{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T04:05:49Z","timestamp":1793505949833,"version":"4.5.0"},"reference-count":63,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T00:00:00Z","timestamp":1755129600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T00:00:00Z","timestamp":1755129600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Commun Biol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Inflammatory bowel disease (IBD) remains a global health challenge linked to intestinal barrier disruption, microbiota dysbiosis, and immune dysregulation, though the interplay of these mechanisms remains poorly defined. Here, we investigated the therapeutic potential of\n                    <jats:italic>Lactobacillus johnsonii<\/jats:italic>\n                    N5 in a murine dextran sulfate sodium (DSS)-induced colitis model. Prophylactic N5 administration alleviated colitis symptoms (weight loss, colon shortening), reduced fecal and serum lipocalin-2 levels, and suppressed colonic pro-inflammatory cytokines (IL-1\u03b2, IL-6). N5 preserved microbial diversity, enhanced mucus secretion, and reinforced mucosal barrier integrity, preventing colitis onset. Therapeutically, N5 attenuated disease progression by downregulating IL-1\u03b2, IL-6, IL-8 expression, restoring\n                    <jats:italic>Lactobacillus<\/jats:italic>\n                    populations, and suppressing\n                    <jats:italic>Escherichia-Shigella<\/jats:italic>\n                    expansion, thereby reducing bacterial translocation and systemic inflammation. N5 promoted Ki67\n                    <jats:sup>+<\/jats:sup>\n                    epithelial proliferation, accelerating mucosal repair. Mechanistically, N5 targeted neutrophil-mediated gut-liver injury, suppressing coagulation pathways in colon-liver transcriptomes, reducing hepatic lesions, platelet aggregation, CD162\n                    <jats:sup>+<\/jats:sup>\n                    neutrophil recruitment, and H3cit\n                    <jats:sup>+<\/jats:sup>\n                    neutrophil extracellular trap (NET) formation. N5\u2019s effects were partially recapitulated by DNase I in vivo and\/or by its metabolites in vitro, suggesting its action involves metabolite-driven NET inhibition alongside DNase-like NET clearance. These findings illuminate N5\u2019s dual role in IBD-prophylactic barrier fortification and therapeutic resolution of neutrophilic inflammation, and highlight its potential as a multifaceted probiotic therapy.\n                  <\/jats:p>","DOI":"10.1038\/s42003-025-08679-4","type":"journal-article","created":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T14:56:06Z","timestamp":1755183366000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Lactobacillus johnsonii alleviates experimental colitis by restoring intestinal barrier function and reducing NET-mediated gut-liver inflammation"],"prefix":"10.1038","volume":"8","author":[{"given":"Hao-Yu","family":"Liu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shicheng","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kennedy Jerry","family":"Ogamune","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinyu","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cuipeng","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wael","family":"Ennab","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ping","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abdelkareem A.","family":"Ahmed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunzeng","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"In Ho","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0500-5292","authenticated-orcid":false,"given":"Demin","family":"Cai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,8,14]]},"reference":[{"key":"8679_CR1","doi-asserted-by":"publisher","first-page":"571","DOI":"10.1016\/S0140-6736(23)00966-2","volume":"402","author":"C Le Berre","year":"2023","unstructured":"Le Berre, C., Honap, S. & Peyrin-Biroulet, L. Ulcerative colitis. Lancet 402, 571\u2013584 (2023).","journal-title":"Lancet"},{"key":"8679_CR2","doi-asserted-by":"publisher","first-page":"992","DOI":"10.1016\/j.immuni.2019.03.017","volume":"50","author":"M