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This review defines the gut-X axis as bidirectional communication between the intestine and extraintestinal systems, and points the intestinal barrier as a selective gatekeeper that regulates thresholds and amplifies gut-derived information flow. We summarize barrier organization, the renewal and repair mechanism to maintain the epithelial integrity under persistent exposure. We then integrate factors shaping barrier steady state, including diet, microbial metabolites, host factors and drugs. Next, we explained how barrier-regulated signal outputs disseminate through immune inflammatory mediators, neural pathways and endocrine metabolic signals, and analyzed how reverse regulation by the brain, liver, lungs and systemic metabolic state reshapes barrier responses. In neuropsychiatric, hepatic, pulmonary, and endocrine metabolic diseases, we focus on the positive feedback cycle, heterogeneity, and the ambiguity in causal direction, and evaluate treatment strategies, covering dietary intervention, microbiota-directed therapies including fecal microbiota transplantation (FMT), and pharmacologic or immunologic methods. Progress will rely on standardized intestinal barrier indicators longitudinal research design to clarify temporal relationship, and hierarchical intervention tests to verify barrier-centered causal hypotheses.<\/jats:p>","DOI":"10.1515\/mr-2026-0009","type":"journal-article","created":{"date-parts":[[2026,6,7]],"date-time":"2026-06-07T23:13:00Z","timestamp":1780873980000},"page":"287-324","source":"Crossref","is-referenced-by-count":0,"title":["Gut mucosal barrier: the frontline of bidirectional regulation of the gut-X axis"],"prefix":"10.1515","volume":"6","author":[{"given":"Xiang","family":"Xu","sequence":"first","affiliation":[{"name":"Department of Gastroenterology , Peking Union Medical College Hospital , Beijing , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaowen","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology , Peking Union Medical College Hospital , Beijing , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuaizhi","family":"Ruan","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology , Peking Union Medical College Hospital , Beijing , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheng","family":"Peng","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology , Peking Union Medical College Hospital , Beijing , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taotao","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology , Peking Union Medical College Hospital , Beijing , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengguang","family":"Yan","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology , Peking Union Medical College Hospital , Beijing , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francis Ka Leung","family":"Chan","sequence":"additional","affiliation":[{"name":"Microbiota I-Center (MagIC) , Hong Kong SAR , China"},{"name":"Center for Gut Microbiota Research, Faculty of Medicine , The Chinese University of Hong Kong , Hong Kong SAR , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4900-0418","authenticated-orcid":false,"given":"Jingnan","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology , Peking Union Medical College Hospital , Beijing , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"374","published-online":{"date-parts":[[2026,6,8]]},"reference":[{"key":"2026083102570591236_j_mr-2026-0009_ref_001","doi-asserted-by":"crossref","unstructured":"Okumura, R, Takeda, K. The role of the mucosal barrier system in maintaining gut symbiosis to prevent intestinal inflammation. Semin Immunopathol 2024;47:2. https:\/\/doi.org\/10.1007\/s00281-024-01026-5.","DOI":"10.1007\/s00281-024-01026-5"},{"key":"2026083102570591236_j_mr-2026-0009_ref_002","doi-asserted-by":"crossref","unstructured":"Zhang, Y, Liu, Y, Liang, X, Wen, Y, Zhao, J, He, Y, et al.. Intestinal barrier in chronic gut and liver diseases: pathogenesis and therapeutic targets. Acta Pharm Sin B 2025;15:5515\u201336. https:\/\/doi.org\/10.1016\/j.apsb.2025.08.028.","DOI":"10.1016\/j.apsb.2025.08.028"},{"key":"2026083102570591236_j_mr-2026-0009_ref_003","doi-asserted-by":"crossref","unstructured":"Lin, X, Yu, Z, Liu, Y, Li, C, Hu, H, Hu, JC, et al.. Gut-X axis. iMeta 2025;4:e270. https:\/\/doi.org\/10.1002\/imt2.270.","DOI":"10.1002\/imt2.270"},{"key":"2026083102570591236_j_mr-2026-0009_ref_004","doi-asserted-by":"crossref","unstructured":"Parker, A, Fonseca, S, Carding, SR. Gut microbes and metabolites as modulators of blood-brain barrier integrity and brain health. Gut Microbes 2020;11:135\u201357. https:\/\/doi.org\/10.1080\/19490976.2019.1638722.","DOI":"10.1080\/19490976.2019.1638722"},{"key":"2026083102570591236_j_mr-2026-0009_ref_005","doi-asserted-by":"crossref","unstructured":"Pu, Q, Lin, P, Gao, P, Wang, Z, Guo, K, Qin, S, et al.. Gut microbiota regulate gut-lung axis inflammatory responses by mediating ILC2 compartmental migration. J\u00a0Immunol 2021;207:257\u201367. https:\/\/doi.org\/10.4049\/jimmunol.2001304.","DOI":"10.4049\/jimmunol.2001304"},{"key":"2026083102570591236_j_mr-2026-0009_ref_006","doi-asserted-by":"crossref","unstructured":"Zeng, S, Rosati, E, Saggau, C, Messner, B, Chu, H, Duan, Y, et al.. Candida albicans-specific Th17\u00a0cell-mediated response contributes to alcohol-associated liver disease. Cell Host Microbe 2023;31:389\u2013404.e7. https:\/\/doi.org\/10.1016\/j.chom.2023.02.001.","DOI":"10.1016\/j.chom.2023.02.001"},{"key":"2026083102570591236_j_mr-2026-0009_ref_007","doi-asserted-by":"crossref","unstructured":"Cryan, JF, O\u2019Riordan, KJ, Cowan, CSM, Sandhu, KV, Bastiaanssen, TFS, Boehme, M, et al.. The microbiota-gut-brain axis. Physiol Rev 2019;99:1877\u20132013. https:\/\/doi.org\/10.1152\/physrev.00018.2018.","DOI":"10.1152\/physrev.00018.2018"},{"key":"2026083102570591236_j_mr-2026-0009_ref_008","doi-asserted-by":"crossref","unstructured":"Sorribas, M, Jakob, MO, Yilmaz, B, Li, H, Stutz, D, Noser, Y, et al.. FXR modulates the gut-vascular barrier by regulating the entry sites for bacterial translocation in experimental cirrhosis. J\u00a0Hepatol 2019;71:1126\u201340. https:\/\/doi.org\/10.1016\/j.jhep.2019.06.017.","DOI":"10.1016\/j.jhep.2019.06.017"},{"key":"2026083102570591236_j_mr-2026-0009_ref_009","doi-asserted-by":"crossref","unstructured":"Gribble, FM, Reimann, F. Enteroendocrine cells: chemosensors in the intestinal epithelium. Annu Rev Physiol 2016;78:277\u201399. https:\/\/doi.org\/10.1146\/annurev-physiol-021115-105439.","DOI":"10.1146\/annurev-physiol-021115-105439"},{"key":"2026083102570591236_j_mr-2026-0009_ref_010","doi-asserted-by":"crossref","unstructured":"Holst, JJ. The physiology of glucagon-like peptide 1. Physiol Rev 2007;87:1409\u201339. https:\/\/doi.org\/10.1152\/physrev.00034.2006.","DOI":"10.1152\/physrev.00034.2006"},{"key":"2026083102570591236_j_mr-2026-0009_ref_011","doi-asserted-by":"crossref","unstructured":"Kaur, H, Kaur, G, Ali, SA. IL-33\u2019s role in the gut immune system: a comprehensive review of its crosstalk and regulation. Life Sci 2023;327:121868. https:\/\/doi.org\/10.1016\/j.lfs.2023.121868.","DOI":"10.1016\/j.lfs.2023.121868"},{"key":"2026083102570591236_j_mr-2026-0009_ref_012","doi-asserted-by":"crossref","unstructured":"Pedersen, HK, Gudmundsdottir, V, Nielsen, HB, Hyotylainen, T, Nielsen, T, Jensen, BAH, et al.. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature 2016;535:376\u201381. https:\/\/doi.org\/10.1038\/nature18646.","DOI":"10.1038\/nature18646"},{"key":"2026083102570591236_j_mr-2026-0009_ref_013","doi-asserted-by":"crossref","unstructured":"Cani, PD, Bibiloni, R, Knauf, C, Waget, A, Neyrinck, AM, Delzenne, NM, et al.. Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice. Diabetes 2008;57:1470\u201381. https:\/\/doi.org\/10.2337\/db07-1403.","DOI":"10.2337\/db07-1403"},{"key":"2026083102570591236_j_mr-2026-0009_ref_014","doi-asserted-by":"crossref","unstructured":"Medina-Rodr\u00edguez, EM, Mart\u00ednez-Raga, J, Sanz, Y. Intestinal barrier, immunity and microbiome: partners in the depression crime. Pharmacol Rev 2024;76:956\u201369. https:\/\/doi.org\/10.1124\/pharmrev.124.001202.","DOI":"10.1124\/pharmrev.124.001202"},{"key":"2026083102570591236_j_mr-2026-0009_ref_015","doi-asserted-by":"crossref","unstructured":"Zheng, D, Liwinski, T, Elinav, E. Interaction between microbiota and immunity in health and disease. Cell Res 2020;30:492\u2013506. https:\/\/doi.org\/10.1038\/s41422-020-0332-7.","DOI":"10.1038\/s41422-020-0332-7"},{"key":"2026083102570591236_j_mr-2026-0009_ref_016","doi-asserted-by":"crossref","unstructured":"Ahmad Kendong, SM, Raja Ali, RA, Nawawi, KNM, Ahmad, HF, Mokhtar, NM. Gut dysbiosis and intestinal barrier dysfunction: potential explanation for early-onset colorectal cancer. Front Cell Infect Microbiol 2021;11:744606. https:\/\/doi.org\/10.3389\/fcimb.2021.744606.","DOI":"10.3389\/fcimb.2021.744606"},{"key":"2026083102570591236_j_mr-2026-0009_ref_017","doi-asserted-by":"crossref","unstructured":"Samuelson, DR, Welsh, DA, Shellito, JE. Regulation of lung immunity and host defense by the intestinal microbiota. Front Microbiol 2015;6:1085. https:\/\/doi.org\/10.3389\/fmicb.2015.01085.","DOI":"10.3389\/fmicb.2015.01085"},{"key":"2026083102570591236_j_mr-2026-0009_ref_018","doi-asserted-by":"crossref","unstructured":"Trompette, A, Gollwitzer, ES, Yadava, K, Sichelstiel, AK, Sprenger, N, Ngom-Bru, C, et al.. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med 2014;20:159\u201366. https:\/\/doi.org\/10.1038\/nm.3444.","DOI":"10.1038\/nm.3444"},{"key":"2026083102570591236_j_mr-2026-0009_ref_019","doi-asserted-by":"crossref","unstructured":"Canfora, EE, Jocken, JW, Blaak, EE. Short-chain fatty acids in control of body weight and insulin sensitivity. Nat Rev Endocrinol 2015;11:577\u201391. https:\/\/doi.org\/10.1038\/nrendo.2015.128.","DOI":"10.1038\/nrendo.2015.128"},{"key":"2026083102570591236_j_mr-2026-0009_ref_020","doi-asserted-by":"crossref","unstructured":"Zhao, J, Bi, W, Xiao, S, Lan, X, Cheng, X, Zhang, J, et al.. Neuroinflammation induced by lipopolysaccharide causes cognitive impairment in mice. Sci Rep 2019;9:5790. https:\/\/doi.org\/10.1038\/s41598-019-42286-8.","DOI":"10.1038\/s41598-019-42286-8"},{"key":"2026083102570591236_j_mr-2026-0009_ref_021","doi-asserted-by":"crossref","unstructured":"Bonaz, B, Bazin, T, Pellissier, S. The vagus nerve at the interface of the microbiota-gut-brain axis. 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Resistant starch intake facilitates weight loss in humans by reshaping the gut microbiota. Nat Metab 2024;6:578\u201397. https:\/\/doi.org\/10.1038\/s42255-024-00988-y.","DOI":"10.1038\/s42255-024-00988-y"},{"key":"2026083102570591236_j_mr-2026-0009_ref_025","doi-asserted-by":"crossref","unstructured":"Vazquez-Roque, MI, Camilleri, M, Smyrk, T, Murray, JA, Marietta, E, O\u2019Neill, J, et al.. A controlled trial of gluten-free diet in patients with irritable bowel syndrome-diarrhea: effects on bowel frequency and intestinal function. Gastroenterology 2013;144:903\u201311.e3. https:\/\/doi.org\/10.1053\/j.gastro.2013.01.049.","DOI":"10.1053\/j.gastro.2013.01.049"},{"key":"2026083102570591236_j_mr-2026-0009_ref_026","doi-asserted-by":"crossref","unstructured":"Zhou, Q, Verne, ML, Fields, JZ, Lefante, JJ, Basra, S, Salameh, H, et al.. Randomised placebo-controlled trial of dietary glutamine supplements for postinfectious irritable bowel syndrome. 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Nat Immunol 2024;25:1218\u201330. https:\/\/doi.org\/10.1038\/s41590-024-01867-0.","DOI":"10.1038\/s41590-024-01867-0"},{"key":"2026083102570591236_j_mr-2026-0009_ref_031","doi-asserted-by":"crossref","unstructured":"Wagner, F, Mansfield, JC, Lekkerkerker, AN, Wang, Y, Keir, M, Dash, A, et al.. Dose escalation randomised study of efmarodocokin alfa in healthy volunteers and patients with ulcerative colitis. Gut 2023;72:1451\u201361. https:\/\/doi.org\/10.1136\/gutjnl-2022-328387.","DOI":"10.1136\/gutjnl-2022-328387"},{"key":"2026083102570591236_j_mr-2026-0009_ref_032","doi-asserted-by":"crossref","unstructured":"Lin, X, Gaudino, SJ, Jang, KK, Bahadur, T, Singh, A, Banerjee, A, et al.. IL-17RA-signaling in Lgr5+ intestinal stem cells induces expression of transcription factor ATOH1 to promote secretory cell lineage commitment. Immunity 2022;55:237\u201353.e8. https:\/\/doi.org\/10.1016\/j.immuni.2021.12.016.","DOI":"10.1016\/j.immuni.2021.12.016"},{"key":"2026083102570591236_j_mr-2026-0009_ref_033","doi-asserted-by":"crossref","unstructured":"Na, YR, Jung, D, Stakenborg, M, Jang, H, Gu, GJ, Jeong, MR, et al.. Prostaglandin E(2) receptor PTGER4-expressing macrophages promote intestinal epithelial barrier regeneration upon inflammation. Gut 2021;70:2249\u201360. https:\/\/doi.org\/10.1136\/gutjnl-2020-322146.","DOI":"10.1136\/gutjnl-2020-322146"},{"key":"2026083102570591236_j_mr-2026-0009_ref_034","doi-asserted-by":"crossref","unstructured":"Volk, N, Lacy, B. Anatomy and physiology of the small bowel. Gastrointest Endosc Clin N Am 2017;27:1\u201313. https:\/\/doi.org\/10.1016\/j.giec.2016.08.001.","DOI":"10.1016\/j.giec.2016.08.001"},{"key":"2026083102570591236_j_mr-2026-0009_ref_035","doi-asserted-by":"crossref","unstructured":"Barker, N, van Es, JH, Kuipers, J, Kujala, P, van den Born, M, Cozijnsen, M, et al.. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 2007;449:1003\u20137. https:\/\/doi.org\/10.1038\/nature06196.","DOI":"10.1038\/nature06196"},{"key":"2026083102570591236_j_mr-2026-0009_ref_036","doi-asserted-by":"crossref","unstructured":"Gu, Y, Forostyan, T, Sabbadini, R, Rosenblatt, J. Epithelial cell extrusion requires the sphingosine-1-phosphate receptor 2 pathway. J\u00a0Cell Biol 2011;193:667\u201376. https:\/\/doi.org\/10.1083\/jcb.201010075.","DOI":"10.1083\/jcb.201010075"},{"key":"2026083102570591236_j_mr-2026-0009_ref_037","doi-asserted-by":"crossref","unstructured":"Eisenhoffer, GT, Loftus, PD, Yoshigi, M, Otsuna, H, Chien, CB, Morcos, PA, et al.. Crowding induces live cell extrusion to maintain homeostatic cell numbers in epithelia. Nature 2012;484:546\u20139. https:\/\/doi.org\/10.1038\/nature10999.","DOI":"10.1038\/nature10999"},{"key":"2026083102570591236_j_mr-2026-0009_ref_038","doi-asserted-by":"crossref","unstructured":"Beumer, J, Clevers, H. Regulation and plasticity of intestinal stem cells during homeostasis and regeneration. Development 2016;143:3639\u201349. https:\/\/doi.org\/10.1242\/dev.133132.","DOI":"10.1242\/dev.133132"},{"key":"2026083102570591236_j_mr-2026-0009_ref_039","doi-asserted-by":"crossref","unstructured":"MacDonald, TT. Epithelial proliferation in response to gastrointestinal inflammation. Ann N Y Acad Sci 1992;664:202\u20139. https:\/\/doi.org\/10.1111\/j.1749-6632.1992.tb39761.x.","DOI":"10.1111\/j.1749-6632.1992.tb39761.x"},{"key":"2026083102570591236_j_mr-2026-0009_ref_040","doi-asserted-by":"crossref","unstructured":"Godl, K, Johansson, MEV, Lidell, ME, M\u00f6rgelin, M, Karlsson, H, Olson, FJ, et al.. The N terminus of the MUC2 mucin forms trimers that are held together within a trypsin-resistant core fragment. J\u00a0Biol Chem 2002;277:47248\u201356. https:\/\/doi.org\/10.1074\/jbc.m208483200.","DOI":"10.1074\/jbc.M208483200"},{"key":"2026083102570591236_j_mr-2026-0009_ref_041","doi-asserted-by":"crossref","unstructured":"Nilsson, HE, Ambort, D, B\u00e4ckstr\u00f6m, M, Thomsson, E, Koeck, PJB, Hansson, GC, et al.. Intestinal MUC2 mucin supramolecular topology by packing and release resting on D3 domain assembly. J\u00a0Mol Biol 2014;426:2567\u201379. https:\/\/doi.org\/10.1016\/j.jmb.2014.04.027.","DOI":"10.1016\/j.jmb.2014.04.027"},{"key":"2026083102570591236_j_mr-2026-0009_ref_042","doi-asserted-by":"crossref","unstructured":"Bergstrom, KSB, Xia, L. Mucin-type O-glycans and their roles in intestinal homeostasis. Glycobiology 2013;23:1026\u201337. https:\/\/doi.org\/10.1093\/glycob\/cwt045.","DOI":"10.1093\/glycob\/cwt045"},{"key":"2026083102570591236_j_mr-2026-0009_ref_043","doi-asserted-by":"crossref","unstructured":"An, G, Wei, B, Xia, B, McDaniel, JM, Ju, T, Cummings, RD, et al.. Increased susceptibility to colitis and colorectal tumors in mice lacking core 3-derived O-glycans. J\u00a0Exp Med 2007;204:1417\u201329. https:\/\/doi.org\/10.1084\/jem.20061929.","DOI":"10.1084\/jem.20061929"},{"key":"2026083102570591236_j_mr-2026-0009_ref_044","doi-asserted-by":"crossref","unstructured":"Fu, J, Wei, B, Wen, T, Johansson, MEV, Liu, X, Bradford, E, et al.. Loss of intestinal core 1\u2013derived O-glycans causes spontaneous colitis in mice. J\u00a0Clin Investig 2011;121:1657\u201366. https:\/\/doi.org\/10.1172\/jci45538.","DOI":"10.1172\/JCI45538"},{"key":"2026083102570591236_j_mr-2026-0009_ref_045","doi-asserted-by":"crossref","unstructured":"Yao, Y, Kim, G, Shafer, S, Chen, Z, Kubo, S, Ji, Y, et al.. Mucus sialylation determines intestinal host-commensal homeostasis. Cell 2022;185:1172\u201388.e28. https:\/\/doi.org\/10.1016\/j.cell.2022.02.013.","DOI":"10.1016\/j.cell.2022.02.013"},{"key":"2026083102570591236_j_mr-2026-0009_ref_046","doi-asserted-by":"crossref","unstructured":"Taniguchi, M, Okumura, R, Matsuzaki, T, Nakatani, A, Sakaki, K, Okamoto, S, et al.. Sialylation shapes mucus architecture inhibiting bacterial invasion in the colon. Mucosal Immunol 2023;16:624\u201341. https:\/\/doi.org\/10.1016\/j.mucimm.2023.06.004.","DOI":"10.1016\/j.mucimm.2023.06.004"},{"key":"2026083102570591236_j_mr-2026-0009_ref_047","doi-asserted-by":"crossref","unstructured":"Okumura, R, Kurakawa, T, Nakano, T, Kayama, H, Kinoshita, M, Motooka, D, et al.. Lypd8 promotes the segregation of flagellated microbiota and colonic epithelia. Nature 2016;532:117\u201321. https:\/\/doi.org\/10.1038\/nature17406.","DOI":"10.1038\/nature17406"},{"key":"2026083102570591236_j_mr-2026-0009_ref_048","doi-asserted-by":"crossref","unstructured":"Hsu, CC, Okumura, R, Takeda, K. Human LYPD8 protein inhibits motility of flagellated bacteria. Inflamm Regen 2017;37:23. https:\/\/doi.org\/10.1186\/s41232-017-0056-3.","DOI":"10.1186\/s41232-017-0056-3"},{"key":"2026083102570591236_j_mr-2026-0009_ref_049","doi-asserted-by":"crossref","unstructured":"Okumura, R, Kodama, T, Hsu, CC, Sahlgren, BH, Hamano, S, Kurakawa, T, et al.. Lypd8 inhibits attachment of pathogenic bacteria to colonic epithelia. Mucosal Immunol 2020;13:75\u201385. https:\/\/doi.org\/10.1038\/s41385-019-0219-4.","DOI":"10.1038\/s41385-019-0219-4"},{"key":"2026083102570591236_j_mr-2026-0009_ref_050","doi-asserted-by":"crossref","unstructured":"van Putten, JPM, Strijbis, K. Transmembrane mucins: signaling receptors at the intersection of inflammation and cancer. J\u00a0Innate Immun 2017;9:281\u201399. https:\/\/doi.org\/10.1159\/000453594.","DOI":"10.1159\/000453594"},{"key":"2026083102570591236_j_mr-2026-0009_ref_051","doi-asserted-by":"crossref","unstructured":"McGuckin, MA, Every, AL, Skene, CD, Linden, SK, Chionh, YT, Swierczak, A, et al.. Muc1 mucin limits both Helicobacter pylori colonization of the murine gastric mucosa and associated gastritis. Gastroenterology 2007;133:1210\u20138. https:\/\/doi.org\/10.1053\/j.gastro.2007.07.003.","DOI":"10.1053\/j.gastro.2007.07.003"},{"key":"2026083102570591236_j_mr-2026-0009_ref_052","doi-asserted-by":"crossref","unstructured":"McAuley, JL, Linden, SK, Png, CW, King, RM, Pennington, HL, Gendler, SJ, et al.. MUC1 cell surface mucin is a critical element of the mucosal barrier to infection. J\u00a0Clin Investig 2007;117:2313\u201324. https:\/\/doi.org\/10.1172\/jci26705.","DOI":"10.1172\/JCI26705"},{"key":"2026083102570591236_j_mr-2026-0009_ref_053","doi-asserted-by":"crossref","unstructured":"Lind\u00e9n, SK, Sheng, YH, Every, AL, Miles, KM, Skoog, EC, Florin, THJ, et al.. MUC1 limits Helicobacter pylori infection both by steric hindrance and by acting as a releasable decoy. PLoS Pathog 2009;5:e1000617. https:\/\/doi.org\/10.1371\/journal.ppat.1000617.","DOI":"10.1371\/journal.ppat.1000617"},{"key":"2026083102570591236_j_mr-2026-0009_ref_054","doi-asserted-by":"crossref","unstructured":"Zhou, C, Liu, Z, Liu, Y, Fu, W, Ding, X, Liu, J, et al.. Gene silencing of porcine MUC13 and ITGB5 candidate genes towards Escherichia coli F4ac adhesion. PLoS One 2013;8:e70303. https:\/\/doi.org\/10.1371\/journal.pone.0070303.","DOI":"10.1371\/journal.pone.0070303"},{"key":"2026083102570591236_j_mr-2026-0009_ref_055","doi-asserted-by":"crossref","unstructured":"Resta-Lenert, S, Das, S, Batra, SK, Ho, SB. Muc17 protects intestinal epithelial cells from enteroinvasive E.\u00a0coli infection by promoting epithelial barrier integrity. Am J Physiol Gastrointest Liver Physiol 2011;300:G1144\u201355. https:\/\/doi.org\/10.1152\/ajpgi.00138.2010.","DOI":"10.1152\/ajpgi.00138.2010"},{"key":"2026083102570591236_j_mr-2026-0009_ref_056","doi-asserted-by":"crossref","unstructured":"Suzuki, T. Regulation of intestinal epithelial permeability by tight junctions. Cell Mol Life Sci 2013;70:631\u201359. https:\/\/doi.org\/10.1007\/s00018-012-1070-x.","DOI":"10.1007\/s00018-012-1070-x"},{"key":"2026083102570591236_j_mr-2026-0009_ref_057","doi-asserted-by":"crossref","unstructured":"Tamura, A, Kitano, Y, Hata, M, Katsuno, T, Moriwaki, K, Sasaki, H, et al.. Megaintestine in claudin-15-deficient mice. Gastroenterology 2008;134:523\u201334.e3. https:\/\/doi.org\/10.1053\/j.gastro.2007.11.040.","DOI":"10.1053\/j.gastro.2007.11.040"},{"key":"2026083102570591236_j_mr-2026-0009_ref_058","doi-asserted-by":"crossref","unstructured":"Muto, S, Hata, M, Taniguchi, J, Tsuruoka, S, Moriwaki, K, Saitou, M, et al.. Claudin-2-deficient mice are defective in the leaky and cation-selective paracellular permeability properties of renal proximal tubules. Proc Natl Acad Sci U S A 2010;107:8011\u20136. https:\/\/doi.org\/10.1073\/pnas.0912901107.","DOI":"10.1073\/pnas.0912901107"},{"key":"2026083102570591236_j_mr-2026-0009_ref_059","doi-asserted-by":"crossref","unstructured":"Ding, L, Lu, Z, Foreman, O, Tatum, R, Lu, Q, Renegar, R, et al.. Inflammation and disruption of the mucosal architecture in claudin-7-deficient mice. Gastroenterology 2012;142:305\u201315. https:\/\/doi.org\/10.1053\/j.gastro.2011.10.025.","DOI":"10.1053\/j.gastro.2011.10.025"},{"key":"2026083102570591236_j_mr-2026-0009_ref_060","doi-asserted-by":"crossref","unstructured":"Sato, T, van Es, JH, Snippert, HJ, Stange, DE, Vries, RG, van den Born, M, et al.. Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts. Nature 2011;469:415\u20138. https:\/\/doi.org\/10.1038\/nature09637.","DOI":"10.1038\/nature09637"},{"key":"2026083102570591236_j_mr-2026-0009_ref_061","doi-asserted-by":"crossref","unstructured":"Brogden, KA. Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria? Nat Rev Microbiol 2005;3:238\u201350. https:\/\/doi.org\/10.1038\/nrmicro1098.","DOI":"10.1038\/nrmicro1098"},{"key":"2026083102570591236_j_mr-2026-0009_ref_062","doi-asserted-by":"crossref","unstructured":"Selsted, ME, Harwig, SS, Ganz, T, Schilling, JW, Lehrer, RI. Primary structures of three human neutrophil defensins. J\u00a0Clin Investig 1985;76:1436\u20139. https:\/\/doi.org\/10.1172\/jci112121.","DOI":"10.1172\/JCI112121"},{"key":"2026083102570591236_j_mr-2026-0009_ref_063","doi-asserted-by":"crossref","unstructured":"Selsted, ME, Ouellette, AJ. Mammalian defensins in the antimicrobial immune response. Nat Immunol 2005;6:551\u20137. https:\/\/doi.org\/10.1038\/ni1206.","DOI":"10.1038\/ni1206"},{"key":"2026083102570591236_j_mr-2026-0009_ref_064","doi-asserted-by":"crossref","unstructured":"Wilde, CG, Griffith, JE, Marra, MN, Snable, JL, Scott, RW. Purification and characterization of human neutrophil peptide 4, a novel member of the defensin family. J\u00a0Biol Chem 1989;264:11200\u20133. https:\/\/doi.org\/10.1016\/s0021-9258(18)60449-1.","DOI":"10.1016\/S0021-9258(18)60449-1"},{"key":"2026083102570591236_j_mr-2026-0009_ref_065","doi-asserted-by":"crossref","unstructured":"Wilson, CL, Ouellette, AJ, Satchell, DP, Ayabe, T, L\u00f3pez-Boado, YS, Stratman, JL, et al.. Regulation of intestinal alpha-defensin activation by the metalloproteinase matrilysin in innate host defense. Science 1999;286:113\u20137. https:\/\/doi.org\/10.1126\/science.286.5437.113.","DOI":"10.1126\/science.286.5437.113"},{"key":"2026083102570591236_j_mr-2026-0009_ref_066","doi-asserted-by":"crossref","unstructured":"Iimura, M, Gallo, RL, Hase, K, Miyamoto, Y, Eckmann, L, Kagnoff, MF. Cathelicidin mediates innate intestinal defense against colonization with epithelial adherent bacterial pathogens. J\u00a0Immunol 2005;174:4901\u20137. https:\/\/doi.org\/10.4049\/jimmunol.174.8.4901.","DOI":"10.4049\/jimmunol.174.8.4901"},{"key":"2026083102570591236_j_mr-2026-0009_ref_067","doi-asserted-by":"crossref","unstructured":"Lehotzky, RE, Partch, CL, Mukherjee, S, Cash, HL, Goldman, WE, Gardner, KH, et al.. Molecular basis for peptidoglycan recognition by a bactericidal lectin. Proc Natl Acad Sci USA 2010;107:7722\u20137. https:\/\/doi.org\/10.1073\/pnas.0909449107.","DOI":"10.1073\/pnas.0909449107"},{"key":"2026083102570591236_j_mr-2026-0009_ref_068","doi-asserted-by":"crossref","unstructured":"Cash, HL, Whitham, CV, Behrendt, CL, Hooper, LV. Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science 2006;313:1126\u201330. https:\/\/doi.org\/10.1126\/science.1127119.","DOI":"10.1126\/science.1127119"},{"key":"2026083102570591236_j_mr-2026-0009_ref_069","doi-asserted-by":"crossref","unstructured":"Mukherjee, S, Zheng, H, Derebe, MG, Callenberg, KM, Partch, CL, Rollins, D, et al.. Antibacterial membrane attack by a pore-forming intestinal C-type lectin. Nature 2014;505:103\u20137. https:\/\/doi.org\/10.1038\/nature12729.","DOI":"10.1038\/nature12729"},{"key":"2026083102570591236_j_mr-2026-0009_ref_070","doi-asserted-by":"crossref","unstructured":"Miki, T, Holst, O, Hardt, WD. The bactericidal activity of the C-type lectin RegIII\u03b2 against gram-negative bacteria involves binding to lipid A. J\u00a0Biol Chem 2012;287:34844\u201355. https:\/\/doi.org\/10.1074\/jbc.m112.399998.","DOI":"10.1074\/jbc.M112.399998"},{"key":"2026083102570591236_j_mr-2026-0009_ref_071","doi-asserted-by":"crossref","unstructured":"Vaishnava, S, Yamamoto, M, Severson, KM, Ruhn, KA, Yu, X, Koren, O, et al.. The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science 2011;334:255\u20138. https:\/\/doi.org\/10.1126\/science.1209791.","DOI":"10.1126\/science.1209791"},{"key":"2026083102570591236_j_mr-2026-0009_ref_072","doi-asserted-by":"crossref","unstructured":"Ragland, SA, Criss, AK. From bacterial killing to immune modulation: recent insights into the functions of lysozyme. PLoS Pathog 2017;13:e1006512. https:\/\/doi.org\/10.1371\/journal.ppat.1006512.","DOI":"10.1371\/journal.ppat.1006512"},{"key":"2026083102570591236_j_mr-2026-0009_ref_073","doi-asserted-by":"crossref","unstructured":"Dennis, EA. Diversity of group types, regulation, and function of phospholipase A2. J\u00a0Biol Chem 1994;269:13057\u201360. https:\/\/doi.org\/10.1016\/s0021-9258(17)36794-7.","DOI":"10.1016\/S0021-9258(17)36794-7"},{"key":"2026083102570591236_j_mr-2026-0009_ref_074","doi-asserted-by":"crossref","unstructured":"Rozenfeld, RA, Liu, X, DePlaen, I, Hsueh, W. Role of gut flora on intestinal group II phospholipase A2 activity and intestinal injury in shock. Am J Physiol Gastrointest Liver Physiol 2001;281:G957\u201363. https:\/\/doi.org\/10.1152\/ajpgi.2001.281.4.g957.","DOI":"10.1152\/ajpgi.2001.281.4.G957"},{"key":"2026083102570591236_j_mr-2026-0009_ref_075","doi-asserted-by":"crossref","unstructured":"Propheter, DC, Chara, AL, Harris, TA, Ruhn, KA, Hooper, LV. Resistin-like molecule \u03b2 is a bactericidal protein that promotes spatial segregation of the microbiota and the colonic epithelium. Proc Natl Acad Sci USA 2017;114:11027\u201333. https:\/\/doi.org\/10.1073\/pnas.1711395114.","DOI":"10.1073\/pnas.1711395114"},{"key":"2026083102570591236_j_mr-2026-0009_ref_076","doi-asserted-by":"crossref","unstructured":"Hogan, SP, Seidu, L, Blanchard, C, Groschwitz, K, Mishra, A, Karow, ML, et al.. Resistin-like molecule beta regulates innate colonic function: barrier integrity and inflammation susceptibility. J\u00a0Allergy Clin Immunol 2006;118:257\u201368. https:\/\/doi.org\/10.1016\/j.jaci.2006.04.039.","DOI":"10.1016\/j.jaci.2006.04.039"},{"key":"2026083102570591236_j_mr-2026-0009_ref_077","doi-asserted-by":"crossref","unstructured":"Hu, Z, Zhang, C, Sifuentes-Dominguez, L, Zarek, CM, Propheter, DC, Kuang, Z, et al.. Small proline-rich protein 2A is a gut bactericidal protein deployed during helminth infection. Science 2021;374:eabe6723. https:\/\/doi.org\/10.1126\/science.abe6723.","DOI":"10.1126\/science.abe6723"},{"key":"2026083102570591236_j_mr-2026-0009_ref_078","doi-asserted-by":"crossref","unstructured":"Hooper, LV, Stappenbeck, TS, Hong, CV, Gordon, JI. Angiogenins: a new class of microbicidal proteins involved in innate immunity. Nat Immunol 2003;4:269\u201373. https:\/\/doi.org\/10.1038\/ni888.","DOI":"10.1038\/ni888"},{"key":"2026083102570591236_j_mr-2026-0009_ref_079","doi-asserted-by":"crossref","unstructured":"Sultana, MF, Suzuki, M, Yamasaki, F, Kubota, W, Takahashi, K, Abo, H, et al.. Identification of crucial amino acid residues for antimicrobial activity of angiogenin 4 and its modulation of gut microbiota in mice. Front Microbiol 2022;13:900948. https:\/\/doi.org\/10.3389\/fmicb.2022.900948.","DOI":"10.3389\/fmicb.2022.900948"},{"key":"2026083102570591236_j_mr-2026-0009_ref_080","doi-asserted-by":"crossref","unstructured":"Yuan, Q, Walker, WA. Innate immunity of the gut: mucosal defense in health and disease. J\u00a0Pediatr Gastroenterol Nutr 2004;38:463\u201373. https:\/\/doi.org\/10.1002\/j.1536-4801.2004.tb12203.x.","DOI":"10.1002\/j.1536-4801.2004.tb12203.x"},{"key":"2026083102570591236_j_mr-2026-0009_ref_081","doi-asserted-by":"crossref","unstructured":"Vitale, S, Picascia, S, Gianfrani, C. The cross-talk between enterocytes and intraepithelial lymphocytes. Mol Cell Pediatr 2016;3:20. https:\/\/doi.org\/10.1186\/s40348-016-0048-4.","DOI":"10.1186\/s40348-016-0048-4"},{"key":"2026083102570591236_j_mr-2026-0009_ref_082","doi-asserted-by":"crossref","unstructured":"Stagg, AJ. Intestinal dendritic cells in health and gut inflammation. Front Immunol 2018;9:2883. https:\/\/doi.org\/10.3389\/fimmu.2018.02883.","DOI":"10.3389\/fimmu.2018.02883"},{"key":"2026083102570591236_j_mr-2026-0009_ref_083","doi-asserted-by":"crossref","unstructured":"Ma, H, Tao, W, Zhu, S. T lymphocytes in the intestinal mucosa: defense and tolerance. Cell Mol Immunol 2019;16:216\u201324. https:\/\/doi.org\/10.1038\/s41423-019-0208-2.","DOI":"10.1038\/s41423-019-0208-2"},{"key":"2026083102570591236_j_mr-2026-0009_ref_084","doi-asserted-by":"crossref","unstructured":"Bot\u00eda-S\u00e1nchez, M, Alarc\u00f3n-Riquelme, ME, Galicia, G. B\u00a0cells and microbiota in autoimmunity. Int J Mol Sci 2021;22:4846. https:\/\/doi.org\/10.3390\/ijms22094846.","DOI":"10.3390\/ijms22094846"},{"key":"2026083102570591236_j_mr-2026-0009_ref_085","doi-asserted-by":"crossref","unstructured":"Medina-Rodriguez, EM, Madorma, D, O\u2019Connor, G, Mason, BL, Han, D, Deo, SK, et al.. Identification of a signaling mechanism by which the microbiome regulates Th17\u00a0cell-mediated depressive-like behaviors in mice. Am J Psychiatry 2020;177:974\u201390. https:\/\/doi.org\/10.1176\/appi.ajp.2020.19090960.","DOI":"10.1176\/appi.ajp.2020.19090960"},{"key":"2026083102570591236_j_mr-2026-0009_ref_086","doi-asserted-by":"crossref","unstructured":"Guan, Q. A comprehensive review and update on the pathogenesis of inflammatory bowel disease. J\u00a0Immunol Res 2019;2019:7247238. https:\/\/doi.org\/10.1155\/2019\/7247238.","DOI":"10.1155\/2019\/7247238"},{"key":"2026083102570591236_j_mr-2026-0009_ref_087","doi-asserted-by":"crossref","unstructured":"Kayama, H, Okumura, R, Takeda, K. Interaction between the microbiota, epithelia, and immune cells in the intestine. Annu Rev Immunol 2020;38:23\u201348. https:\/\/doi.org\/10.1146\/annurev-immunol-070119-115104.","DOI":"10.1146\/annurev-immunol-070119-115104"},{"key":"2026083102570591236_j_mr-2026-0009_ref_088","doi-asserted-by":"crossref","unstructured":"Gou, HZ, Zhang, YL, Ren, LF, Li, ZJ, Zhang, L. How do intestinal probiotics restore the intestinal barrier? Front Microbiol 2022;13:929346. https:\/\/doi.org\/10.3389\/fmicb.2022.929346.","DOI":"10.3389\/fmicb.2022.929346"},{"key":"2026083102570591236_j_mr-2026-0009_ref_089","doi-asserted-by":"crossref","unstructured":"Corr, SC, Hill, C, Gahan, CGM. Understanding the mechanisms by which probiotics inhibit gastrointestinal pathogens. Adv Food Nutr Res 2009;56:1\u201315. https:\/\/doi.org\/10.1016\/S1043-4526(08)00601-3.","DOI":"10.1016\/S1043-4526(08)00601-3"},{"key":"2026083102570591236_j_mr-2026-0009_ref_090","doi-asserted-by":"crossref","unstructured":"Hyn\u00f6nen, U, Palva, A. Lactobacillus surface layer proteins: structure, function and applications. Appl Microbiol Biotechnol 2013;97:5225\u201343. https:\/\/doi.org\/10.1007\/s00253-013-4962-2.","DOI":"10.1007\/s00253-013-4962-2"},{"key":"2026083102570591236_j_mr-2026-0009_ref_091","doi-asserted-by":"crossref","unstructured":"Sherman, PM, Johnson-Henry, KC, Yeung, HP, Ngo, PSC, Goulet, J, Tompkins, TA. Probiotics reduce enterohemorrhagic Escherichia coli O157:H7- and enteropathogenic E.\u00a0coli O127:H6-induced changes in polarized T84 epithelial cell monolayers by reducing bacterial adhesion and cytoskeletal rearrangements. Infect Immun 2005;73:5183\u20138. https:\/\/doi.org\/10.1128\/iai.73.8.5183-5188.2005.","DOI":"10.1128\/IAI.73.8.5183-5188.2005"},{"key":"2026083102570591236_j_mr-2026-0009_ref_092","doi-asserted-by":"crossref","unstructured":"Smajs, D, Bure\u0161, J, Smarda, J, Chaloupkov\u00e1, E, Kv\u011btina, J, F\u00f6rstl, M, et al.. Experimental administration of the probiotic Escherichia coli strain nissle 1917 results in decreased diversity of E.\u00a0coli strains in pigs. Curr Microbiol 2012;64:205\u201310. https:\/\/doi.org\/10.1007\/s00284-011-0051-x.","DOI":"10.1007\/s00284-011-0051-x"},{"key":"2026083102570591236_j_mr-2026-0009_ref_093","doi-asserted-by":"crossref","unstructured":"Meng, Y, Wang, J, Wang, Z, Zhang, G, Liu, L, Huo, G, et al.. Lactobacillus plantarum KLDS1.0318 ameliorates impaired intestinal immunity and metabolic disorders in cyclophosphamide-treated mice. Front Microbiol 2019;10:731. https:\/\/doi.org\/10.3389\/fmicb.2019.00731.","DOI":"10.3389\/fmicb.2019.00731"},{"key":"2026083102570591236_j_mr-2026-0009_ref_094","doi-asserted-by":"crossref","unstructured":"van Es, JH, Sato, T, van de Wetering, M, Lyubimova, A, Yee Nee, AN, Gregorieff, A, et al.. Dll1+ secretory progenitor cells revert to stem cells upon crypt damage. Nat Cell Biol 2012;14:1099\u2013104. https:\/\/doi.org\/10.1038\/ncb2581.","DOI":"10.1038\/ncb2581"},{"key":"2026083102570591236_j_mr-2026-0009_ref_095","doi-asserted-by":"crossref","unstructured":"Tomic, G, Morrissey, E, Kozar, S, Ben-Moshe, S, Hoyle, A, Azzarelli, R, et al.. Phospho-regulation of ATOH1 is required for plasticity of secretory progenitors and tissue regeneration. Cell Stem Cell 2018;23:436\u201343.e7. https:\/\/doi.org\/10.1016\/j.stem.2018.07.002.","DOI":"10.1016\/j.stem.2018.07.002"},{"key":"2026083102570591236_j_mr-2026-0009_ref_096","doi-asserted-by":"crossref","unstructured":"Sato, T, Vries, RG, Snippert, HJ, van de Wetering, M, Barker, N, Stange, DE, et al.. Single Lgr5 stem cells build crypt-villus structures in\u00a0vitro without a mesenchymal niche. Nature 2009;459:262\u20135. https:\/\/doi.org\/10.1038\/nature07935.","DOI":"10.1038\/nature07935"},{"key":"2026083102570591236_j_mr-2026-0009_ref_097","doi-asserted-by":"crossref","unstructured":"Angus, HCK, Butt, AG, Schultz, M, Kemp, RA. Intestinal organoids as a tool for inflammatory bowel disease research. Front Med 2020;6:334. https:\/\/doi.org\/10.3389\/fmed.2019.00334.","DOI":"10.3389\/fmed.2019.00334"},{"key":"2026083102570591236_j_mr-2026-0009_ref_098","doi-asserted-by":"crossref","unstructured":"Christ, A, Lauterbach, M, Latz, E. Western diet and the immune system: an inflammatory connection. Immunity 2019;51:794\u2013811. https:\/\/doi.org\/10.1016\/j.immuni.2019.09.020.","DOI":"10.1016\/j.immuni.2019.09.020"},{"key":"2026083102570591236_j_mr-2026-0009_ref_099","doi-asserted-by":"crossref","unstructured":"Zheng, M, Zhai, Y, Yu, Y, Shen, J, Chu, S, Focaccia, E, et al.. TNF compromises intestinal bile-acid tolerance dictating colitis progression and limited infliximab response. Cell Metab 2024;36:2086\u2013103.e9. https:\/\/doi.org\/10.1016\/j.cmet.2024.06.008.","DOI":"10.1016\/j.cmet.2024.06.008"},{"key":"2026083102570591236_j_mr-2026-0009_ref_100","doi-asserted-by":"crossref","unstructured":"Liu, TC, Kern, JT, Jain, U, Sonnek, NM, Xiong, S, Simpson, KF, et al.. Western diet induces Paneth cell defects through microbiome alterations and farnesoid X receptor and type I interferon activation. Cell Host Microbe 2021;29:988\u20131001.e6. https:\/\/doi.org\/10.1016\/j.chom.2021.04.004.","DOI":"10.1016\/j.chom.2021.04.004"},{"key":"2026083102570591236_j_mr-2026-0009_ref_101","doi-asserted-by":"crossref","unstructured":"Yang, J, Wei, H, Zhou, Y, Szeto, CH, Li, C, Lin, Y, et al.. High-fat diet promotes colorectal tumorigenesis through modulating gut microbiota and metabolites. Gastroenterology 2022;162:135\u201349.e2. https:\/\/doi.org\/10.1053\/j.gastro.2021.08.041.","DOI":"10.1053\/j.gastro.2021.08.041"},{"key":"2026083102570591236_j_mr-2026-0009_ref_102","doi-asserted-by":"crossref","unstructured":"Febbraio, MA, Karin, M. \u201cSweet death\u201d: fructose as a metabolic toxin that targets the gut-liver axis. Cell Metab 2021;33:2316\u201328. https:\/\/doi.org\/10.1016\/j.cmet.2021.09.004.","DOI":"10.1016\/j.cmet.2021.09.004"},{"key":"2026083102570591236_j_mr-2026-0009_ref_103","doi-asserted-by":"crossref","unstructured":"Thaiss, CA, Levy, M, Grosheva, I, Zheng, D, Soffer, E, Blacher, E, et al.. Hyperglycemia drives intestinal barrier dysfunction and risk for enteric infection. Science 2018;359:1376\u201383. https:\/\/doi.org\/10.1126\/science.aar3318.","DOI":"10.1126\/science.aar3318"},{"key":"2026083102570591236_j_mr-2026-0009_ref_104","doi-asserted-by":"crossref","unstructured":"Marchix, J, Goddard, G, Helmrath, MA. Host-gut microbiota crosstalk in intestinal adaptation. Cell Mol Gastroenterol Hepatol 2018;6:149\u201362. https:\/\/doi.org\/10.1016\/j.jcmgh.2018.01.024.","DOI":"10.1016\/j.jcmgh.2018.01.024"},{"key":"2026083102570591236_j_mr-2026-0009_ref_105","doi-asserted-by":"crossref","unstructured":"Venkatraman, A, Ramakrishna, BS, Shaji, RV, Kumar, NS, Pulimood, A, Patra, S. Amelioration of dextran sulfate colitis by butyrate: role of heat shock protein 70 and NF-kappaB. Am J Physiol Gastrointest Liver Physiol 2003;285:G177\u201384. https:\/\/doi.org\/10.1152\/ajpgi.00307.2002.","DOI":"10.1152\/ajpgi.00307.2002"},{"key":"2026083102570591236_j_mr-2026-0009_ref_106","doi-asserted-by":"crossref","unstructured":"Ahmad, MS, Krishnan, S, Ramakrishna, BS, Mathan, M, Pulimood, AB, Murthy, SN. Butyrate and glucose metabolism by colonocytes in experimental colitis in mice. Gut 2000;46:493\u20139. https:\/\/doi.org\/10.1136\/gut.46.4.493.","DOI":"10.1136\/gut.46.4.493"},{"key":"2026083102570591236_j_mr-2026-0009_ref_107","doi-asserted-by":"crossref","unstructured":"Byndloss, MX, Olsan, EE, Rivera-Ch\u00e1vez, F, Tiffany, CR, Cevallos, SA, Lokken, KL, et al.. Microbiota-activated PPAR-\u03b3 signaling inhibits dysbiotic Enterobacteriaceae expansion. Science 2017;357:570\u20135. https:\/\/doi.org\/10.1126\/science.aam9949.","DOI":"10.1126\/science.aam9949"},{"key":"2026083102570591236_j_mr-2026-0009_ref_108","doi-asserted-by":"crossref","unstructured":"Shimotoyodome, A, Meguro, S, Hase, T, Tokimitsu, I, Sakata, T. Short chain fatty acids but not lactate or succinate stimulate mucus release in the rat colon. Comp Biochem Physiol Part A Mol Integr Physiol 2000;125:525\u201331. https:\/\/doi.org\/10.1016\/s1095-6433(00)00183-5.","DOI":"10.1016\/S1095-6433(00)00183-5"},{"key":"2026083102570591236_j_mr-2026-0009_ref_109","doi-asserted-by":"crossref","unstructured":"Finnie, IA, Dwarakanath, AD, Taylor, BA, Rhodes, JM. Colonic