007\/s11306-018-1367-3","volume":"14","author":"D Broadhurst","year":"2018","unstructured":"Broadhurst, D., Goodacre, R., Reinke, S. N., Kuligowski, J., Wilson, I. D., Lewis, M. R., & Dunn, W. B. (2018). Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies. Metabolomics, 14(6), 72. https:\/\/doi.org\/10.1007\/s11306-018-1367-3","journal-title":"Metabolomics"},{"issue":"3","key":"2288_CR8","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1021\/acs.jnatprod.9b00176","volume":"82","author":"LK Caesar","year":"2019","unstructured":"Caesar, L. K., Kellogg, J. J., Kvalheim, O. M., & Cech, N. B. (2019). Opportunities and limitations for untargeted mass spectrometry metabolomics to identify biologically active constituents in complex natural product mixtures. Journal of Natural Products, 82(3), 469\u2013484. https:\/\/doi.org\/10.1021\/acs.jnatprod.9b00176","journal-title":"Journal of Natural Products"},{"issue":"6","key":"2288_CR9","doi-asserted-by":"publisher","first-page":"406","DOI":"10.3390\/metabo11060406","volume":"11","author":"C Caffaratti","year":"2021","unstructured":"Caffaratti, C., Plazy, C., Mery, G., Tidjani, A. R., Fiorini, F., Thiroux, S., et al. (2021). What we know so Far about the Metabolite-Mediated Microbiota-Intestinal immunity dialogue and how to hear the sound of this crosstalk. Metabolites, 11(6), 406. https:\/\/doi.org\/10.3390\/metabo11060406","journal-title":"Metabolites"},{"issue":"4","key":"2288_CR10","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1038\/s41579-022-00805-x","volume":"21","author":"SL Collins","year":"2023","unstructured":"Collins, S. L., Stine, J. G., Bisanz, J. E., Okafor, C. D., & Patterson, A. D. (2023). Bile acids and the gut microbiota: Metabolic interactions and impacts on disease. Nature Reviews Microbiology, 21(4), 236\u2013247. https:\/\/doi.org\/10.1038\/s41579-022-00805-x","journal-title":"Nature Reviews Microbiology"},{"issue":"5","key":"2288_CR11","doi-asserted-by":"publisher","first-page":"1597","DOI":"10.1007\/s00726-011-0846-x","volume":"42","author":"ZL Dai","year":"2012","unstructured":"Dai, Z. L., Li, X. L., Xi, P. B., Zhang, J., Wu, G., & Zhu, W. Y. (2012). Metabolism of select amino acids in bacteria from the pig small intestine. Amino Acids, 42(5), 1597\u20131608. https:\/\/doi.org\/10.1007\/s00726-011-0846-x","journal-title":"Amino Acids"},{"issue":"8","key":"2288_CR12","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1038\/s41575-019-0157-3","volume":"16","author":"B Dalile","year":"2019","unstructured":"Dalile, B., Van Oudenhove, L., Vervliet, B., & Verbeke, K. (2019). The role of short-chain fatty acids in microbiota\u2013gut\u2013brain communication. Nature Reviews Gastroenterology & Hepatology, 16(8), 461\u2013478. https:\/\/doi.org\/10.1038\/s41575-019-0157-3","journal-title":"Nature Reviews Gastroenterology & Hepatology"},{"key":"2288_CR13","doi-asserted-by":"publisher","DOI":"10.26434\/chemrxiv-2023-98n6q","author":"T Damiani","year":"2023","unstructured":"Damiani, T., Heuckeroth, S., Smirnov, A., Mokshyna, O., Brungs, C., & Korf, A. (2023). Mass spectrometry data processing in MZmine 3: feature detection and annotation. ChemRxiv. https:\/\/doi.org\/10.26434\/chemrxiv-2023-98n6q","journal-title":"ChemRxiv"},{"key":"2288_CR14","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1007\/978-1-0716-0239-3_3","volume":"2104","author":"X Du","year":"2020","unstructured":"Du, X., Smirnov, A., Pluskal, T., Jia, W., & Sumner, S. (2020). Metabolomics data preprocessing using ADAP and MZmine 2. Methods