Friedrich","year":"2019","unstructured":"Friedrich, M., Pohin, M. & Powrie, F. Cytokine networks in the pathophysiology of inflammatory bowel disease. Immunity 50, 992\u20131006 (2019).","journal-title":"Immunity"},{"key":"8679_CR3","doi-asserted-by":"publisher","first-page":"1970","DOI":"10.1038\/s41591-021-01520-5","volume":"27","author":"M Friedrich","year":"2021","unstructured":"Friedrich, M. et al. IL-1-driven stromal-neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies. Nat. Med. 27, 1970\u20131981 (2021).","journal-title":"Nat. Med."},{"key":"8679_CR4","doi-asserted-by":"publisher","first-page":"103062","DOI":"10.1016\/j.jaut.2023.103062","volume":"141","author":"R Wu","year":"2023","unstructured":"Wu, R., Xiong, R., Li, Y., Chen, J. & Yan, R. Gut microbiome, metabolome, host immunity associated with inflammatory bowel disease and intervention of fecal microbiota transplantation. J. Autoimmun. 141, 103062 (2023).","journal-title":"J. Autoimmun."},{"key":"8679_CR5","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1111\/apha.12695","volume":"217","author":"D Ahl","year":"2016","unstructured":"Ahl, D. et al. Lactobacillus reuteri increases mucus thickness and ameliorates dextran sulphate sodium-induced colitis in mice. Acta Physiol.217, 300\u2013310 (2016).","journal-title":"Acta Physiol."},{"key":"8679_CR6","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.865982","volume":"13","author":"HY Liu","year":"2022","unstructured":"Liu, H. Y. et al. Epithelial heat shock proteins mediate the protective effects of Limosilactobacillus reuteri in dextran sulfate sodium-induced colitis. Front. Immunol. 13, 865982 (2022).","journal-title":"Front. Immunol."},{"key":"8679_CR7","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1053\/j.gastro.2020.09.056","volume":"160","author":"M Lee","year":"2021","unstructured":"Lee, M. & Chang, E. B. Inflammatory bowel diseases (IBD) and the microbiome\u2014searching the crime scene for clues. Gastroenterology 160, 524\u2013537 (2021).","journal-title":"Gastroenterology"},{"key":"8679_CR8","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1080\/19490976.2019.1662712","volume":"11","author":"W Panpetch","year":"2020","unstructured":"Panpetch, W. et al. Additional Candida albicans administration enhances the severity of dextran sulfate solution induced colitis mouse model through leaky gut-enhanced systemic inflammation and gut-dysbiosis but attenuated by Lactobacillus rhamnosus L34. Gut Microbes 11, 465\u2013480 (2020).","journal-title":"Gut Microbes"},{"key":"8679_CR9","doi-asserted-by":"publisher","first-page":"1620","DOI":"10.1053\/j.gastro.2004.03.024","volume":"126","author":"RB Sartor","year":"2004","unstructured":"Sartor, R. B. Therapeutic manipulation of the enteric microflora in inflammatory bowel diseases: antibiotics, probiotics, and prebiotics. Gastroenterology 126, 1620\u20131633 (2004).","journal-title":"Gastroenterology"},{"key":"8679_CR10","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1016\/j.exphem.2019.11.008","volume":"80","author":"CRC Zhang","year":"2019","unstructured":"Zhang, C. R. C. et al. Inflammatory cytokines promote clonal hematopoiesis with specific mutations in ulcerative colitis patients. Exp. Hematol. 80, 36\u201341.e33 (2019).","journal-title":"Exp. Hematol."},{"key":"8679_CR11","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1093\/ecco-jcc\/jjz132","volume":"14","author":"T Li","year":"2020","unstructured":"Li, T. et al. Neutrophil extracellular traps induce intestinal damage and thrombotic tendency in inflammatory bowel disease. J. Crohns Colitis 14, 240\u2013253 (2020).","journal-title":"J. Crohns Colitis"},{"key":"8679_CR12","doi-asserted-by":"publisher","first-page":"3.20.21","DOI":"10.1002\/0471142735.im0320s110","volume":"110","author":"M Swamydas","year":"2015","unstructured":"Swamydas, M., Luo, Y., Dorf, M. E. & Lionakis, M. S. Isolation of mouse neutrophils. Curr. Protoc. Immunol. 110, 3.20.21\u201323.20.15 (2015).","journal-title":"Curr. Protoc. Immunol."