mucin synthesis is increased by sodium butyrate. Gut 1995;36:93\u20139. https:\/\/doi.org\/10.1136\/gut.36.1.93.","DOI":"10.1136\/gut.36.1.93"},{"key":"2026083102570591236_j_mr-2026-0009_ref_110","doi-asserted-by":"crossref","unstructured":"Barcelo, A, Claustre, J, Moro, F, Chayvialle, JA, Cuber, JC, Plaisanci\u00e9, P. Mucin secretion is modulated by luminal factors in the isolated vascularly perfused rat colon. Gut 2000;46:218\u201324. https:\/\/doi.org\/10.1136\/gut.46.2.218.","DOI":"10.1136\/gut.46.2.218"},{"key":"2026083102570591236_j_mr-2026-0009_ref_111","doi-asserted-by":"crossref","unstructured":"Sakata, T, Setoyama, H. Local stimulatory effect of short-chain fatty acids on the mucus release from the hindgut mucosa of rats (Rattus norvegicus). Comp Biochem Physiol Part A Physiol 1995;111:429\u201332. https:\/\/doi.org\/10.1016\/0300-9629(95)00033-4.","DOI":"10.1016\/0300-9629(95)00033-4"},{"key":"2026083102570591236_j_mr-2026-0009_ref_112","doi-asserted-by":"crossref","unstructured":"Burger-van Paassen, N, Vincent, A, Puiman, PJ, van der Sluis, M, Bouma, J, Boehm, G, et al.. The regulation of intestinal mucin MUC2 expression by short-chain fatty acids: implications for epithelial protection. Biochem J 2009;420:211\u20139. https:\/\/doi.org\/10.1042\/BJ20082222.","DOI":"10.1042\/BJ20082222"},{"key":"2026083102570591236_j_mr-2026-0009_ref_113","doi-asserted-by":"crossref","unstructured":"Collins, SL, Stine, JG, Bisanz, JE, Okafor, CD, Patterson, AD. Bile acids and the gut microbiota: metabolic interactions and impacts on disease. Nat Rev Microbiol 2023;21:236\u201347. https:\/\/doi.org\/10.1038\/s41579-022-00805-x.","DOI":"10.1038\/s41579-022-00805-x"},{"key":"2026083102570591236_j_mr-2026-0009_ref_114","doi-asserted-by":"crossref","unstructured":"Golden, JM, Escobar, OH, Nguyen, MVL, Mallicote, MU, Kavarian, P, Frey, MR, et al.. Ursodeoxycholic acid protects against intestinal barrier breakdown by promoting enterocyte migration via EGFR- and COX-2-dependent mechanisms. Am J Physiol Gastrointest Liver Physiol 2018;315:G259\u201371. https:\/\/doi.org\/10.1152\/ajpgi.00354.2017.","DOI":"10.1152\/ajpgi.00354.2017"},{"key":"2026083102570591236_j_mr-2026-0009_ref_115","doi-asserted-by":"crossref","unstructured":"Alemi, F, Poole, DP, Chiu, J, Schoonjans, K, Cattaruzza, F, Grider, JR, et al.. The receptor TGR5 mediates the prokinetic actions of intestinal bile acids and is required for normal defecation in mice. Gastroenterology 2013;144:145\u201354. https:\/\/doi.org\/10.1053\/j.gastro.2012.09.055.","DOI":"10.1053\/j.gastro.2012.09.055"},{"key":"2026083102570591236_j_mr-2026-0009_ref_116","doi-asserted-by":"crossref","unstructured":"Hubbard, TD, Murray, IA, Bisson, WH, Lahoti, TS, Gowda, K, Amin, SG, et al.. Adaptation of the human aryl hydrocarbon receptor to sense microbiota-derived indoles. Sci Rep 2015;5:12689. https:\/\/doi.org\/10.1038\/srep12689.","DOI":"10.1038\/srep12689"},{"key":"2026083102570591236_j_mr-2026-0009_ref_117","doi-asserted-by":"crossref","unstructured":"Venkatesh, M, Mukherjee, S, Wang, H, Li, H, Sun, K, Benechet, AP, et al.. Symbiotic bacterial metabolites regulate gastrointestinal barrier function via the xenobiotic sensor PXR and toll-like receptor 4. Immunity 2014;41:296\u2013310. https:\/\/doi.org\/10.1016\/j.immuni.2014.06.014.","DOI":"10.1016\/j.immuni.2014.06.014"},{"key":"2026083102570591236_j_mr-2026-0009_ref_118","doi-asserted-by":"crossref","unstructured":"Metidji, A, Omenetti, S, Crotta, S, Li, Y, Nye, E, Ross, E, et al.. The environmental sensor AHR protects from inflammatory damage by maintaining intestinal stem cell homeostasis and barrier integrity. Immunity 2018;49:353\u201362.e5. https:\/\/doi.org\/10.1016\/j.immuni.2018.07.010.","DOI":"10.1016\/j.immuni.2018.07.010"},{"key":"2026083102570591236_j_mr-2026-0009_ref_119","doi-asserted-by":"crossref","unstructured":"Shimada, Y, Kinoshita, M, Harada, K, Mizutani, M, Masahata, K, Kayama, H, et al.. Commensal bacteria-dependent indole production enhances epithelial barrier function in the colon. PLoS One 2013;8:e80604. https:\/\/doi.org\/10.1371\/journal.pone.0080604.","DOI":"10.1371\/journal.pone.0080604"},{"key":"2026083102570591236_j_mr-2026-0009_ref_120","doi-asserted-by":"crossref","unstructured":"Sazonovs, A, Stevens, CR, Venkataraman, GR, Yuan, K, Avila, B, Abreu, MT, et al.. Large-scale sequencing identifies multiple genes and rare variants associated with Crohn\u2019s disease susceptibility. Nat Genet 2022;54:1275\u201383. https:\/\/doi.org\/10.1038\/s41588-022-01156-2.","DOI":"10.1038\/s41588-022-01156-2"},{"key":"2026083102570591236_j_mr-2026-0009_ref_121","doi-asserted-by":"crossref","unstructured":"Gettler, K, Levantovsky, R, Moscati, A, Giri, M, Wu, Y, Hsu, NY, et al.. Common and rare variant prediction and penetrance of IBD in a large, multi-ethnic, health system-based biobank cohort. Gastroenterology 2021;160:1546\u201357. https:\/\/doi.org\/10.1053\/j.gastro.2020.12.034.","DOI":"10.1053\/j.gastro.2021.03.009"},{"key":"2026083102570591236_j_mr-2026-0009_ref_122","doi-asserted-by":"crossref","unstructured":"Glocker, EO, Kotlarz, D, Boztug, K, Gertz, EM, Sch\u00e4ffer, AA, Noyan, F, et al.. Inflammatory bowel disease and mutations affecting the interleukin-10 receptor. N\u00a0Engl J Med 2009;361:2033\u201345. https:\/\/doi.org\/10.1056\/nejmoa0907206.","DOI":"10.1056\/NEJMoa0907206"},{"key":"2026083102570591236_j_mr-2026-0009_ref_123","doi-asserted-by":"crossref","unstructured":"Shao, XX, Lin, DP, Sun, L, Wu, CQ, Yang, W, Jiang, Y. Association of ulcerative colitis with solute-linked carrier family 26 member A3 gene polymorphisms and its expression in colonic tissues in Chinese patients. Int J Colorectal Dis 2018;33:1169\u201372. https:\/\/doi.org\/10.1007\/s00384-018-3097-4.","DOI":"10.1007\/s00384-018-3097-4"},{"key":"2026083102570591236_j_mr-2026-0009_ref_124","doi-asserted-by":"crossref","unstructured":"Vinayaga-Pavan, M, Frampton, M, Pontikos, N, Levine, AP, Smith, PJ, Jonasson, JG, et al.. Elevation in cell cycle and protein metabolism gene transcription in inactive colonic tissue from Icelandic patients with ulcerative colitis. Inflamm Bowel Dis 2019;25:317\u201327. https:\/\/doi.org\/10.1093\/ibd\/izy350.","DOI":"10.1093\/ibd\/izy350"},{"key":"2026083102570591236_j_mr-2026-0009_ref_125","doi-asserted-by":"crossref","unstructured":"Kumar, A, Priyamvada, S, Ge, Y, Jayawardena, D, Singhal, M, Anbazhagan, AN, et al.. A novel role of SLC26A3 in the maintenance of intestinal epithelial barrier integrity. Gastroenterology 2021;160:1240\u201355.e3. https:\/\/doi.org\/10.1053\/j.gastro.2020.11.008.","DOI":"10.1053\/j.gastro.2020.11.008"},{"key":"2026083102570591236_j_mr-2026-0009_ref_126","doi-asserted-by":"crossref","unstructured":"Fazio, A, Bordoni, D, Kuiper, JWP, Weber-Stiehl, S, Stengel, ST, Arnold, P, et al.. DNA methyltransferase 3A controls intestinal epithelial barrier function and regeneration in the colon. Nat Commun 2022;13:6266. https:\/\/doi.org\/10.1038\/s41467-022-33844-2.","DOI":"10.1038\/s41467-022-33844-2"},{"key":"2026083102570591236_j_mr-2026-0009_ref_127","doi-asserted-by":"crossref","unstructured":"Gutierrez Lopez, DE, Lashinger, LM, Weinstock, GM, Bray, MS. Circadian rhythms and the gut microbiome synchronize the host\u2019s metabolic response to diet. Cell Metab 2021;33:873\u201387. https:\/\/doi.org\/10.1016\/j.cmet.2021.03.015.","DOI":"10.1016\/j.cmet.2021.03.015"},{"key":"2026083102570591236_j_mr-2026-0009_ref_128","doi-asserted-by":"crossref","unstructured":"Tuganbaev, T, Mor, U, Bashiardes, S, Liwinski, T, Nobs, SP, Leshem, A, et al.. Diet diurnally regulates small intestinal microbiome-epithelial-immune homeostasis and enteritis. Cell 2020;182:1441\u201359.e21. https:\/\/doi.org\/10.1016\/j.cell.2020.08.027.","DOI":"10.1016\/j.cell.2020.08.027"},{"key":"2026083102570591236_j_mr-2026-0009_ref_129","doi-asserted-by":"crossref","unstructured":"Talbot, J, Hahn, P, Kroehling, L, Nguyen, H, Li, D, Littman, DR. Feeding-dependent VIP neuron-ILC3 circuit regulates the intestinal barrier. Nature 2020;579:575\u201380. https:\/\/doi.org\/10.1038\/s41586-020-2039-9.","DOI":"10.1038\/s41586-020-2039-9"},{"key":"2026083102570591236_j_mr-2026-0009_ref_130","doi-asserted-by":"crossref","unstructured":"Guo, X, Wang, J, Xu, H, Wang, Y, Cao, Y, Wen, Y, et al.. Obesity induced disruption on diurnal rhythm of insulin sensitivity via gut microbiome-bile acid metabolism. Biochim Biophys Acta Mol Cell Biol Lipids 2024;1869:159419. https:\/\/doi.org\/10.1016\/j.bbalip.2023.159419.","DOI":"10.1016\/j.bbalip.2023.159419"},{"key":"2026083102570591236_j_mr-2026-0009_ref_131","doi-asserted-by":"crossref","unstructured":"Choi, H, Rao, MC, Chang, EB. Gut microbiota as a transducer of dietary cues to regulate host circadian rhythms and metabolism. Nat Rev Gastroenterol Hepatol 2021;18:679\u201389. https:\/\/doi.org\/10.1038\/s41575-021-00452-2.","DOI":"10.1038\/s41575-021-00452-2"},{"key":"2026083102570591236_j_mr-2026-0009_ref_132","doi-asserted-by":"crossref","unstructured":"Fawad, JA, Luzader, DH, Hanson, GF, Moutinho, TJ, McKinney, CA, Mitchell, PG, et al.. Histone deacetylase inhibition by gut microbe-generated short-chain fatty acids entrains intestinal epithelial circadian rhythms. Gastroenterology 2022;163:1377\u201390.e11. https:\/\/doi.org\/10.1053\/j.gastro.2022.07.051.","DOI":"10.1053\/j.gastro.2022.07.051"},{"key":"2026083102570591236_j_mr-2026-0009_ref_133","doi-asserted-by":"crossref","unstructured":"Brooks, JF2nd, Behrendt, CL, Ruhn, KA, Lee, S, Raj, P, Takahashi, JS, et al.. The microbiota coordinates diurnal rhythms in innate immunity with the circadian clock. Cell 2021;184:4154\u201367.e12. https:\/\/doi.org\/10.1016\/j.cell.2021.07.001.","DOI":"10.1016\/j.cell.2021.07.001"},{"key":"2026083102570591236_j_mr-2026-0009_ref_134","doi-asserted-by":"crossref","unstructured":"Willing, BP, Russell, SL, Finlay, BB. Shifting the balance: antibiotic effects on host-microbiota mutualism. Nat Rev Microbiol 2011;9:233\u201343. https:\/\/doi.org\/10.1038\/nrmicro2536.","DOI":"10.1038\/nrmicro2536"},{"key":"2026083102570591236_j_mr-2026-0009_ref_135","doi-asserted-by":"crossref","unstructured":"Patel, VC, Lee, S, McPhail, MJW, Da Silva, K, Guilly, S, Zamalloa, A, et al.. Rifaximin-\u03b1 reduces gut-derived inflammation and mucin degradation in cirrhosis and encephalopathy: RIFSYS randomised controlled trial. J\u00a0Hepatol 2022;76:332\u201342. https:\/\/doi.org\/10.1016\/j.jhep.2021.09.010.","DOI":"10.1016\/j.jhep.2021.09.010"},{"key":"2026083102570591236_j_mr-2026-0009_ref_136","doi-asserted-by":"crossref","unstructured":"Xu, D, Gao, J, Gillilland, M3rd, Wu, X, Song, I, Kao, JY, et al.. Rifaximin alters intestinal bacteria and prevents stress-induced gut inflammation and visceral hyperalgesia in rats. Gastroenterology 2014;146:484\u201396.e4. https:\/\/doi.org\/10.1053\/j.gastro.2013.10.026.","DOI":"10.1053\/j.gastro.2013.10.026"},{"key":"2026083102570591236_j_mr-2026-0009_ref_137","doi-asserted-by":"crossref","unstructured":"Feng, Y, Huang, Y, Wang, Y, Wang, P, Song, H, Wang, F. Antibiotics induced intestinal tight junction barrier dysfunction is associated with microbiota dysbiosis, activated NLRP3 inflammasome and autophagy. PLoS One 2019;14:e0218384. https:\/\/doi.org\/10.1371\/journal.pone.0218384.","DOI":"10.1371\/journal.pone.0218384"},{"key":"2026083102570591236_j_mr-2026-0009_ref_138","doi-asserted-by":"crossref","unstructured":"Sawaed, J, Zelik, L, Levin, Y, Feeney, R, Naama, M, Gordon, A, et al.. Antibiotics damage the colonic mucus barrier in a microbiota-independent manner. Sci Adv 2024;10:eadp4119. https:\/\/doi.org\/10.1126\/sciadv.adp4119.","DOI":"10.1126\/sciadv.adp4119"},{"key":"2026083102570591236_j_mr-2026-0009_ref_139","doi-asserted-by":"crossref","unstructured":"Li, T, Ding, N, Guo, H, Hua, R, Lin, Z, Tian, H, et al.. A gut microbiota-bile acid axis promotes intestinal homeostasis upon aspirin-mediated damage. Cell Host Microbe 2024;32:191\u2013208.e9. https:\/\/doi.org\/10.1016\/j.chom.2023.12.015.","DOI":"10.1016\/j.chom.2023.12.015"},{"key":"2026083102570591236_j_mr-2026-0009_ref_140","doi-asserted-by":"crossref","unstructured":"Rodrigues, D, Souza, T, Jennen, DGJ, Lemmens, L, Kleinjans, JCS, de Kok, TM. Drug-induced gene expression profile changes in relation to intestinal toxicity: State-of-the-art and new approaches. Cancer Treat Rev 2019;77:57\u201366. https:\/\/doi.org\/10.1016\/j.ctrv.2019.06.004.","DOI":"10.1016\/j.ctrv.2019.06.004"},{"key":"2026083102570591236_j_mr-2026-0009_ref_141","doi-asserted-by":"crossref","unstructured":"Wu, D, Hu, L, Han, M, Deng, Y, Zhang, Y, Ren, G, et al.. PD-1 signaling facilitates activation of lymphoid tissue inducer cells by restraining fatty acid oxidation. Nat Metab 2022;4:867\u201382. https:\/\/doi.org\/10.1038\/s42255-022-00595-9.","DOI":"10.1038\/s42255-022-00595-9"},{"key":"2026083102570591236_j_mr-2026-0009_ref_142","doi-asserted-by":"crossref","unstructured":"Soularue, E, Lepage, P, Colombel, JF, Coutzac, C, Faleck, D, Marthey, L, et al.. Enterocolitis due to immune checkpoint inhibitors: a systematic review. Gut 2018;67:2056\u201367. https:\/\/doi.org\/10.1136\/gutjnl-2018-316948.","DOI":"10.1136\/gutjnl-2018-316948"},{"key":"2026083102570591236_j_mr-2026-0009_ref_143","doi-asserted-by":"crossref","unstructured":"Ichinohe, T, Pang, IK, Kumamoto, Y, Peaper, DR, Ho, JH, Murray, TS, et al.. Microbiota regulates immune defense against respiratory tract influenza A virus infection. Proc Natl Acad Sci USA 2011;108:5354\u20139. https:\/\/doi.org\/10.1073\/pnas.1019378108.","DOI":"10.1073\/pnas.1019378108"},{"key":"2026083102570591236_j_mr-2026-0009_ref_144","doi-asserted-by":"crossref","unstructured":"Arpaia, N, Campbell, C, Fan, X, Dikiy, S, van der Veeken, J, deRoos, P, et al.. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 2013;504:451\u20135. https:\/\/doi.org\/10.1038\/nature12726.","DOI":"10.1038\/nature12726"},{"key":"2026083102570591236_j_mr-2026-0009_ref_145","doi-asserted-by":"crossref","unstructured":"Cani, PD, Amar, J, Iglesias, MA, Poggi, M, Knauf, C, Bastelica, D, et al.. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 2007;56:1761\u201372. https:\/\/doi.org\/10.2337\/db06-1491.","DOI":"10.2337\/db06-1491"},{"key":"2026083102570591236_j_mr-2026-0009_ref_146","doi-asserted-by":"crossref","unstructured":"Huang, Y, Mao, K, Chen, X, Sun, MA, Kawabe, T, Li, W, et al.. S1P-dependent interorgan trafficking of group 2 innate lymphoid cells supports host defense. Science 2018;359:114\u20139. https:\/\/doi.org\/10.1126\/science.aam5809.","DOI":"10.1126\/science.aam5809"},{"key":"2026083102570591236_j_mr-2026-0009_ref_147","doi-asserted-by":"crossref","unstructured":"Lee, KC, Chen, P, Maricic, I, Inamine, T, Hu, J, Gong, S, et al.. Intestinal iNKT\u00a0cells migrate to liver and contribute to hepatocyte apoptosis during alcoholic liver disease. Am J Physiol Gastrointest Liver Physiol 2019;316:G585\u201397. https:\/\/doi.org\/10.1152\/ajpgi.00269.2018.","DOI":"10.1152\/ajpgi.00269.2018"},{"key":"2026083102570591236_j_mr-2026-0009_ref_148","doi-asserted-by":"crossref","unstructured":"Rojas, OL, Pr\u00f6bstel, AK, Porfilio, EA, Wang, AA, Charabati, M, Sun, T, et al.. Recirculating intestinal IgA-producing cells regulate neuroinflammation via IL-10. Cell 2019;176:610\u201324.e18. https:\/\/doi.org\/10.1016\/j.cell.2018.11.035.","DOI":"10.1016\/j.cell.2018.11.035"},{"key":"2026083102570591236_j_mr-2026-0009_ref_149","doi-asserted-by":"crossref","unstructured":"Fitzpatrick, Z, Frazer, G, Ferro, A, Clare, S, Bouladoux, N, Ferdinand, J, et al.. Gut-educated IgA plasma cells defend the meningeal venous sinuses. Nature 2020;587:472\u20136. https:\/\/doi.org\/10.1038\/s41586-020-2886-4.","DOI":"10.1038\/s41586-020-2886-4"},{"key":"2026083102570591236_j_mr-2026-0009_ref_150","doi-asserted-by":"crossref","unstructured":"Sanmarco, LM, Wheeler, MA, Guti\u00e9rrez-V\u00e1zquez, C, Polonio, CM, Linnerbauer, M, Pinho-Ribeiro, FA, et al.. Gut-licensed IFN\u03b3+ NK cells drive LAMP1+TRAIL+ anti-inflammatory astrocytes. Nature 2021;590:473\u20139. https:\/\/doi.org\/10.1038\/s41586-020-03116-4.","DOI":"10.1038\/s41586-020-03116-4"},{"key":"2026083102570591236_j_mr-2026-0009_ref_151","doi-asserted-by":"crossref","unstructured":"Erny, D, Hrab\u011b de Angelis, AL, Jaitin, D, Wieghofer, P, Staszewski, O, David, E, et al.. Host microbiota constantly control maturation and function of microglia in the CNS. Nat Neurosci 2015;18:965\u201377. https:\/\/doi.org\/10.1038\/nn.4030.","DOI":"10.1038\/nn.4030"},{"key":"2026083102570591236_j_mr-2026-0009_ref_152","doi-asserted-by":"crossref","unstructured":"Van Hove, H, Martens, L, Scheyltjens, I, De Vlaminck, K, Pombo Antunes, AR, De, PS, et al.. A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment. Nat Neurosci 2019;22:1021\u201335. https:\/\/doi.org\/10.1038\/s41593-019-0393-4.","DOI":"10.1038\/s41593-019-0393-4"},{"key":"2026083102570591236_j_mr-2026-0009_ref_153","doi-asserted-by":"crossref","unstructured":"Thion, MS, Low, D, Silvin, A, Chen, J, Grisel, P, Schulte-Schrepping, J, et al.. Microbiome influences prenatal and adult microglia in a sex-specific manner. Cell 2018;172:500\u201316.e16. https:\/\/doi.org\/10.1016\/j.cell.2017.11.042.","DOI":"10.1016\/j.cell.2017.11.042"},{"key":"2026083102570591236_j_mr-2026-0009_ref_154","doi-asserted-by":"crossref","unstructured":"Rothhammer, V, Mascanfroni, ID, Bunse, L, Takenaka, MC, Kenison, JE, Mayo, L, et al.. Type I interferons and microbial metabolites of tryptophan modulate astrocyte activity and central nervous system inflammation via the aryl hydrocarbon receptor. Nat Med 2016;22:586\u201397. https:\/\/doi.org\/10.1038\/nm.4106.","DOI":"10.1038\/nm.4106"},{"key":"2026083102570591236_j_mr-2026-0009_ref_155","doi-asserted-by":"crossref","unstructured":"Agirman, G, Yu, KB, Hsiao, EY. Signaling inflammation across the gut-brain axis. Science 2021;374:1087\u201392. https:\/\/doi.org\/10.1126\/science.abi6087.","DOI":"10.1126\/science.abi6087"},{"key":"2026083102570591236_j_mr-2026-0009_ref_156","doi-asserted-by":"crossref","unstructured":"Bluthe, RM, Michaud, B, Kelley, KW, Dantzer, R. Vagotomy blocks behavioural effects of interleukin-1 injected via the intraperitoneal route but not via other systemic routes. Neuroreport 1996;7:2823\u20137. https:\/\/doi.org\/10.1097\/00001756-199611040-00083.","DOI":"10.1097\/00001756-199611040-00083"},{"key":"2026083102570591236_j_mr-2026-0009_ref_157","doi-asserted-by":"crossref","unstructured":"Rao, S, Schieber, AMP, O\u2019Connor, CP, Leblanc, M, Michel, D, Ayres, JS. Pathogen-mediated inhibition of anorexia promotes host survival and transmission. Cell 2017;168:503\u201316.e12. https:\/\/doi.org\/10.1016\/j.cell.2017.01.006.","DOI":"10.1016\/j.cell.2017.01.006"},{"key":"2026083102570591236_j_mr-2026-0009_ref_158","doi-asserted-by":"crossref","unstructured":"Yam, MF, Loh, YC, Tan, CS, Khadijah Adam, S, Abdul Manan, N, Basir, R. General pathways of pain sensation and the major neurotransmitters involved in pain regulation. Int J Mol Sci 2018;19:2164. https:\/\/doi.org\/10.3390\/ijms19082164.","DOI":"10.3390\/ijms19082164"},{"key":"2026083102570591236_j_mr-2026-0009_ref_159","doi-asserted-by":"crossref","unstructured":"Pinho-Ribeiro, FA, Verri, WA, Chiu, IM. Nociceptor sensory neuron-immune interactions in pain and inflammation. Trends Immunol 2017;38:5\u201319. https:\/\/doi.org\/10.1016\/j.it.2016.10.001.","DOI":"10.1016\/j.it.2016.10.001"},{"key":"2026083102570591236_j_mr-2026-0009_ref_160","doi-asserted-by":"crossref","unstructured":"Huh, JR, Veiga-Fernandes, H. Neuroimmune circuits in inter-organ communication. Nat Rev Immunol 2020;20:217\u201328. https:\/\/doi.org\/10.1038\/s41577-019-0247-z.","DOI":"10.1038\/s41577-019-0247-z"},{"key":"2026083102570591236_j_mr-2026-0009_ref_161","doi-asserted-by":"crossref","unstructured":"White, JP, Xiong, S, Malvin, NP, Khoury-Hanold, W, Heuckeroth, RO, Stappenbeck, TS, et al.. Intestinal dysmotility syndromes following systemic infection by flaviviruses. Cell 2018;175:1198\u2013212.e12. https:\/\/doi.org\/10.1016\/j.cell.2018.08.069.","DOI":"10.1016\/j.cell.2018.08.069"},{"key":"2026083102570591236_j_mr-2026-0009_ref_162","doi-asserted-by":"crossref","unstructured":"Lai, NY, Musser, MA, Pinho-Ribeiro, FA, Baral, P, Jacobson, A, Ma, P, et al.. Gut-innervating nociceptor neurons regulate peyer\u2019s patch microfold cells and SFB levels to mediate Salmonella host defense. Cell 2020;180:33\u201349.e22. https:\/\/doi.org\/10.1016\/j.cell.2019.11.014.","DOI":"10.1016\/j.cell.2019.11.014"},{"key":"2026083102570591236_j_mr-2026-0009_ref_163","doi-asserted-by":"crossref","unstructured":"Deczkowska, A, Amit, I, Schwartz, M. Microglial immune checkpoint mechanisms. Nat Neurosci 2018;21:779\u201386. https:\/\/doi.org\/10.1038\/s41593-018-0145-x.","DOI":"10.1038\/s41593-018-0145-x"},{"key":"2026083102570591236_j_mr-2026-0009_ref_164","doi-asserted-by":"crossref","unstructured":"Gyoneva, S, Traynelis, SF. Norepinephrine modulates the motility of resting and activated microglia via different adrenergic receptors. J\u00a0Biol Chem 2013;288:15291\u2013302. https:\/\/doi.org\/10.1074\/jbc.m113.458901.","DOI":"10.1074\/jbc.M113.458901"},{"key":"2026083102570591236_j_mr-2026-0009_ref_165","doi-asserted-by":"crossref","unstructured":"Pathak, P, Xie, C, Nichols, RG, Ferrell, JM, Boehme, S, Krausz, KW, et al.. Intestine farnesoid X receptor agonist and the gut microbiota activate G-protein bile acid receptor-1 signaling to improve metabolism. Hepatology 2018;68:1574\u201388. https:\/\/doi.org\/10.1002\/hep.29857.","DOI":"10.1002\/hep.29857"},{"key":"2026083102570591236_j_mr-2026-0009_ref_166","doi-asserted-by":"crossref","unstructured":"Koh, A, De Vadder, F, Kovatcheva-Datchary, P, B\u00e4ckhed, F. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell 2016;165:1332\u201345. https:\/\/doi.org\/10.1016\/j.cell.2016.05.041.","DOI":"10.1016\/j.cell.2016.05.041"},{"key":"2026083102570591236_j_mr-2026-0009_ref_167","doi-asserted-by":"crossref","unstructured":"De Silva, A, Bloom, SR. Gut hormones and appetite control: a focus on PYY and GLP-1 as therapeutic targets in obesity. Gut Liver 2012;6:10\u201320. https:\/\/doi.org\/10.5009\/gnl.2012.6.1.10.","DOI":"10.5009\/gnl.2012.6.1.10"},{"key":"2026083102570591236_j_mr-2026-0009_ref_168","doi-asserted-by":"crossref","unstructured":"MacDonald, PE, El-kholy, W, Riedel, MJ, Salapatek, AM, Light, PE, Wheeler, MB. The multiple actions of GLP-1 on the process of glucose-stimulated insulin secretion. Diabetes 2002;51:S434\u201342. https:\/\/doi.org\/10.2337\/diabetes.51.2007.s434.","DOI":"10.2337\/diabetes.51.2007.S434"},{"key":"2026083102570591236_j_mr-2026-0009_ref_169","doi-asserted-by":"crossref","unstructured":"Priyadarshini, M, Villa, SR, Fuller, M, Wicksteed, B, MacKay, CR, Alquier, T, et al.. An acetate-specific GPCR, FFAR2, regulates insulin secretion. Mol Endocrinol 2015;29:1055\u201366. https:\/\/doi.org\/10.1210\/me.2015-1007.","DOI":"10.1210\/me.2015-1007"},{"key":"2026083102570591236_j_mr-2026-0009_ref_170","doi-asserted-by":"crossref","unstructured":"McNelis, JC, Lee, YS, Mayoral, R, van der Kant, R, Johnson, AM, Wollam, J, et al.. GPR43 potentiates \u03b2-cell function in obesity. Diabetes 2015;64:3203\u201317. https:\/\/doi.org\/10.2337\/db14-1938.","DOI":"10.2337\/db14-1938"},{"key":"2026083102570591236_j_mr-2026-0009_ref_171","doi-asserted-by":"crossref","unstructured":"Pingitore, A, Chambers, ES, Hill, T, Maldonado, IR, Liu, B, Bewick, G, et al.. The diet-derived short chain fatty acid propionate improves beta-cell function in humans and stimulates insulin secretion from human islets in\u00a0vitro. Diabetes Obes Metab 2017;19:257\u201365. https:\/\/doi.org\/10.1111\/dom.12811.","DOI":"10.1111\/dom.12811"},{"key":"2026083102570591236_j_mr-2026-0009_ref_172","doi-asserted-by":"crossref","unstructured":"Tirosh, A, Calay, ES, Tuncman, G, Claiborn, KC, Inouye, KE, Eguchi, K, et al.. The short-chain fatty acid propionate increases glucagon and FABP4 production, impairing insulin action in mice and humans. Sci Transl Med 2019;11:eaav0120. https:\/\/doi.org\/10.1126\/scitranslmed.aav0120.","DOI":"10.1126\/scitranslmed.aav0120"},{"key":"2026083102570591236_j_mr-2026-0009_ref_173","doi-asserted-by":"crossref","unstructured":"Scott, SA, Fu, J, Chang, PV. Microbial tryptophan metabolites regulate gut barrier function via the aryl hydrocarbon receptor. Proc Natl Acad Sci USA 2020;117:19376\u201387. https:\/\/doi.org\/10.1073\/pnas.2000047117.","DOI":"10.1073\/pnas.2000047117"},{"key":"2026083102570591236_j_mr-2026-0009_ref_174","doi-asserted-by":"crossref","unstructured":"Kim, G, Chen, Z, Li, J, Luo, J, Castro-Martinez, F, Wisniewski, J, et al.. Gut-liver axis calibrates intestinal stem cell fitness. Cell 2024;187:914\u201330.e20. https:\/\/doi.org\/10.1016\/j.cell.2024.01.001.","DOI":"10.1016\/j.cell.2024.01.001"},{"key":"2026083102570591236_j_mr-2026-0009_ref_175","doi-asserted-by":"crossref","unstructured":"Hendrikx, T, Lang, S, Rajcic, D, Wang, Y, McArdle, S, Kim, K, et al.. Hepatic pIgR-mediated secretion of IgA limits bacterial translocation and prevents ethanol-induced liver disease in mice. Gut 2023;72:1959\u201370. https:\/\/doi.org\/10.1136\/gutjnl-2022-328265.","DOI":"10.1136\/gutjnl-2022-328265"},{"key":"2026083102570591236_j_mr-2026-0009_ref_176","doi-asserted-by":"crossref","unstructured":"Miyamoto, Y, Kikuta, J, Matsui, T, Hasegawa, T, Fujii, K, Okuzaki, D, et al.. Periportal macrophages protect against commensal-driven liver inflammation. Nature 2024;629:901\u20139. https:\/\/doi.org\/10.1038\/s41586-024-07372-6.","DOI":"10.1038\/s41586-024-07372-6"},{"key":"2026083102570591236_j_mr-2026-0009_ref_177","doi-asserted-by":"crossref","unstructured":"Xu, R, Liu, P, Zhang, T, Wu, Q, Zeng, M, Ma, Y, et al.. Progressive deterioration of the upper respiratory tract and the gut microbiomes in children during the early infection stages of COVID-19. J\u00a0Genet Genom 2021;48:803\u201314. https:\/\/doi.org\/10.1016\/j.jgg.2021.05.004.","DOI":"10.1016\/j.jgg.2021.05.004"},{"key":"2026083102570591236_j_mr-2026-0009_ref_178","doi-asserted-by":"crossref","unstructured":"Al Khatib, HA, Mathew, S, Smatti, MK, Eltai, NO, Pathan, SA, Al Thani, AA, et al.. Profiling of intestinal microbiota in patients infected with respiratory influenza A and B viruses. Pathogens 2021;10:761. https:\/\/doi.org\/10.3390\/pathogens10060761.","DOI":"10.3390\/pathogens10060761"},{"key":"2026083102570591236_j_mr-2026-0009_ref_179","doi-asserted-by":"crossref","unstructured":"Qin, N, Zheng, B, Yao, J, Guo, L, Zuo, J, Wu, L, et al.. Influence of H7N9 virus infection and associated treatment on human gut