in Molecular Biology (Clifton N J), 2104, 25\u201348. https:\/\/doi.org\/10.1007\/978-1-0716-0239-3_3","journal-title":"Methods in Molecular Biology (Clifton N J)"},{"issue":"4","key":"2288_CR15","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1038\/s41592-019-0344-8","volume":"16","author":"K D\u00fchrkop","year":"2019","unstructured":"D\u00fchrkop, K., Fleischauer, M., Ludwig, M., Aksenov, A. A., Melnik, A. V., Meusel, M., et al. (2019). SIRIUS 4: A rapid tool for turning tandem mass spectra into metabolite structure information. Nature Methods, 16(4), 299\u2013302. https:\/\/doi.org\/10.1038\/s41592-019-0344-8","journal-title":"Nature Methods"},{"issue":"8","key":"2288_CR16","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1136\/gut.29.8.1035","volume":"29","author":"DF Evans","year":"1988","unstructured":"Evans, D. F., Pye, G., Bramley, R., Clark, A. G., Dyson, T. J., & Hardcastle, J. D. (1988). Measurement of Gastrointestinal pH profiles in normal ambulant human subjects. Gut, 29(8), 1035\u20131041. https:\/\/doi.org\/10.1136\/gut.29.8.1035","journal-title":"Gut"},{"key":"2288_CR17","doi-asserted-by":"publisher","first-page":"1853","DOI":"10.3389\/fimmu.2018.01853","volume":"9","author":"S Fiorucci","year":"2018","unstructured":"Fiorucci, S., Biagioli, M., Zampella, A., & Distrutti, E. (2018). Bile acids activated receptors regulate innate immunity. Frontiers in Immunology, 9, 1853. https:\/\/doi.org\/10.3389\/fimmu.2018.01853","journal-title":"Frontiers in Immunology"},{"issue":"3","key":"2288_CR18","doi-asserted-by":"publisher","first-page":"674","DOI":"10.1007\/s10620-020-06715-3","volume":"66","author":"S Fiorucci","year":"2021","unstructured":"Fiorucci, S., Carino, A., Baldoni, M., Santucci, L., Costanzi, E., Graziosi, L., et al. (2021). Bile acid signaling in inflammatory bowel diseases. Digestive Diseases and Sciences, 66(3), 674\u2013693. https:\/\/doi.org\/10.1007\/s10620-020-06715-3","journal-title":"Digestive Diseases and Sciences"},{"key":"2288_CR19","doi-asserted-by":"publisher","DOI":"10.1038\/s42255-023-00777-z","author":"J Folz","year":"2023","unstructured":"Folz, J., Culver, R. N., Morales, J. M., Grembi, J., Triadafilopoulos, G., Relman, D. A., et al. (2023). Human metabolome variation along the upper intestinal tract. Nature Metabolism. https:\/\/doi.org\/10.1038\/s42255-023-00777-z","journal-title":"Nature Metabolism"},{"issue":"19","key":"2288_CR20","doi-asserted-by":"publisher","first-page":"9405","DOI":"10.1039\/d1fo01574e","volume":"12","author":"JS Folz","year":"2021","unstructured":"Folz, J. S., Shalon, D., & Fiehn, O. (2021). Metabolomics analysis of time-series human small intestine lumen samples collected in vivo. Food & Function, 12(19), 9405\u20139415. https:\/\/doi.org\/10.1039\/d1fo01574e","journal-title":"Food & Function"},{"issue":"7998","key":"2288_CR21","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., Collins, S. L., Panitchpakdi, M., Belda-Ferre, P., Stewart, A. K., Terrazas, C., M., et al. (2024). Reverse metabolomics for the discovery of chemical structures from humans. Nature, 626(7998), 419\u2013426. https:\/\/doi.org\/10.1038\/s41586-023-06906-8","journal-title":"Nature"},{"issue":"3","key":"2288_CR22","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1007\/s10545-017-0130-7","volume":"41","author":"I Gertsman","year":"2018","unstructured":"Gertsman, I., & Barshop, B. A. (2018). Promises and pitfalls of untargeted metabolomics. Journal of Inherited Metabolic Disease, 41(3), 