},{"key":"8679_CR13","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1016\/j.jcmgh.2021.03.002","volume":"12","author":"B Drury","year":"2021","unstructured":"Drury, B., Hardisty, G., Gray, R. D. & Ho, G. T. Neutrophil extracellular traps in inflammatory bowel disease: pathogenic mechanisms and clinical translation. Cell Mol. Gastroenterol. Hepatol. 12, 321\u2013333 (2021).","journal-title":"Cell Mol. Gastroenterol. Hepatol."},{"key":"8679_CR14","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2021.1968257","volume":"13","author":"G Li","year":"2021","unstructured":"Li, G. et al. Microbiota metabolite butyrate constrains neutrophil functions and ameliorates mucosal inflammation in inflammatory bowel disease. Gut Microbes 13, 1968257 (2021).","journal-title":"Gut Microbes"},{"key":"8679_CR15","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1042\/cs1010395","volume":"101","author":"K Leiper","year":"2001","unstructured":"Leiper, K. et al. Interaction between bacterial peptides, neutrophils and goblet cells: a possible mechanism for neutrophil recruitment and goblet cell depletion in colitis. Clin. Sci.101, 395\u2013402 (2001).","journal-title":"Clin. Sci."},{"key":"8679_CR16","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1111\/1751-2980.12540","volume":"18","author":"GX Zhou","year":"2017","unstructured":"Zhou, G. X. & Liu, Z. J. Potential roles of neutrophils in regulating intestinal mucosal inflammation of inflammatory bowel disease. J. Dig. Dis. 18, 495\u2013503 (2017).","journal-title":"J. Dig. Dis."},{"key":"8679_CR17","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1038\/nrgastro.2017.183","volume":"15","author":"M Honda","year":"2018","unstructured":"Honda, M. & Kubes, P. Neutrophils and neutrophil extracellular traps in the liver and gastrointestinal system. Nat. Rev. Gastroenterol. Hepatol. 15, 206\u2013221 (2018).","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"8679_CR18","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms7673","volume":"6","author":"E Kolaczkowska","year":"2015","unstructured":"Kolaczkowska, E. et al. Molecular mechanisms of NET formation and degradation revealed by intravital imaging in the liver vasculature. Nat. Commun. 6, 6673 (2015).","journal-title":"Nat. Commun."},{"key":"8679_CR19","doi-asserted-by":"publisher","first-page":"275","DOI":"10.3390\/biomedicines8080275","volume":"8","author":"EY Lin","year":"2020","unstructured":"Lin, E. Y. et al. Neutrophil extracellular traps impair intestinal barrier function during experimental colitis. Biomedicines 8, 275 (2020).","journal-title":"Biomedicines"},{"key":"8679_CR20","doi-asserted-by":"publisher","DOI":"10.1002\/advs.202300560","volume":"10","author":"L Zhang","year":"2023","unstructured":"Zhang, L. et al. Exosomes-transferred LINC00668 contributes to thrombosis by promoting nets formation in inflammatory bowel disease. Adv. Sci.10, e2300560 (2023).","journal-title":"Adv. Sci."},{"key":"8679_CR21","first-page":"130","volume":"994","author":"M Cao","year":"2017","unstructured":"Cao, M. et al. Neutrophil extracellular traps exacerbate inflammatory responses and thrombotic tendency in both a murine colitis model and patients with inflammatory bowel disease. Blood 994, 130 (2017).","journal-title":"Blood"},{"key":"8679_CR22","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/ecco-jcc\/jjy215","volume":"13","author":"V Dinallo","year":"2019","unstructured":"Dinallo, V. et al. Neutrophil extracellular traps sustain inflammatory signals in ulcerative colitis. J. Crohns Colitis 13, 772\u2013784 (2019).","journal-title":"J. Crohns Colitis"},{"key":"8679_CR23","doi-asserted-by":"publisher","first-page":"2052","DOI":"10.1097\/MIB.0000000000000460","volume":"21","author":"TB Bennike","year":"2015","unstructured":"Bennike, T. B. et al. Neutrophil extracellular traps in ulcerative colitis: a proteome analysis of intestinal biopsies. Inflamm. Bowel Dis. 21, 2052\u20132067 (2015).","journal-title":"Inflamm. Bowel Dis."},{"key":"8679_CR24","doi-asserted-by":"publisher","first-page":"976","DOI":"10.1128\/IAI.01389-15","volume":"84","author":"JK Crane","year":"2016","unstructured":"Crane, J. K., Broome, J. E. & Lis, A. Biological activities of uric acid in infection due to enteropathogenic and Shiga-toxigenic Escherichia coli. Infect. Immun. 