microbiota. Sci Rep 2015;5:14771. https:\/\/doi.org\/10.1038\/srep14771.","DOI":"10.1038\/srep14771"},{"key":"2026083102570591236_j_mr-2026-0009_ref_180","doi-asserted-by":"crossref","unstructured":"Hu, X, Zhao, Y, Yang, Y, Gong, W, Sun, X, Yang, L, et al.. Akkermansia muciniphila improves host defense against influenza virus infection. Front Microbiol 2021;11:586476. https:\/\/doi.org\/10.3389\/fmicb.2020.586476.","DOI":"10.3389\/fmicb.2020.586476"},{"key":"2026083102570591236_j_mr-2026-0009_ref_181","doi-asserted-by":"crossref","unstructured":"Wang, L, Cai, Y, Garssen, J, Henricks, PAJ, Folkerts, G, Braber, S. The bidirectional gut-lung axis in chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2023;207:1145\u201360. https:\/\/doi.org\/10.1164\/rccm.202206-1066tr.","DOI":"10.1164\/rccm.202206-1066TR"},{"key":"2026083102570591236_j_mr-2026-0009_ref_182","doi-asserted-by":"crossref","unstructured":"Wu, H, Tremaroli, V, Schmidt, C, Lundqvist, A, Olsson, LM, Kr\u00e4mer, M, et al.. The gut microbiota in prediabetes and diabetes: a population-based cross-sectional study. Cell Metab 2020;32:379\u201390.e3. https:\/\/doi.org\/10.1016\/j.cmet.2020.06.011.","DOI":"10.1016\/j.cmet.2020.06.011"},{"key":"2026083102570591236_j_mr-2026-0009_ref_185","doi-asserted-by":"crossref","unstructured":"Lee, GO, McCormick, BJJ, Seidman, JC, Kosek, MN, Haque, R, Olortegui, MP, et al.. Infant nutritional status, feeding practices, enteropathogen exposure, socioeconomic status, and illness are associated with gut barrier function as assessed by the lactulose mannitol test in the MAL-ED birth cohort. Am J Trop Med Hyg 2017;97:281\u201390. https:\/\/doi.org\/10.4269\/ajtmh.16-0830.","DOI":"10.4269\/ajtmh.16-0830"},{"key":"2026083102570591236_j_mr-2026-0009_ref_186","doi-asserted-by":"crossref","unstructured":"Olivera, PA, Martinez-Lozano, H, Leibovitzh, H, Xue, M, Neustaeter, A, Espin-Garcia, O, et al.. Healthy first-degree relatives from multiplex families vs simplex families have higher subclinical intestinal inflammation, a distinct fecal microbial signature, and harbor a higher risk of developing Crohn\u2019s disease. Gastroenterology 2025;168:99\u2013110.e2. https:\/\/doi.org\/10.1053\/j.gastro.2024.08.031.","DOI":"10.1053\/j.gastro.2024.09.051"},{"key":"2026083102570591236_j_mr-2026-0009_ref_187","doi-asserted-by":"crossref","unstructured":"Turpin, W, Lee, SH, Raygoza Garay, JA, Madsen, KL, Meddings, JB, Bedrani, L, et al.. Increased intestinal permeability is associated with later development of Crohn\u2019s disease. Gastroenterology 2020;159:2092\u2013100.e5. https:\/\/doi.org\/10.1053\/j.gastro.2020.08.005.","DOI":"10.1053\/j.gastro.2020.08.005"},{"key":"2026083102570591236_j_mr-2026-0009_ref_183","doi-asserted-by":"crossref","unstructured":"Khoshbin, K, Khanna, L, Maselli, D, Atieh, J, Breen-Lyles, M, Arndt, K, et al.. Development and validation of test for \u201cleaky gut\u201d small intestinal and colonic permeability using sugars in healthy adults. Gastroenterology 2021;161:463\u201375.e13. https:\/\/doi.org\/10.1053\/j.gastro.2021.04.020.","DOI":"10.1053\/j.gastro.2021.04.020"},{"key":"2026083102570591236_j_mr-2026-0009_ref_184","doi-asserted-by":"crossref","unstructured":"Grover, M, Camilleri, M, Hines, J, Burton, D, Ryks, M, Wadhwa, A, et al.. (13) C mannitol as a novel biomarker for measurement of intestinal permeability. Neurogastroenterol Motil 2016;28:1114\u20139. https:\/\/doi.org\/10.1111\/nmo.12802.","DOI":"10.1111\/nmo.12802"},{"key":"2026083102570591236_j_mr-2026-0009_ref_188","doi-asserted-by":"crossref","unstructured":"D\u2019Agostino, L, Daniele, B, Pignata, S, Barone, MV, Ciacci, C, Sollazzo, R, et al.. Postheparin plasma diamine oxidase increases in patients with coeliac disease during gluten free diet. Gut 1987;28:131\u20134. https:\/\/doi.org\/10.1136\/gut.28.suppl.131.","DOI":"10.1136\/gut.28.Suppl.131"},{"key":"2026083102570591236_j_mr-2026-0009_ref_189","doi-asserted-by":"crossref","unstructured":"D\u2019Agostino, L, Daniele, B, Pallone, F, Pignata, S, Leoni, M, Mazzacca, G. Postheparin plasma diamine oxidase in patients with small bowel Crohn\u2019s disease. Gastroenterology 1988;95:1503\u20139. https:\/\/doi.org\/10.1016\/s0016-5085(88)80069-6.","DOI":"10.1016\/S0016-5085(88)80069-6"},{"key":"2026083102570591236_j_mr-2026-0009_ref_193","doi-asserted-by":"crossref","unstructured":"Tulkens, J, Vergauwen, G, Van Deun, J, Geeurickx, E, Dhondt, B, Lippens, L, et al.. Increased levels of systemic LPS-positive bacterial extracellular vesicles in patients with intestinal barrier dysfunction. Gut 2020;69:191\u20133. https:\/\/doi.org\/10.1136\/gutjnl-2018-317726.","DOI":"10.1136\/gutjnl-2018-317726"},{"key":"2026083102570591236_j_mr-2026-0009_ref_194","doi-asserted-by":"crossref","unstructured":"Leibovitzh, H, Lee, SH, Raygoza Garay, JA, Espin-Garcia, O, Xue, M, Neustaeter, A, et al.. Immune response and barrier dysfunction-related proteomic signatures in preclinical phase of Crohn\u2019s disease highlight earliest events of pathogenesis. Gut 2023;72:1462\u201371. https:\/\/doi.org\/10.1136\/gutjnl-2022-328421.","DOI":"10.1136\/gutjnl-2022-328421"},{"key":"2026083102570591236_j_mr-2026-0009_ref_196","doi-asserted-by":"crossref","unstructured":"Vancamelbeke, M, Vermeire, S. The intestinal barrier: a fundamental role in health and disease. Expert Rev Gastroenterol Hepatol 2017;11:821\u201334. https:\/\/doi.org\/10.1080\/17474124.2017.1343143.","DOI":"10.1080\/17474124.2017.1343143"},{"key":"2026083102570591236_j_mr-2026-0009_ref_197","doi-asserted-by":"crossref","unstructured":"Ravelli, A, Villanacci, V. Tricks of the trade: how to avoid histological pitfalls in celiac disease. Pathol Res Pract 2012;208:197\u2013202. https:\/\/doi.org\/10.1016\/j.prp.2012.01.008.","DOI":"10.1016\/j.prp.2012.01.008"},{"key":"2026083102570591236_j_mr-2026-0009_ref_198","doi-asserted-by":"crossref","unstructured":"Robert, ME, Crowe, SE, Burgart, L, Yantiss, RK, Lebwohl, B, Greenson, JK, et al.. Statement on best practices in the use of pathology as a diagnostic tool for celiac disease: a guide for clinicians and pathologists. Am J Surg Pathol 2018;42:e44\u201358. https:\/\/doi.org\/10.1097\/pas.0000000000001107.","DOI":"10.1097\/PAS.0000000000001107"},{"key":"2026083102570591236_j_mr-2026-0009_ref_199","doi-asserted-by":"crossref","unstructured":"Feakins, R, Borralho Nunes, P, Driessen, A, Gordon, IO, Zidar, N, Baldin, P, et al.. Definitions of histological abnormalities in inflammatory bowel disease: an ECCO position paper. J\u00a0Crohns Colitis 2024;18:175\u201391. https:\/\/doi.org\/10.1093\/ecco-jcc\/jjad142.","DOI":"10.1093\/ecco-jcc\/jjad142"},{"key":"2026083102570591236_j_mr-2026-0009_ref_264","doi-asserted-by":"crossref","unstructured":"Levine, A, Wine, E, Assa, A, Sigall Boneh, R, Shaoul, R, Kori, M, et al.. Crohn\u2019s disease exclusion diet plus partial enteral nutrition induces sustained remission in a randomized controlled trial. Gastroenterology 2019;157:440\u201350.e8. https:\/\/doi.org\/10.1053\/j.gastro.2019.04.021.","DOI":"10.1053\/j.gastro.2019.04.021"},{"key":"2026083102570591236_j_mr-2026-0009_ref_268","doi-asserted-by":"crossref","unstructured":"Kim, S, Shin, YC, Kim, TY, Kim, Y, Lee, YS, Lee, SH, et al.. Mucin degrader Akkermansia muciniphila accelerates intestinal stem cell-mediated epithelial development. Gut Microbes 2021;13:1\u201320. https:\/\/doi.org\/10.1080\/19490976.2021.1892441.","DOI":"10.1080\/19490976.2021.1892441"},{"key":"2026083102570591236_j_mr-2026-0009_ref_269","doi-asserted-by":"crossref","unstructured":"Wu, H, Xie, S, Miao, J, Li, Y, Wang, Z, Wang, M, et al.. Lactobacillus reuteri maintains intestinal epithelial regeneration and repairs damaged intestinal mucosa. Gut Microbes 2020;11:997\u20131014. https:\/\/doi.org\/10.1080\/19490976.2020.1734423.","DOI":"10.1080\/19490976.2020.1734423"},{"key":"2026083102570591236_j_mr-2026-0009_ref_270","doi-asserted-by":"crossref","unstructured":"Seo, B, Jeon, K, Moon, S, Lee, K, Kim, WK, Jeong, H, et al.. Roseburia spp. abundance associates with alcohol consumption in humans and its administration ameliorates alcoholic fatty liver in mice. Cell Host Microbe 2020;27:25\u201340.e6. https:\/\/doi.org\/10.1016\/j.chom.2019.11.001.","DOI":"10.1016\/j.chom.2019.11.001"},{"key":"2026083102570591236_j_mr-2026-0009_ref_272","doi-asserted-by":"crossref","unstructured":"Zhang, Y, Wang, Y, Zhang, X, Wang, P, Shi, F, Zhang, Z, et al.. Gastrointestinal self-adaptive and nutrient self-sufficient Akkermansia muciniphila\u2013gelatin porous microgels for synergistic therapy of ulcerative colitis. ACS Nano 2024;18:26807\u201327. https:\/\/doi.org\/10.1021\/acsnano.4c07658.","DOI":"10.1021\/acsnano.4c07658"},{"key":"2026083102570591236_j_mr-2026-0009_ref_273","doi-asserted-by":"crossref","unstructured":"Chen, Y, Lin, S, Wang, L, Zhang, Y, Chen, H, Fu, Z, et al.. Reinforcement of the intestinal mucosal barrier via mucus-penetrating PEGylated bacteria. Nat Biomed Eng 2024;8:823\u201341. https:\/\/doi.org\/10.1038\/s41551-024-01224-4.","DOI":"10.1038\/s41551-024-01224-4"},{"key":"2026083102570591236_j_mr-2026-0009_ref_274","doi-asserted-by":"crossref","unstructured":"Cao, F, Jin, L, Gao, Y, Ding, Y, Wen, H, Qian, Z, et al.. Artificial-enzymes-armed Bifidobacterium longum probiotics for alleviating intestinal inflammation and microbiota dysbiosis. Nat Nanotechnol 2023;18:617\u201327. https:\/\/doi.org\/10.1038\/s41565-023-01346-x.","DOI":"10.1038\/s41565-023-01346-x"},{"key":"2026083102570591236_j_mr-2026-0009_ref_275","doi-asserted-by":"crossref","unstructured":"Guo, P, Wang, W, Xiang, Q, Pan, C, Qiu, Y, Li, T, et al.. Engineered probiotic ameliorates ulcerative colitis by restoring gut microbiota and redox homeostasis. Cell Host Microbe 2024;32:1502\u201318.e9. https:\/\/doi.org\/10.1016\/j.chom.2024.07.028.","DOI":"10.1016\/j.chom.2024.07.028"},{"key":"2026083102570591236_j_mr-2026-0009_ref_271","doi-asserted-by":"crossref","unstructured":"Zhang, Y, Liu, R, Chen, Y, Cao, Z, Liu, C, Bao, R, et al.. Akkermansia muciniphila supplementation in patients with overweight\/obese type 2 diabetes: efficacy depends on its baseline levels in the gut. Cell Metab 2025;37:592\u2013605.e6. https:\/\/doi.org\/10.1016\/j.cmet.2024.12.010.","DOI":"10.1016\/j.cmet.2024.12.010"},{"key":"2026083102570591236_j_mr-2026-0009_ref_224","doi-asserted-by":"crossref","unstructured":"Mouries, J, Brescia, P, Silvestri, A, Spadoni, I, Sorribas, M, Wiest, R, et al.. Microbiota-driven gut vascular barrier disruption is a prerequisite for non-alcoholic steatohepatitis development. J\u00a0Hepatol 2019;71:1216\u201328. https:\/\/doi.org\/10.1016\/j.jhep.2019.08.005.","DOI":"10.1016\/j.jhep.2019.08.005"},{"key":"2026083102570591236_j_mr-2026-0009_ref_278","doi-asserted-by":"crossref","unstructured":"Chen, L, Jiao, T, Liu, W, Luo, Y, Wang, J, Guo, X, et al.. Hepatic cytochrome P450 8B1 and cholic acid potentiate intestinal epithelial injury in colitis by suppressing intestinal stem cell renewal. Cell Stem Cell 2022;29:1366\u201381.e9. https:\/\/doi.org\/10.1016\/j.stem.2022.08.008.","DOI":"10.1016\/j.stem.2022.08.008"},{"key":"2026083102570591236_j_mr-2026-0009_ref_279","doi-asserted-by":"crossref","unstructured":"Sorrentino, G, Perino, A, Yildiz, E, El Alam, G, Bou Sleiman, M, Gioiello, A, et al.. Bile acids signal via TGR5 to activate intestinal stem cells and epithelial regeneration. Gastroenterology 2020;159:956\u201368.e8. https:\/\/doi.org\/10.1053\/j.gastro.2020.05.067.","DOI":"10.1053\/j.gastro.2020.05.067"},{"key":"2026083102570591236_j_mr-2026-0009_ref_280","doi-asserted-by":"crossref","unstructured":"Friedman, ES, Li, Y, Shen, TD, Jiang, J, Chau, L, Adorini, L, et al.. FXR-dependent modulation of the human small intestinal microbiome by the bile acid derivative obeticholic acid. Gastroenterology 2018;155:1741\u201352.e5. https:\/\/doi.org\/10.1053\/j.gastro.2018.08.022.","DOI":"10.1053\/j.gastro.2018.08.022"},{"key":"2026083102570591236_j_mr-2026-0009_ref_282","doi-asserted-by":"crossref","unstructured":"He, GW, Lin, L, DeMartino, J, Zheng, X, Staliarova, N, Dayton, T, et al.. Optimized human intestinal organoid model reveals interleukin-22-dependency of Paneth cell formation. Cell Stem Cell 2022;29:1333\u201345.e6. https:\/\/doi.org\/10.1016\/j.stem.2022.11.001.","DOI":"10.1016\/j.stem.2022.08.002"},{"key":"2026083102570591236_j_mr-2026-0009_ref_283","doi-asserted-by":"crossref","unstructured":"Chiang, HY, Lu, HH, Sudhakar, JN, Chen, YW, Shih, NS, Weng, YT, et al.. IL-22 initiates an IL-18-dependent epithelial response circuit to enforce intestinal host defence. Nat Commun 2022;13:874. https:\/\/doi.org\/10.1038\/s41467-022-28478-3.","DOI":"10.1038\/s41467-022-28478-3"},{"key":"2026083102570591236_j_mr-2026-0009_ref_281","doi-asserted-by":"crossref","unstructured":"Liu, J, Ren, H, Zhang, C, Li, J, Qiu, Q, Zhang, N, et al.. Orally-delivered, cytokine-engineered extracellular vesicles for targeted treatment of inflammatory bowel disease. Small 2023;19:e2304023. https:\/\/doi.org\/10.1002\/smll.202304023.","DOI":"10.1002\/smll.202304023"},{"key":"2026083102570591236_j_mr-2026-0009_ref_276","doi-asserted-by":"crossref","unstructured":"Su, L, Nalle, SC, Shen, L, Turner, ES, Singh, G, Breskin, LA, et al.. TNFR2 activates MLCK-dependent tight junction dysregulation to cause apoptosis-mediated barrier loss and experimental colitis. Gastroenterology 