355\u2013366. https:\/\/doi.org\/10.1007\/s10545-017-0130-7","journal-title":"Journal of Inherited Metabolic Disease"},{"issue":"1","key":"2288_CR23","doi-asserted-by":"publisher","first-page":"26164","DOI":"10.3402\/mehd.v26.26164","volume":"26","author":"D Graf","year":"2015","unstructured":"Graf, D., Di Cagno, R., F\u00e5k, F., Flint, H. J., Nyman, M., Saarela, M., & Watzl, B. (2015). Contribution of diet to the composition of the human gut microbiota. Microbial Ecology in Health and Disease, 26(1), 26164. https:\/\/doi.org\/10.3402\/mehd.v26.26164","journal-title":"Microbial Ecology in Health and Disease"},{"issue":"5","key":"2288_CR24","doi-asserted-by":"publisher","first-page":"662","DOI":"10.1016\/j.chom.2015.03.005","volume":"17","author":"CJ Kelly","year":"2015","unstructured":"Kelly, C. J., Zheng, L., Campbell, E. L., Saeedi, B., Scholz, C. C., Bayless, A. J., et al. (2015). Crosstalk between Microbiota-Derived Short-Chain fatty acids and intestinal epithelial HIF augments tissue barrier function. Cell Host & Microbe, 17(5), 662\u2013671. https:\/\/doi.org\/10.1016\/j.chom.2015.03.005","journal-title":"Cell Host & Microbe"},{"issue":"6","key":"2288_CR25","doi-asserted-by":"publisher","first-page":"1332","DOI":"10.1016\/j.cell.2016.05.041","volume":"165","author":"A Koh","year":"2016","unstructured":"Koh, A., De Vadder, F., Kovatcheva-Datchary, P., & B\u00e4ckhed, F. (2016). From dietary Fiber to host physiology: Short-Chain fatty acids as key bacterial metabolites. Cell, 165(6), 1332\u20131345. https:\/\/doi.org\/10.1016\/j.cell.2016.05.041","journal-title":"Cell"},{"key":"2288_CR26","doi-asserted-by":"publisher","DOI":"10.1038\/s41577-024-01057-x","author":"MH Lee","year":"2024","unstructured":"Lee, M. H., Nuccio, S. P., Mohanty, I., Hagey, L. R., Dorrestein, P. C., Chu, H., & Raffatellu, M. (2024). How bile acids and the microbiota interact to shape host immunity. Nature Reviews Immunology. https:\/\/doi.org\/10.1038\/s41577-024-01057-x","journal-title":"Nature Reviews Immunology"},{"key":"2288_CR27","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1016\/j.biochi.2020.09.007","volume":"178","author":"I Lema","year":"2020","unstructured":"Lema, I., Ara\u00fajo, J. R., Rolhion, N., & Demignot, S. (2020). Jejunum: The understudied meeting place of dietary lipids and the microbiota. Biochimie, 178, 124\u2013136. https:\/\/doi.org\/10.1016\/j.biochi.2020.09.007","journal-title":"Biochimie"},{"issue":"5","key":"2288_CR28","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1016\/j.chom.2024.04.004","volume":"32","author":"TT Li","year":"2024","unstructured":"Li, T. T., Chen, X., Huo, D., Arifuzzaman, M., Qiao, S., Jin, W. B., et al. (2024). Microbiota metabolism of intestinal amino acids impacts host nutrient homeostasis and physiology. Cell Host & Microbe, 32(5), 661\u2013675e10. https:\/\/doi.org\/10.1016\/j.chom.2024.04.004","journal-title":"Cell Host & Microbe"},{"key":"2288_CR29","doi-asserted-by":"publisher","unstructured":"Magn\u00fasd\u00f3ttir, S., Ravcheev, D., de Cr\u00e9cy-Lagard, V., & Thiele, I. (2015). Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes. Frontiers in Genetics, 6.