84, 976\u2013988 (2016).","journal-title":"Infect. Immun."},{"key":"8679_CR25","doi-asserted-by":"publisher","first-page":"G181","DOI":"10.1152\/ajpgi.00053.2015","volume":"309","author":"L Vong","year":"2015","unstructured":"Vong, L. et al. Selective enrichment of commensal gut bacteria protects against Citrobacter rodentium-induced colitis. Am. J. Physiol. Gastrointest. Liver Physiol. 309, G181\u2013G192 (2015).","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol."},{"key":"8679_CR26","doi-asserted-by":"publisher","first-page":"1870","DOI":"10.4049\/jimmunol.1302286","volume":"192","author":"L Vong","year":"2014","unstructured":"Vong, L., Lorentz, R. J., Assa, A., Glogauer, M. & Sherman, P. M. Probiotic Lactobacillus rhamnosus inhibits the formation of neutrophil extracellular traps. J. Immunol. 192, 1870\u20131877 (2014).","journal-title":"J. Immunol."},{"key":"8679_CR27","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1038\/nrgastro.2014.66","volume":"11","author":"C Hill","year":"2014","unstructured":"Hill, C. et al. Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat. Rev. Gastroenterol. Hepatol. 11, 506\u2013514 (2014).","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"8679_CR28","doi-asserted-by":"publisher","first-page":"757","DOI":"10.3389\/fmicb.2018.00757","volume":"19","author":"Q Mu","year":"2018","unstructured":"Mu, Q., Tavella, V. J. & Luo, X. M. Role of Lactobacillus reuteri in human health and diseases. Front. Microbiol. 19, 757 (2018).","journal-title":"Front. Microbiol."},{"key":"8679_CR29","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-021-01128-4","volume":"9","author":"HY Liu","year":"2021","unstructured":"Liu, H. Y. et al. Distinct B cell subsets in Peyer\u2019s patches convey probiotic effects by Limosilactobacillus reuteri. Microbiome 9, 198 (2021).","journal-title":"Microbiome"},{"key":"8679_CR30","doi-asserted-by":"publisher","DOI":"10.1016\/j.lfs.2022.121309","volume":"314","author":"C Lin","year":"2023","unstructured":"Lin, C. et al. Differential reinforcement of intestinal barrier function by various Lactobacillus reuteri strains in mice with DSS-induced acute colitis. Life Sci. 314, 121309 (2023).","journal-title":"Life Sci."},{"key":"8679_CR31","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1016\/j.aninu.2023.04.012","volume":"15","author":"L Yuan","year":"2023","unstructured":"Yuan, L. et al. Lactobacillus johnsonii N5 from heat stress-resistant pigs improves gut mucosal immunity and barrier in dextran sodium sulfate-induced colitis. Anim. Nutr. 15, 210\u2013224 (2023).","journal-title":"Anim. Nutr."},{"key":"8679_CR32","doi-asserted-by":"publisher","first-page":"433","DOI":"10.3390\/antiox14040433","volume":"14","author":"HY Liu","year":"2025","unstructured":"Liu, H. Y. et al. Probiotic Lactobacillus johnsonii reduces intestinal inflammation and rebalances splenic Treg\/Th17 responses in dextran sulfate sodium-induced colitis. Antioxidants14, 433 (2025).","journal-title":"Antioxidants"},{"key":"8679_CR33","doi-asserted-by":"publisher","first-page":"2298","DOI":"10.3390\/nu12082298","volume":"12","author":"G Wang","year":"2020","unstructured":"Wang, G. et al. Lactobacillus reuteri Ameliorates intestinal inflammation and modulates gut microbiota and metabolic disorders in dextran sulfate sodium-induced colitis in Mice. Nutrients 12, 2298 (2020).","journal-title":"Nutrients"},{"key":"8679_CR34","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1016\/0016-5085(94)90124-4","volume":"107","author":"CM Surawicz","year":"1994","unstructured":"Surawicz, C. M., Haggitt, R. C., Husseman, M. & McFarland, L. V. Mucosal biopsy diagnosis of colitis: acute self-limited colitis and idiopathic inflammatory bowel disease. Gastroenterology 107, 755\u2013763 (1994).","journal-title":"Gastroenterology"},{"key":"8679_CR35","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.adi1501","volume":"16","author":"M Czech","year":"2024","unstructured":"Czech, M. et al. Lipocalin-2 expression identifies an intestinal regulatory neutrophil population during acute graft-versus-host disease. Sci. Transl. Med. 16, eadi1501 (2024).","journal-title":"Sci. Transl. Med."