2013;145:407\u201315. https:\/\/doi.org\/10.1053\/j.gastro.2013.04.011.","DOI":"10.1053\/j.gastro.2013.04.011"},{"key":"2026083102570591236_j_mr-2026-0009_ref_277","doi-asserted-by":"crossref","unstructured":"Marchelletta, RR, Krishnan, M, Spalinger, MR, Placone, TW, Alvarez, R, Sayoc-Becerra, A, et al.. T\u00a0cell protein tyrosine phosphatase protects intestinal barrier function by restricting epithelial tight junction remodeling. J\u00a0Clin Investig 2021;131:e138230. https:\/\/doi.org\/10.1172\/jci138230.","DOI":"10.1172\/JCI138230"},{"key":"2026083102570591236_j_mr-2026-0009_ref_190","doi-asserted-by":"crossref","unstructured":"Cao, B, Zhao, RY, Li, HH, Xu, XM, Cui, H, Deng, H, et al.. Oral administration of asparagine and 3-indolepropionic acid prolongs survival time of rats with traumatic colon injury. Mil Med Res 2022;9:37. https:\/\/doi.org\/10.1186\/s40779-022-00397-w.","DOI":"10.1186\/s40779-022-00397-w"},{"key":"2026083102570591236_j_mr-2026-0009_ref_191","doi-asserted-by":"crossref","unstructured":"Playford, RJ, Belo, A, Poulsom, R, Fitzgerald, AJ, Harris, K, Pawluczyk, I, et al.. Effects of mouse and human lipocalin homologues 24p3\/lcn2 and neutrophil gelatinase-associated lipocalin on gastrointestinal mucosal integrity and repair. Gastroenterology 2006;131:809\u201317. https:\/\/doi.org\/10.1053\/j.gastro.2006.05.051.","DOI":"10.1053\/j.gastro.2006.05.051"},{"key":"2026083102570591236_j_mr-2026-0009_ref_192","doi-asserted-by":"crossref","unstructured":"Xia, M, Lu, J, Lan, J, Teng, T, Shiao, R, Sun, H, et al.. Elevated IL-22 as a result of stress-induced gut leakage suppresses septal neuron activation to ameliorate anxiety-like behavior. Immunity 2025;58:218\u201331.e12. https:\/\/doi.org\/10.1016\/j.immuni.2024.11.008.","DOI":"10.1016\/j.immuni.2024.11.008"},{"key":"2026083102570591236_j_mr-2026-0009_ref_195","doi-asserted-by":"crossref","unstructured":"Kang, S, Kim, J, Park, A, Koh, M, Shin, W, Park, G, et al.. TRIM40 is a pathogenic driver of inflammatory bowel disease subverting intestinal barrier integrity. Nat Commun 2023;14:700. https:\/\/doi.org\/10.1038\/s41467-023-36424-0.","DOI":"10.1038\/s41467-023-36424-0"},{"key":"2026083102570591236_j_mr-2026-0009_ref_200","doi-asserted-by":"crossref","unstructured":"Hsiao, EY, McBride, SW, Hsien, S, Sharon, G, Hyde, ER, McCue, T, et al.. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell 2013;155:1451\u201363. https:\/\/doi.org\/10.1016\/j.cell.2013.11.024.","DOI":"10.1016\/j.cell.2013.11.024"},{"key":"2026083102570591236_j_mr-2026-0009_ref_201","doi-asserted-by":"crossref","unstructured":"Ashwood, P, Krakowiak, P, Hertz-Picciotto, I, Hansen, R, Pessah, I, Van de Water, J. Elevated plasma cytokines in autism spectrum disorders provide evidence of immune dysfunction and are associated with impaired behavioral outcome. Brain Behav Immun 2011;25:40\u20135. https:\/\/doi.org\/10.1016\/j.bbi.2010.08.003.","DOI":"10.1016\/j.bbi.2010.08.003"},{"key":"2026083102570591236_j_mr-2026-0009_ref_202","doi-asserted-by":"crossref","unstructured":"Xie, J, Huang, L, Li, X, Li, H, Zhou, Y, Zhu, H, et al.. Immunological cytokine profiling identifies TNF-\u03b1 as a key molecule dysregulated in autistic children. Oncotarget 2017;8:82390\u20138. https:\/\/doi.org\/10.18632\/oncotarget.19326.","DOI":"10.18632\/oncotarget.19326"},{"key":"2026083102570591236_j_mr-2026-0009_ref_203","doi-asserted-by":"crossref","unstructured":"Molloy, CA, Morrow, AL, Meinzen-Derr, J, Schleifer, K, Dienger, K, Manning-Courtney, P, et al.. Elevated cytokine levels in children with autism spectrum disorder. J\u00a0Neuroimmunol 2006;172:198\u2013205. https:\/\/doi.org\/10.1016\/j.jneuroim.2005.11.007.","DOI":"10.1016\/j.jneuroim.2005.11.007"},{"key":"2026083102570591236_j_mr-2026-0009_ref_204","doi-asserted-by":"crossref","unstructured":"Iglesias-V\u00e1zquez, L, Van Ginkel, RG, Arija, V, Canals, J. Composition of gut microbiota in children with autism spectrum disorder: a systematic review and meta-analysis. Nutrients 2020;12:792. https:\/\/doi.org\/10.3390\/nu12030792.","DOI":"10.3390\/nu12030792"},{"key":"2026083102570591236_j_mr-2026-0009_ref_205","doi-asserted-by":"crossref","unstructured":"Li, N, Yang, J, Zhang, J, Liang, C, Wang, Y, Chen, B, et al.. Correlation of gut microbiome between ASD children and mothers and potential biomarkers for risk assessment. Genom Proteom Bioinform 2019;17:26\u201338. https:\/\/doi.org\/10.1016\/j.gpb.2019.01.002.","DOI":"10.1016\/j.gpb.2019.01.002"},{"key":"2026083102570591236_j_mr-2026-0009_ref_206","doi-asserted-by":"crossref","unstructured":"Zhao, Y, Wang, Y, Meng, F, Chen, X, Chang, T, Huang, H, et al.. Altered gut microbiota as potential biomarkers for autism spectrum disorder in early childhood. Neuroscience 2023;523:118\u201331. https:\/\/doi.org\/10.1016\/j.neuroscience.2023.04.029.","DOI":"10.1016\/j.neuroscience.2023.04.029"},{"key":"2026083102570591236_j_mr-2026-0009_ref_207","doi-asserted-by":"crossref","unstructured":"Gerges, P, Bangarusamy, DK, Bitar, T, Alameddine, A, Nemer, G, Hleihel, W. Turicibacter and Catenibacterium as potential biomarkers in autism spectrum disorders. Sci Rep 2024;14:23184. https:\/\/doi.org\/10.1038\/s41598-024-73700-5.","DOI":"10.1038\/s41598-024-73700-5"},{"key":"2026083102570591236_j_mr-2026-0009_ref_208","doi-asserted-by":"crossref","unstructured":"Abuljadayel, D, Alotibi, A, Alqothmi, K, Basingab, F, Alhazmi, S, Almuhammadi, A, et al.. Gut microbiota of children with autism spectrum disorder and healthy siblings: a comparative study. Exp Ther Med 2024;28:430. https:\/\/doi.org\/10.3892\/etm.2024.12719.","DOI":"10.3892\/etm.2024.12719"},{"key":"2026083102570591236_j_mr-2026-0009_ref_209","doi-asserted-by":"crossref","unstructured":"Wang, W, Fu, P. Gut microbiota analysis and in\u00a0silico biomarker detection of children with autism spectrum disorder across cohorts. Microorganisms 2023;11:291. https:\/\/doi.org\/10.3390\/microorganisms11020291.","DOI":"10.3390\/microorganisms11020291"},{"key":"2026083102570591236_j_mr-2026-0009_ref_210","doi-asserted-by":"crossref","unstructured":"Dan, Z, Mao, X, Liu, Q, Guo, M, Zhuang, Y, Liu, Z, et al.. Altered gut microbial profile is associated with abnormal metabolism activity of autism spectrum disorder. Gut Microbes 2020;11:1246\u201367. https:\/\/doi.org\/10.1080\/19490976.2020.1747329.","DOI":"10.1080\/19490976.2020.1747329"},{"key":"2026083102570591236_j_mr-2026-0009_ref_211","doi-asserted-by":"crossref","unstructured":"Manghi, P, Filosi, M, Zolfo, M, Casten, LG, Garcia-Valiente, A, Mattevi, S, et al.. Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders. Nat Commun 2024;15:9743. https:\/\/doi.org\/10.1038\/s41467-024-53934-7.","DOI":"10.1038\/s41467-024-53934-7"},{"key":"2026083102570591236_j_mr-2026-0009_ref_212","doi-asserted-by":"crossref","unstructured":"Barone, R, Alaimo, S, Messina, M, Pulvirenti, A, Bastin, J, Group, MA, et al.. A subset of patients with autism spectrum disorders show a distinctive metabolic profile by dried blood spot analyses. Front Psychiatr 2018;9:636. https:\/\/doi.org\/10.3389\/fpsyt.2018.00636.","DOI":"10.3389\/fpsyt.2018.00636"},{"key":"2026083102570591236_j_mr-2026-0009_ref_213","doi-asserted-by":"crossref","unstructured":"Orozco, JS, Hertz-Picciotto, I, Abbeduto, L, Slupsky, CM. Metabolomics analysis of children with autism, idiopathic-developmental delays, and Down syndrome. Transl Psychiatry 2019;9:243. https:\/\/doi.org\/10.1038\/s41398-019-0578-3.","DOI":"10.1038\/s41398-019-0578-3"},{"key":"2026083102570591236_j_mr-2026-0009_ref_214","doi-asserted-by":"crossref","unstructured":"Leboucher, A, Pisani, DF, Martinez-Gili, L, Chilloux, J, Bermudez-Martin, P, Van Dijck, A, et al.. The translational regulator FMRP controls lipid and glucose metabolism in mice and humans. Mol Metabol 2019;21:22\u201335. https:\/\/doi.org\/10.1016\/j.molmet.2019.01.002.","DOI":"10.1016\/j.molmet.2019.01.002"},{"key":"2026083102570591236_j_mr-2026-0009_ref_215","doi-asserted-by":"crossref","unstructured":"West, PR, Amaral, DG, Bais, P, Smith, AM, Egnash, LA, Ross, ME, et al.. Metabolomics as a tool for discovery of biomarkers of autism spectrum disorder in the blood plasma of children. PLoS One 2014;9:e112445. https:\/\/doi.org\/10.1371\/journal.pone.0112445.","DOI":"10.1371\/journal.pone.0112445"},{"key":"2026083102570591236_j_mr-2026-0009_ref_216","doi-asserted-by":"crossref","unstructured":"Lingampelly, SS, Naviaux, JC, Heuer, LS, Monk, JM, Li, K, Wang, L, et al.. Metabolic network analysis of pre-ASD newborns and 5-year-old children with autism spectrum disorder. Commun Biol 2024;7:536. https:\/\/doi.org\/10.1038\/s42003-024-06102-y.","DOI":"10.1038\/s42003-024-06102-y"},{"key":"2026083102570591236_j_mr-2026-0009_ref_217","doi-asserted-by":"crossref","unstructured":"Liu, P, Liu, Z, Wang, J, Wang, J, Gao, M, Zhang, Y, et al.. Immunoregulatory role of the gut microbiota in inflammatory depression. Nat Commun 2024;15:3003. https:\/\/doi.org\/10.1038\/s41467-024-47273-w.","DOI":"10.1038\/s41467-024-47273-w"},{"key":"2026083102570591236_j_mr-2026-0009_ref_218","doi-asserted-by":"crossref","unstructured":"Chen, C, Zhang, D, Wu, D, Chen, F, Li, Z, Hu, Y. Gut microbiome, and immune cells mediated effect on depression: a two-step, two-sample Mendelian randomization analysis. Exp Gerontol 2024;195:112530. https:\/\/doi.org\/10.1016\/j.exger.2024.112530.","DOI":"10.1016\/j.exger.2024.112530"},{"key":"2026083102570591236_j_mr-2026-0009_ref_219","doi-asserted-by":"crossref","unstructured":"Zhu, X, Sakamoto, S, Ishii, C, Smith, MD, Ito, K, Obayashi, M, et al.. Dectin-1 signaling on colonic \u03b3\u03b4 T\u00a0cells promotes psychosocial stress responses. Nat Immunol 2023;24:625\u201336. https:\/\/doi.org\/10.1038\/s41590-023-01447-8.","DOI":"10.1038\/s41590-023-01447-8"},{"key":"2026083102570591236_j_mr-2026-0009_ref_220","doi-asserted-by":"crossref","unstructured":"Haran, JP, Bhattarai, SK, Foley, SE, Dutta, P, Ward, DV, Bucci, V, et al.. Alzheimer\u2019s disease microbiome is associated with dysregulation of the anti-inflammatory P-glycoprotein pathway. mBio 2019;10:e00632-19. https:\/\/doi.org\/10.1128\/mbio.00632-19.","DOI":"10.1128\/mBio.00632-19"},{"key":"2026083102570591236_j_mr-2026-0009_ref_221","doi-asserted-by":"crossref","unstructured":"Grabrucker, S, Marizzoni, M, Silajd\u017ei\u0107, E, Lopizzo, N, Mombelli, E, Nicolas, S, et al.. Microbiota from Alzheimer\u2019s patients induce deficits in cognition and hippocampal neurogenesis. Brain 2023;146:4916\u201334. https:\/\/doi.org\/10.1093\/brain\/awad303.","DOI":"10.1093\/brain\/awad303"},{"key":"2026083102570591236_j_mr-2026-0009_ref_222","doi-asserted-by":"crossref","unstructured":"Zhuang, ZQ, Shen, LL, Li, WW, Fu, X, Zeng, F, Gui, L, et al.. Gut microbiota is altered in patients with Alzheimer\u2019s disease. J\u00a0Alzheimers Dis 2018;63:1337\u201346. https:\/\/doi.org\/10.3233\/jad-180176.","DOI":"10.3233\/JAD-180176"},{"key":"2026083102570591236_j_mr-2026-0009_ref_223","doi-asserted-by":"crossref","unstructured":"Li, J, Zhu, S, Wang, Y, Fan, M, Dai, J, Zhu, C, et al.. Metagenomic association analysis of cognitive impairment in community-dwelling older adults. Neurobiol Dis 2023;180:106081. https:\/\/doi.org\/10.1016\/j.nbd.2023.106081.","DOI":"10.1016\/j.nbd.2023.106081"},{"key":"2026083102570591236_j_mr-2026-0009_ref_225","doi-asserted-by":"crossref","unstructured":"Schwimmer, JB, Johnson, JS, Angeles, JE, Behling, C, Belt, PH, Borecki, I, et al.. Microbiome signatures associated with steatohepatitis and moderate to severe fibrosis in children with nonalcoholic fatty liver disease. Gastroenterology 2019;157:1109\u201322. https:\/\/doi.org\/10.1053\/j.gastro.2019.06.028.","DOI":"10.1053\/j.gastro.2019.08.040"},{"key":"2026083102570591236_j_mr-2026-0009_ref_226","doi-asserted-by":"crossref","unstructured":"Boursier, J, Mueller, O, Barret, M, Machado, M, Fizanne, L, Araujo-Perez, F, et al.. The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota. Hepatology 2016;63:764\u201375. https:\/\/doi.org\/10.1002\/hep.28356.","DOI":"10.1002\/hep.28356"},{"key":"2026083102570591236_j_mr-2026-0009_ref_227","doi-asserted-by":"crossref","unstructured":"Loomba, R, Seguritan, V, Li, W, Long, T, Klitgord, N, Bhatt, A, et al.. Gut microbiome-based metagenomic signature for non-invasive detection of advanced fibrosis in human nonalcoholic fatty liver disease. Cell Metab 2017;25:1054\u201362.e5. https:\/\/doi.org\/10.1016\/j.cmet.2017.04.001.","DOI":"10.1016\/j.cmet.2017.04.001"},{"key":"2026083102570591236_j_mr-2026-0009_ref_228","doi-asserted-by":"crossref","unstructured":"Kuang, J, Wang, J, Li, Y, Li, M, Zhao, M, Ge, K, et al.. Hyodeoxycholic acid alleviates non-alcoholic fatty liver disease through modulating the gut-liver axis. Cell Metab 2023;35:1752\u201366.e8. https:\/\/doi.org\/10.1016\/j.cmet.2023.07.011.","DOI":"10.1016\/j.cmet.2023.07.011"},{"key":"2026083102570591236_j_mr-2026-0009_ref_229","doi-asserted-by":"crossref","unstructured":"Nie, Q, Luo, X, Wang, K, Ding, Y, Jia, S, Zhao, Q, et al.. Gut symbionts alleviate MASH through a secondary bile acid biosynthetic pathway. Cell 2024;187:2717\u201334.e33. https:\/\/doi.org\/10.1016\/j.cell.2024.03.034.","DOI":"10.1016\/j.cell.2024.03.034"},{"key":"2026083102570591236_j_mr-2026-0009_ref_230","doi-asserted-by":"crossref","unstructured":"Chen, B, Sun, L, Zeng, G, Shen, Z, Wang, K, Yin, L, et