\u00a0Retrieved\u00a0August 3, 2023, from,\u00a0https:\/\/www.frontiersin.org\/articles\/https:\/\/doi.org\/10.3389\/fgene.2015.00148.","DOI":"10.3389\/fgene.2015.00148"},{"issue":"11","key":"2288_CR30","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1007\/s11306-020-01744-5","volume":"16","author":"R Mandal","year":"2020","unstructured":"Mandal, R., Cano, R., Davis, C. D., Hayashi, D., Jackson, S. A., Jones, C. M., et al. (2020). Workshop report: Toward the development of a human whole stool reference material for metabolomic and metagenomic gut Microbiome measurements. Metabolomics, 16(11), 119. https:\/\/doi.org\/10.1007\/s11306-020-01744-5","journal-title":"Metabolomics"},{"issue":"3","key":"2288_CR31","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1016\/j.chom.2019.08.011","volume":"26","author":"K Martinez-Guryn","year":"2019","unstructured":"Martinez-Guryn, K., Leone, V., & Chang, E. B. (2019). Regional diversity of the Gastrointestinal Microbiome. Cell Host & Microbe, 26(3), 314\u2013324. https:\/\/doi.org\/10.1016\/j.chom.2019.08.011","journal-title":"Cell Host & Microbe"},{"issue":"4","key":"2288_CR32","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1038\/nrmicro2538","volume":"9","author":"MA McGuckin","year":"2011","unstructured":"McGuckin, M. A., Lind\u00e9n, S. K., Sutton, P., & Florin, T. H. (2011). Mucin dynamics and enteric pathogens. Nature Reviews Microbiology, 9(4), 265\u2013278. https:\/\/doi.org\/10.1038\/nrmicro2538","journal-title":"Nature Reviews Microbiology"},{"issue":"9","key":"2288_CR33","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.1097\/00042737-200109000-00004","volume":"13","author":"V Milovic","year":"2001","unstructured":"Milovic, V. (2001). Polyamines in the gut lumen: Bioavailability and biodistribution. European Journal of Gastroenterology & Hepatology, 13(9), 1021\u20131025. https:\/\/doi.org\/10.1097\/00042737-200109000-00004","journal-title":"European Journal of Gastroenterology & Hepatology"},{"key":"2288_CR34","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2024.02.019","author":"I Mohanty","year":"2024","unstructured":"Mohanty, I., Mannochio-Russo, H., Schweer, J. V., Abiead, Y. E., Bittremieux, W., Xing, S., et al. (2024). The underappreciated diversity of bile acid modifications. Cell. https:\/\/doi.org\/10.1016\/j.cell.2024.02.019","journal-title":"Cell"},{"issue":"1","key":"2288_CR35","doi-asserted-by":"publisher","first-page":"2105","DOI":"10.1038\/s41467-021-22212-1","volume":"12","author":"A Nakamura","year":"2021","unstructured":"Nakamura, A., Kurihara, S., Takahashi, D., Ohashi, W., Nakamura, Y., Kimura, S., et al. (2021). Symbiotic polyamine metabolism regulates epithelial proliferation and macrophage differentiation in the colon. Nature Communications, 12(1), 2105. https:\/\/doi.org\/10.1038\/s41467-021-22212-1","journal-title":"Nature Communications"},{"issue":"4","key":"2288_CR36","doi-asserted-by":"publisher","first-page":"2930","DOI":"10.3390\/nu7042930","volume":"7","author":"EPJG Neis","year":"2015","unstructured":"Neis, E. P. J. G., Dejong, C. H. C., & Rensen, S. S. (2015). The role of microbial amino acid metabolism in host metabolism. Nutrients, 7(4), 2930\u20132946. https:\/\/doi.org\/10.3390\/nu7042930","journal-title":"Nutrients"},{"issue":"6086","key":"2288_CR37","doi-asserted-by":"publisher","first-page":"1262","DOI":"10.1126\/science.1223813","volume":"336","author":"JK Nicholson","year":"2012","unstructured":"Nicholson, J. K., Holmes, E., Kinross, J., Burcelin, R., Gibson, G., Jia, W., & Pettersson, S. (2012). Host-Gut microbiota metabolic interactions. Science, 336(6086), 1262\u20131267. https:\/\/doi.org\/10.1126\/science.1223813","journal-title":"Science"},{"issue":"9","key":"2288_CR38","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1038\/s41592-020-0933-6","volume":"17","author":"LF Nothias","year":"2020","unstructured":"Nothias, L. F., Petras, D., Schmid, R., D\u00fchrkop, K., Rainer, J., Sarvepalli, A., et