},{"key":"8679_CR36","first-page":"2327","volume":"21","author":"J Stallhofer","year":"2015","unstructured":"Stallhofer, J. et al. Lipocalin-2 is a disease activity marker in inflammatory bowel disease regulated by IL-17A, IL-22, and TNF-\u03b1 and modulated by IL23R genotype status. Inflamm. Bowel Dis. 21, 2327\u20132340 (2015).","journal-title":"Inflamm. Bowel Dis."},{"key":"8679_CR37","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1038\/s41564-022-01094-z","volume":"7","author":"SC Forster","year":"2022","unstructured":"Forster, S. C. et al. Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis. Nat. Microbiol. 7, 590\u2013599 (2022).","journal-title":"Nat. Microbiol."},{"key":"8679_CR38","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-022-01347-3","volume":"10","author":"J Yang","year":"2022","unstructured":"Yang, J. et al. RhoB affects colitis through modulating cell signaling and intestinal microbiome. Microbiome 10, 149 (2022).","journal-title":"Microbiome"},{"key":"8679_CR39","doi-asserted-by":"publisher","first-page":"e1009476","DOI":"10.1371\/journal.ppat.1009476","volume":"17","author":"N Parmar","year":"2021","unstructured":"Parmar, N. et al. Intestinal-epithelial LSD1 controls goblet cell maturation and effector responses required for gut immunity to bacterial and helminth infection. PLoS Pathog. 17, e1009476 (2021).","journal-title":"PLoS Pathog."},{"key":"8679_CR40","doi-asserted-by":"publisher","first-page":"2186","DOI":"10.1182\/blood-2018-10-862243","volume":"133","author":"DF Noubouossie","year":"2019","unstructured":"Noubouossie, D. F., Reeves, B. N., Strahl, B. D. & Key, N. S. Neutrophils: back in the thrombosis spotlight. Blood 133, 2186\u20132197 (2019).","journal-title":"Blood"},{"key":"8679_CR41","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.141217","volume":"5","author":"Y Weng","year":"2020","unstructured":"Weng, Y. et al. Liver epithelial focal adhesion kinase modulates fibrogenesis and hedgehog signaling. JCI Insight 5, e141217 (2020).","journal-title":"JCI Insight"},{"key":"8679_CR42","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/s40580-024-00414-9","volume":"11","author":"CJ Wang","year":"2024","unstructured":"Wang, C. J. et al. Polymeric DNase-I nanozymes targeting neutrophil extracellular traps for the treatment of bowel inflammation. Nano Converg. 11, 6 (2024).","journal-title":"Nano Converg."},{"key":"8679_CR43","doi-asserted-by":"publisher","DOI":"10.1016\/j.nmni.2025.101567","volume":"64","author":"A Ahmadi","year":"2025","unstructured":"Ahmadi, A. et al. Comparative analysis of dominant gut microbiota in Inflammatory Bowel Disease patients and healthy individuals: a case-control study. N. Microbes N. Infect. 64, 101567 (2025).","journal-title":"N. Microbes N. Infect."},{"key":"8679_CR44","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1038\/s41420-023-01666-w","volume":"9","author":"C Li","year":"2023","unstructured":"Li, C., Peng, K., Xiao, S., Long, Y. & Yu, Q. The role of Lactobacillus in inflammatory bowel disease: from actualities to prospects. Cell Death Discov. 9, 361 (2023).","journal-title":"Cell Death Discov."},{"key":"8679_CR45","doi-asserted-by":"publisher","first-page":"2142","DOI":"10.1136\/gutjnl-2018-317571","volume":"68","author":"S van der Post","year":"2019","unstructured":"van der Post, S. et al. Structural weakening of the colonic mucus barrier is an early event in ulcerative colitis pathogenesis. Gut Microbes 68, 2142\u20132151 (2019).","journal-title":"Gut Microbes"},{"key":"8679_CR46","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1136\/gutjnl-2012-303207","volume":"63","author":"ME Johansson","year":"2014","unstructured":"Johansson, M. E. et al. Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis. Gut Microbes 63, 281\u2013291 (2014).","journal-title":"Gut Microbes"},{"key":"8679_CR47","doi-asserted-by":"publisher","DOI":"10.1126\/sciimmunol.aaw4341","volume":"4","author":"R Caruso","year":"2019","unstructured":"Caruso, R. et al. A specific gene-microbe interaction drives the development of Crohn\u2019s disease-like colitis in mice. Sci. Immunol. 