al.. Gut bacteria alleviate smoking-related NASH by degrading gut nicotine. Nature 2022;610:562\u20138. https:\/\/doi.org\/10.1038\/s41586-022-05299-4.","DOI":"10.1038\/s41586-022-05299-4"},{"key":"2026083102570591236_j_mr-2026-0009_ref_231","doi-asserted-by":"crossref","unstructured":"Qin, N, Yang, F, Li, A, Prifti, E, Chen, Y, Shao, L, et al.. Alterations of the human gut microbiome in liver cirrhosis. Nature 2014;513:59\u201364. https:\/\/doi.org\/10.1038\/nature13568.","DOI":"10.1038\/nature13568"},{"key":"2026083102570591236_j_mr-2026-0009_ref_232","doi-asserted-by":"crossref","unstructured":"Bajaj, JS, Liu, EJ, Kheradman, R, Fagan, A, Heuman, DM, White, M, et al.. Fungal dysbiosis in cirrhosis. Gut 2018;67:1146\u201354. https:\/\/doi.org\/10.1136\/gutjnl-2016-313170.","DOI":"10.1136\/gutjnl-2016-313170"},{"key":"2026083102570591236_j_mr-2026-0009_ref_233","doi-asserted-by":"crossref","unstructured":"Mazagova, M, Wang, L, Anfora, AT, Wissmueller, M, Lesley, SA, Miyamoto, Y, et al.. Commensal microbiota is hepatoprotective and prevents liver fibrosis in mice. FASEB J 2015;29:1043\u201355. https:\/\/doi.org\/10.1096\/fj.14-259515.","DOI":"10.1096\/fj.14-259515"},{"key":"2026083102570591236_j_mr-2026-0009_ref_234","doi-asserted-by":"crossref","unstructured":"Kasahara, N, Imi, Y, Amano, R, Shinohara, M, Okada, K, Hosokawa, Y, et al.. A gut microbial metabolite of linoleic acid ameliorates liver fibrosis by inhibiting TGF-\u03b2 signaling in hepatic stellate cells. Sci Rep 2023;13:18983. https:\/\/doi.org\/10.1038\/s41598-023-46404-5.","DOI":"10.1038\/s41598-023-46404-5"},{"key":"2026083102570591236_j_mr-2026-0009_ref_235","doi-asserted-by":"crossref","unstructured":"Yuan, X, Yang, J, Huang, Y, Li, J, Li, Y. Gut microbiota metabolite 3-indolepropionic acid directly activates hepatic stellate cells by ROS\/JNK\/p38 signaling pathways. Biomolecules 2023;13:1464. https:\/\/doi.org\/10.3390\/biom13101464.","DOI":"10.3390\/biom13101464"},{"key":"2026083102570591236_j_mr-2026-0009_ref_236","doi-asserted-by":"crossref","unstructured":"Sun, Z, Zhu, QL, Shen, Y, Yan, T, Zhou, X. Dynamic changes of gut and lung microorganisms during chronic obstructive pulmonary disease exacerbations. Kaohsiung J Med Sci 2020;36:107\u201313. https:\/\/doi.org\/10.1002\/kjm2.12147.","DOI":"10.1002\/kjm2.12147"},{"key":"2026083102570591236_j_mr-2026-0009_ref_237","doi-asserted-by":"crossref","unstructured":"Notarbartolo, V, Giuffr\u00e8, M, Montante, C, Corsello, G, Carta, M. Composition of human breast milk microbiota and its role in children\u2019s health. Pediatr Gastroenterol Hepatol Nutr 2022;25:194\u2013210. https:\/\/doi.org\/10.5223\/pghn.2022.25.3.194.","DOI":"10.5223\/pghn.2022.25.3.194"},{"key":"2026083102570591236_j_mr-2026-0009_ref_238","doi-asserted-by":"crossref","unstructured":"Dumas, A, Bernard, L, Poquet, Y, Lugo-Villarino, G, Neyrolles, O. The role of the lung microbiota and the gut-lung axis in respiratory infectious diseases. Cell Microbiol 2018;20:e12966. https:\/\/doi.org\/10.1111\/cmi.12966.","DOI":"10.1111\/cmi.12966"},{"key":"2026083102570591236_j_mr-2026-0009_ref_239","doi-asserted-by":"crossref","unstructured":"Li, N, Yang, Z, Liao, B, Pan, T, Pu, J, Hao, B, et al.. Chronic exposure to ambient particulate matter induces gut microbial dysbiosis in a rat COPD model. Respir Res 2020;21:271. https:\/\/doi.org\/10.1186\/s12931-020-01529-3.","DOI":"10.1186\/s12931-020-01529-3"},{"key":"2026083102570591236_j_mr-2026-0009_ref_240","doi-asserted-by":"crossref","unstructured":"Bowerman, KL, Rehman, SF, Vaughan, A, Lachner, N, Budden, KF, Kim, RY, et al.. Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease. Nat Commun 2020;11:5886. https:\/\/doi.org\/10.1038\/s41467-020-19701-0.","DOI":"10.1038\/s41467-020-19701-0"},{"key":"2026083102570591236_j_mr-2026-0009_ref_241","doi-asserted-by":"crossref","unstructured":"Chan, KG, Ng, KT, Pang, YK, Chong, TM, Kamarulzaman, A, Yin, WF, et al.. Genome anatomy of Streptococcus parasanguinis strain C1A, isolated from a patient with acute exacerbation of chronic obstructive pulmonary disease, reveals unusual genomic features. Genome Announc 2015;3:e00541-15. https:\/\/doi.org\/10.1128\/genomea.00541-15.","DOI":"10.1128\/genomeA.00541-15"},{"key":"2026083102570591236_j_mr-2026-0009_ref_242","doi-asserted-by":"crossref","unstructured":"Stokholm, J, Blaser, MJ, Thorsen, J, Rasmussen, MA, Waage, J, Vinding, RK, et al.. Maturation of the gut microbiome and risk of asthma in childhood. Nat Commun 2018;9:141. https:\/\/doi.org\/10.1038\/s41467-017-02573-2.","DOI":"10.1038\/s41467-017-02573-2"},{"key":"2026083102570591236_j_mr-2026-0009_ref_243","doi-asserted-by":"crossref","unstructured":"Stiemsma, LT, Arrieta, MC, Dimitriu, PA, Cheng, J, Thorson, L, Lefebvre, DL, et al.. Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma. Clin Sci (Lond) 2016;130:2199\u2013207. https:\/\/doi.org\/10.1042\/cs20160349.","DOI":"10.1042\/CS20160349"},{"key":"2026083102570591236_j_mr-2026-0009_ref_244","doi-asserted-by":"crossref","unstructured":"Kahhaleh, FG, Barrientos, G, Conrad, ML. The gut-lung axis and asthma susceptibility in early life. Acta Physiol 2024;240:e14092. https:\/\/doi.org\/10.1111\/apha.14092.","DOI":"10.1111\/apha.14092"},{"key":"2026083102570591236_j_mr-2026-0009_ref_245","doi-asserted-by":"crossref","unstructured":"Shukla, SD, Budden, KF, Neal, R, Hansbro, PM. Microbiome effects on immunity, health and disease in the lung. Clin Transl Immunol 2017;6:e133. https:\/\/doi.org\/10.1038\/cti.2017.6.","DOI":"10.1038\/cti.2017.6"},{"key":"2026083102570591236_j_mr-2026-0009_ref_246","doi-asserted-by":"crossref","unstructured":"Wang, W, Luo, X, Zhang, Q, He, X, Zhang, Z, Wang, X. Bifidobacterium infantis relieves allergic asthma in mice by regulating Th1\/Th2. Med Sci Monit 2020;26:e920583. https:\/\/doi.org\/10.12659\/msm.920583.","DOI":"10.12659\/MSM.920583"},{"key":"2026083102570591236_j_mr-2026-0009_ref_247","doi-asserted-by":"crossref","unstructured":"Ghiamati Yazdi, F, Zakeri, A, van Ark, I, Leusink-Muis, T, Braber, S, Soleimanian-Zad, S, et al.. Crude turmeric extract improves the suppressive effects of Lactobacillus rhamnosus GG on allergic inflammation in a murine model of house dust mite-induced asthma. Front Immunol 2020;11:1092. https:\/\/doi.org\/10.3389\/fimmu.2020.01092.","DOI":"10.3389\/fimmu.2020.01092"},{"key":"2026083102570591236_j_mr-2026-0009_ref_248","doi-asserted-by":"crossref","unstructured":"Li, L, Fang, Z, Lee, YK, Zhao, J, Zhang, H, Peng, H, et al.. Efficacy and safety of Lactobacillus reuteri CCFM1040 in allergic rhinitis and asthma: a randomized, placebo-controlled trial. Front Nutr 2022;9:862934. https:\/\/doi.org\/10.3389\/fnut.2022.862934.","DOI":"10.3389\/fnut.2022.862934"},{"key":"2026083102570591236_j_mr-2026-0009_ref_249","doi-asserted-by":"crossref","unstructured":"Grayson, MH, Camarda, LE, Hussain, SA, Zemple, SJ, Hayward, M, Lam, V, et al.. Intestinal microbiota disruption reduces regulatory T\u00a0cells and increases respiratory viral infection mortality through increased IFN\u03b3 production. Front Immunol 2018;9:1587. https:\/\/doi.org\/10.3389\/fimmu.2018.01587.","DOI":"10.3389\/fimmu.2018.01587"},{"key":"2026083102570591236_j_mr-2026-0009_ref_250","doi-asserted-by":"crossref","unstructured":"Aljumaah, MR, Bhatia, U, Roach, J, Gunstad, J, Azcarate Peril, MA. The gut microbiome, mild cognitive impairment, and probiotics: a randomized clinical trial in middle-aged and older adults. Clin Nutr 2022;41:2565\u201376. https:\/\/doi.org\/10.1016\/j.clnu.2022.09.012.","DOI":"10.1016\/j.clnu.2022.09.012"},{"key":"2026083102570591236_j_mr-2026-0009_ref_251","doi-asserted-by":"crossref","unstructured":"Hu, Y, Feng, Y, Wu, J, Liu, F, Zhang, Z, Hao, Y, et al.. The gut microbiome signatures discriminate healthy from pulmonary tuberculosis patients. Front Cell Infect Microbiol 2019;9:90. https:\/\/doi.org\/10.3389\/fcimb.2019.00090.","DOI":"10.3389\/fcimb.2019.00090"},{"key":"2026083102570591236_j_mr-2026-0009_ref_252","doi-asserted-by":"crossref","unstructured":"Li, W, Zhu, Y, Liao, Q, Wang, Z, Wan, C. Characterization of gut microbiota in children with pulmonary tuberculosis. BMC Pediatr 2019;19:445. https:\/\/doi.org\/10.1186\/s12887-019-1782-2.","DOI":"10.1186\/s12887-019-1782-2"},{"key":"2026083102570591236_j_mr-2026-0009_ref_253","doi-asserted-by":"crossref","unstructured":"Vijay-Kumar, M, Bovilla, VR, Yeoh, BS, Golonka, RM, Saha, P, Joe, B, et al.. Bacterial flagellin is a dominant, stable innate immune activator in the gastrointestinal contents of mice and rats. Gut Microbes 2023;15:2185031. https:\/\/doi.org\/10.1080\/19490976.2023.2185031.","DOI":"10.1080\/19490976.2023.2185031"},{"key":"2026083102570591236_j_mr-2026-0009_ref_254","doi-asserted-by":"crossref","unstructured":"Knapp, S. Gut to lung. Gut 2016;65:544\u20135. https:\/\/doi.org\/10.1136\/gutjnl-2015-310599.","DOI":"10.1136\/gutjnl-2015-310599"},{"key":"2026083102570591236_j_mr-2026-0009_ref_255","doi-asserted-by":"crossref","unstructured":"Gauguet, S, D\u2019Ortona, S, Ahnger-Pier, K, Duan, B, Surana, NK, Lu, R, et al.. Intestinal microbiota of mice influences resistance to Staphylococcus aureus pneumonia. Infect Immun 2015;83:4003\u201314. https:\/\/doi.org\/10.1128\/iai.00037-15.","DOI":"10.1128\/IAI.00037-15"},{"key":"2026083102570591236_j_mr-2026-0009_ref_256","doi-asserted-by":"crossref","unstructured":"Mishra, SP, Wang, B, Jain, S, Ding, J, Rejeski, J, Furdui, CM, et al.. A mechanism by which gut microbiota elevates permeability and inflammation in obese\/diabetic mice and human gut. Gut 2023;72:1848\u201365. https:\/\/doi.org\/10.1136\/gutjnl-2022-327365.","DOI":"10.1136\/gutjnl-2022-327365"},{"key":"2026083102570591236_j_mr-2026-0009_ref_257","doi-asserted-by":"crossref","unstructured":"Takeuchi, T, Kameyama, K, Miyauchi, E, Nakanishi, Y, Kanaya, T, Fujii, T, et al.. Fatty acid overproduction by gut commensal microbiota exacerbates obesity. Cell Metab 2023;35:361\u201375.e9. https:\/\/doi.org\/10.1016\/j.cmet.2022.12.013.","DOI":"10.1016\/j.cmet.2022.12.013"},{"key":"2026083102570591236_j_mr-2026-0009_ref_258","doi-asserted-by":"crossref","unstructured":"Grasset, E, Puel, A, Charpentier, J, Collet, X, Christensen, JE, Terc\u00e9, F, et al.. A specific gut microbiota dysbiosis of type 2 diabetic mice induces GLP-1 resistance through an enteric NO-dependent and gut-brain axis mechanism. Cell Metab 2017;25:1075\u201390.e5. https:\/\/doi.org\/10.1016\/j.cmet.2017.04.013.","DOI":"10.1016\/j.cmet.2017.04.013"},{"key":"2026083102570591236_j_mr-2026-0009_ref_259","doi-asserted-by":"crossref","unstructured":"Qin, J, Li, Y, Cai, Z, Li, S, Zhu, J, Zhang, F, et al.. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 2012;490:55\u201360. https:\/\/doi.org\/10.1038\/nature11450.","DOI":"10.1038\/nature11450"},{"key":"2026083102570591236_j_mr-2026-0009_ref_260","doi-asserted-by":"crossref","unstructured":"Karlsson, FH, Tremaroli, V, Nookaew, I, Bergstr\u00f6m, G, Behre, CJ, Fagerberg, B, et al.. Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 2013;498:99\u2013103. https:\/\/doi.org\/10.1038\/nature12198.","DOI":"10.1038\/nature12198"},{"key":"2026083102570591236_j_mr-2026-0009_ref_261","doi-asserted-by":"crossref","unstructured":"Molinaro, A, Bel Lassen, P, Henricsson, M, Wu, H, Adriouch, S, Belda, E, et al.. Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology. Nat Commun 2020;11:5881. https:\/\/doi.org\/10.1038\/s41467-020-19589-w.","DOI":"10.1038\/s41467-020-20412-9"},{"key":"2026083102570591236_j_mr-2026-0009_ref_262","doi-asserted-by":"crossref","unstructured":"Shin, NR, Lee, JC, Lee, HY, Kim, MS, Whon, TW, Lee, MS, et al.. An increase in theAkkermansiaspp. population induced by metformin treatment improves glucose homeostasis in diet-induced obese mice. Gut 2014;63:727\u201335. https:\/\/doi.org\/10.1136\/gutjnl-2012-303839.","DOI":"10.1136\/gutjnl-2012-303839"},{"key":"2026083102570591236_j_mr-2026-0009_ref_263","doi-asserted-by":"crossref","unstructured":"Wrzosek, L, Ciocan, D, Hugot, C, Spatz, M, Dupeux, M, Houron, C, et al.. Microbiota tryptophan metabolism induces aryl hydrocarbon receptor activation and improves alcohol-induced liver injury. Gut 2021;70:1299\u2013308. https:\/\/doi.org\/10.1136\/gutjnl-2020-321565.","DOI":"10.1136\/gutjnl-2020-321565"},{"key":"2026083102570591236_j_mr-2026-0009_ref_265","doi-asserted-by":"crossref","unstructured":"Zhou, X, Chakraborty, D, Murray, IA, Coslo, D, Kehs, Z, Vijay, A, et al.. Aryl hydrocarbon receptor activation coordinates mouse small intestinal epithelial cell programming. Lab Invest 2023;103:100012. https:\/\/doi.org\/10.1016\/j.labinv.2022.100012.","DOI":"10.1016\/j.labinv.2022.100012"},{"key":"2026083102570591236_j_mr-2026-0009_ref_266","doi-asserted-by":"crossref","unstructured":"Hu, XL, Xiao, W, Lei, Y, Green, A, Lee, X, Maradana, MR, et al.. Aryl hydrocarbon receptor utilises cellular zinc signals to maintain the gut epithelial barrier. Nat Commun 2023;14:5431. https:\/\/doi.org\/10.1038\/s41467-023-41168-y.","DOI":"10.1038\/s41467-023-41168-y"},{"key":"2026083102570591236_j_mr-2026-0009_ref_267","doi-asserted-by":"crossref","unstructured":"Singh, R, Chandrashekharappa, S, Bodduluri, SR, Baby, BV, Hegde, B, Kotla, NG, et al.. Enhancement of the gut barrier integrity by a microbial\u00a0metabolite through the Nrf2 pathway. 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