al. (2020). Feature-based molecular networking in the GNPS analysis environment. Nature Methods, 17(9), 905\u2013908. https:\/\/doi.org\/10.1038\/s41592-020-0933-6","journal-title":"Nature Methods"},{"issue":"1","key":"2288_CR39","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1016\/j.cmet.2017.05.008","volume":"26","author":"TS Postler","year":"2017","unstructured":"Postler, T. S., & Ghosh, S. (2017). Understanding the holobiont: How microbial metabolites affect human health and shape the immune system. Cell Metabolism, 26(1), 110\u2013130. https:\/\/doi.org\/10.1016\/j.cmet.2017.05.008","journal-title":"Cell Metabolism"},{"key":"2288_CR40","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2023-329614","author":"M Rehan","year":"2023","unstructured":"Rehan, M., Al-Bahadly, I., Thomas, D. G., Young, W., Cheng, L. K., & Avci, E. (2023). Smart capsules for sensing and sampling the gut: Status, challenges and prospects. Gut. https:\/\/doi.org\/10.1136\/gutjnl-2023-329614","journal-title":"Gut"},{"issue":"1","key":"2288_CR41","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1080\/19490976.2015.1127483","volume":"7","author":"JM Ridlon","year":"2016","unstructured":"Ridlon, J. M., Harris, S. C., Bhowmik, S., Kang, D. J., & Hylemon, P. B. (2016). Consequences of bile salt biotransformations by intestinal bacteria. Gut Microbes, 7(1), 22\u201339. https:\/\/doi.org\/10.1080\/19490976.2015.1127483","journal-title":"Gut Microbes"},{"key":"2288_CR42","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1016\/j.aca.2020.12.025","volume":"1147","author":"M Roca","year":"2021","unstructured":"Roca, M., Alcoriza, M. I., Garcia-Ca\u00f1averas, J. C., & Lahoz, A. (2021). Reviewing the metabolome coverage provided by LC-MS: Focus on sample Preparation and chromatography-A tutorial. Analytica Chimica Acta, 1147, 38\u201355. https:\/\/doi.org\/10.1016\/j.aca.2020.12.025","journal-title":"Analytica Chimica Acta"},{"issue":"3","key":"2288_CR43","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1007\/s00726-012-1371-2","volume":"45","author":"A San Gabriel","year":"2013","unstructured":"San Gabriel, A., & Uneyama, H. (2013). Amino acid sensing in the Gastrointestinal tract. Amino Acids, 45(3), 451\u2013461. https:\/\/doi.org\/10.1007\/s00726-012-1371-2","journal-title":"Amino Acids"},{"issue":"4","key":"2288_CR44","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1038\/s41587-023-01690-2","volume":"41","author":"R Schmid","year":"2023","unstructured":"Schmid, R., Heuckeroth, S., Korf, A., Smirnov, A., Myers, O., Dyrlund, T. S., et al. (2023). Integrative analysis of multimodal mass spectrometry data in MZmine 3. Nature Biotechnology, 41(4), 447\u2013449. https:\/\/doi.org\/10.1038\/s41587-023-01690-2","journal-title":"Nature Biotechnology"},{"issue":"12","key":"2288_CR45","doi-asserted-by":"publisher","first-page":"1897","DOI":"10.1007\/s13361-016-1469-y","volume":"27","author":"AC Schrimpe-Rutledge","year":"2016","unstructured":"Schrimpe-Rutledge, A. C., Codreanu, S. G., Sherrod, S. D., & McLean, J. A. (2016). Untargeted metabolomics Strategies\u2014Challenges and emerging directions. Journal of the American Society for Mass Spectrometry, 27(12), 1897\u20131905. https:\/\/doi.org\/10.1007\/s13361-016-1469-y","journal-title":"Journal of the American Society for Mass Spectrometry"},{"issue":"4","key":"2288_CR46","doi-asserted-by":"publisher","first-page":"2097","DOI":"10.1021\/es5002105","volume":"48","author":"EL Schymanski","year":"2014","unstructured":"Schymanski, E. L., Jeon, J., Gulde, R., Fenner, K., Ruff, M., Singer, H. P., & Hollender, J. (2014). Identifying small molecules via high resolution mass spectrometry: Communicating confidence. Environmental Science & Technology, 48(4), 2097\u20132098. https:\/\/doi.org\/10.1021\/es5002105","journal-title":"Environmental Science & Technology"},{"key":"2288_CR47","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-05989-7","author":"D Shalon","year":"2023","unstructured":"Shalon, D., Culver, R. N., Grembi, J. A., Folz, J., Treit, P. V., Shi, H., et al. (2023). Profiling the human intestinal environment under physiological conditions. Nature. https:\/\/doi.org\/10.1038\/s41586-023-05989-7","journal-title":"Nature"},{"key":"2288_CR48","doi-asserted-by":"crossref","unstructured":"Steinbach, E., Belda, E., Alili, R., Adriouch, S., Luminal, J., Group, C. M. A. M. (2023). in M. D. (Je\/Col-M.,. Comparative analysis of the duodenojejunal microbiome with the oral and fecal microbiome unveils its role in human severe obesity. medRxiv, 2023\u201312.","DOI":"10.1101\/2023.12.15.23299964"},{"key":"2288_CR49","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2020.00151","author":"Q Tang","year":"2020","unstructured":"Tang, Q., Jin, G., Wang, G., Liu, T., Liu, X., Wang, B., & Cao, H. (2020). Current sampling methods for gut microbiota: A call for more precise devices. Frontiers in Cellular and Infection Microbiology. https:\/\/doi.org\/10.3389\/fcimb.2020.00151","journal-title":"Frontiers in Cellular and Infection Microbiology"},{"issue":"1","key":"2288_CR50","doi-asserted-by":"publisher","first-page":"15","DOI":"10.3390\/mps7010015","volume":"7","author":"A Tronel","year":"2024","unstructured":"Tronel, A., Silvent, A. S., Buelow, E., Giai, J., Leroy, C., Proust, M., et al. (2024). Pilot study: Safety and performance validation of an ingestible medical device for collecting small intestinal liquid in healthy volunteers. Methods and Protocols, 7(1), 15. https:\/\/doi.org\/10.3390\/mps7010015","journal-title":"Methods and Protocols"},{"issue":"1","key":"2288_CR51","doi-asserted-by":"publisher","first-page":"362","DOI":"10.1038\/s41467-019-14177-z","volume":"11","author":"A Vich Vila","year":"2020","unstructured":"Vich Vila, A., Collij, V., Sanna, S., Sinha, T., Imhann, F., Bourgonje, A. R., et al. (2020). Impact of commonly used drugs on the composition and metabolic function of the gut microbiota. Nature Communications, 11(1), 362. https:\/\/doi.org\/10.1038\/s41467-019-14177-z","journal-title":"Nature Communications"},{"key":"2288_CR52","doi-asserted-by":"publisher","DOI":"10.1101\/2024.04.04.24305299","author":"G Wang","year":"2024","unstructured":"Wang, G., Bundalovic-Torma, C., Menon, S., Bruehlmann, S., Wilsack, L., & Rehak, R. (2024a). Clinical sampling of small intestine luminal content for microbiome multi-omics analysis: A performance analysis of the small intestine microbiome aspiration (simba) capsule and benchmarking against endoscopy. medRxiv. https:\/\/doi.org\/10.1101\/2024.04.04.24305299","journal-title":"medRxiv"},{"key":"2288_CR53","doi-asserted-by":"publisher","DOI":"10.1101\/2024.04.02.24305212","author":"G Wang","year":"2024","unstructured":"Wang, G., Menon, S., Wilsack, L., Rehak, R., Lou, L., & Turbide, C. (2024b). Spatially and temporally precise microbiome profiling in the small intestine using the SIMBA capsule with X-ray tracking. medRxiv. https:\/\/doi.org\/10.1101\/2024.04.02.24305212","journal-title":"medRxiv"},{"issue":"7","key":"2288_CR54","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1038\/nrd.2016.32","volume":"15","author":"DS Wishart","year":"2016","unstructured":"Wishart, D. S. (2016). Emerging applications of metabolomics in drug discovery and precision medicine. Nature Reviews Drug Discovery, 15(7), 473\u2013484. https:\/\/doi.org\/10.1038\/nrd.2016.32","journal-title":"Nature Reviews Drug Discovery"},{"issue":"6","key":"2288_CR55","doi-asserted-by":"publisher","first-page":"3092","DOI":"10.1039\/C9RA08985C","volume":"10","author":"X Zhang","year":"2020","unstructured":"Zhang, X., Li, Q., Xu, Z., & Dou, J. (2020). Mass spectrometry-based metabolomics in health and medical science: A systematic review. RSC Advances, 10(6), 3092\u20133104. https:\/\/doi.org\/10.1039\/C9RA08985C","journal-title":"RSC Advances"},{"issue":"7","key":"2288_CR56","doi-asserted-by":"publisher","first-page":"1415","DOI":"10.1038\/ismej.2011.212","volume":"6","author":"EG Zoetendal","year":"2012","unstructured":"Zoetendal, E. G., Raes, J., van den Bogert, B., Arumugam, M., Booijink, C. C., Troost, F. J., et al. (2012). The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. The ISME Journal, 6(7), 1415\u20131426. https:\/\/doi.org\/10.1038\/ismej.2011.212","journal-title":"The ISME Journal"}],"container-title":["Metabolomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11306-025-02288-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11306-025-02288-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11306-025-02288-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,15]],"date-time":"2025-09-15T15:05:14Z","timestamp":1757948714000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s11306-025-02288-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,19]]},"references-count":56,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2025,8]]}},"alternative-id":["2288"],"URL":"https:\/\/doi.org\/10.1007\/s11306-025-02288-2","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.09.16.613180","asserted-by":"object"}]},"ISSN":["1573-3890"],"issn-type":[{"value":"1573-3890","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,6,19]]},"assertion":[{"value":"4 February 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 June 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 June 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"A.T and T.S, as employee and CEO\/co-founders of Pelican Health, respectively, which markets intestinal sampling capsules, may face a conflict of interest due to their roles within the company. PCD is an advisor and holds equity in Cybele, BileOmix and Sirenas and a Scientific co-founder, advisor and holds equity to Ometa, Enveda, and Arome with prior approval by UC-San Diego. PCD also consulted for DSM animal health in 2023. All the authors, except T.S and A.T. declare that they have no conflict of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}},{"value":"This research was approved by the CHUGA institutional review board and authorized after its filing with the CNIL according to the French procedure for a monocentric study and has been granted ethical approval by the Personal Protection Committee (23 February 2022 and 9 March 2023) and, by the French National Agency for the Safety of Medicines and Health Products (ANSM) (2 June 2022 and 20 March 2023), and it has formally been registered as a study (NCT05477069) (Tronel et al.,\n                      \n                      ).","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval"}}],"article-number":"84"}}