4, eaaw4341 (2019).","journal-title":"Sci. Immunol."},{"key":"8679_CR48","doi-asserted-by":"publisher","first-page":"738","DOI":"10.1160\/TH15-09-0710","volume":"115","author":"Z He","year":"2016","unstructured":"He, Z. et al. Phosphotidylserine exposure and neutrophil extracellular traps enhance procoagulant activity in patients with inflammatory bowel disease. Thromb. Haemost. 115, 738\u2013751 (2016).","journal-title":"Thromb. Haemost."},{"key":"8679_CR49","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1111\/pin.12715","volume":"68","author":"Y Gottlieb","year":"2018","unstructured":"Gottlieb, Y. et al. Neutrophil extracellular traps in pediatric inflammatory bowel disease. Pathol. Int 68, 517\u2013523 (2018).","journal-title":"Pathol. Int"},{"key":"8679_CR50","doi-asserted-by":"publisher","first-page":"672","DOI":"10.3390\/microorganisms12040672","volume":"12","author":"K Wang","year":"2024","unstructured":"Wang, K. et al. Characterization of Probiotic Properties and Whole-Genome Analysis of Lactobacillus johnsonii N5 and N7 Isolated from Swine. Microorganisms 12, 672 (2024).","journal-title":"Microorganisms"},{"key":"8679_CR51","doi-asserted-by":"crossref","unstructured":"Sumby, P. et al. Extracellular deoxyribonuclease made by group A Streptococcus assists pathogenesis by enhancing evasion of the innate immune response. Proc. Natl Acad. Sci. 102, 1679\u20131684 (2005).","DOI":"10.1073\/pnas.0406641102"},{"key":"8679_CR52","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-58933-8","volume":"14","author":"X Gu","year":"2024","unstructured":"Gu, X. et al. The antioxidant activity and metabolomic analysis of the supernatant of Streptococcus alactolyticus strain FGM. Sci. Rep. 14, 8413 (2024).","journal-title":"Sci. Rep."},{"key":"8679_CR53","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1097\/MIB.0000000000000591","volume":"22","author":"L Vong","year":"2016","unstructured":"Vong, L., Yeung, C. W., Pinnell, L. J. & Sherman, P. M. Adherent-invasive Escherichia coli exacerbates antibiotic-associated intestinal dysbiosis and neutrophil extracellular trap activation. Inflamm. Bowel Dis. 22, 42\u201354 (2016).","journal-title":"Inflamm. Bowel Dis."},{"key":"8679_CR54","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-55015-1","volume":"15","author":"J Kim","year":"2024","unstructured":"Kim, J. et al. A microbiota-derived metabolite, 3-phenyllactic acid, prolongs healthspan by enhancing mitochondrial function and stress resilience via SKN-1\/ATFS-1 in C. elegans. Nat. Commun. 15, 10773 (2024).","journal-title":"Nat. Commun."},{"key":"8679_CR55","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1053\/j.gastro.2011.04.007","volume":"141","author":"I Monteleone","year":"2011","unstructured":"Monteleone, I. et al. Aryl hydrocarbon receptor-induced signals up-regulate IL-22 production and inhibit inflammation in the gastrointestinal tract. Gastroenterology 141, 237\u2013248 (2011). 248.e231.","journal-title":"Gastroenterology"},{"key":"8679_CR56","doi-asserted-by":"publisher","first-page":"1639","DOI":"10.1111\/jam.13459","volume":"122","author":"NJ Nealon","year":"2017","unstructured":"Nealon, N. J., Worcester, C. R. & Ryan, E. P. Lactobacillus paracasei metabolism of rice bran reveals metabolome associated with Salmonella Typhimurium growth reduction. J. Appl. Microbiol. 122, 1639\u20131656 (2017).","journal-title":"J. Appl. Microbiol."},{"key":"8679_CR57","doi-asserted-by":"publisher","first-page":"640","DOI":"10.1021\/pr4007624","volume":"13","author":"CR Evans","year":"2014","unstructured":"Evans, C. R. et al. Untargeted LC-MS metabolomics of bronchoalveolar lavage fluid differentiates acute respiratory distress syndrome from health. J. Proteome Res. 13, 640\u2013649 (2014).","journal-title":"J. Proteome Res."},{"key":"8679_CR58","doi-asserted-by":"publisher","first-page":"918","DOI":"10.1038\/nbt.2377","volume":"30","author":"MC Chambers","year":"2012","unstructured":"Chambers, M. C. et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 30, 918\u2013920 (2012).","journal-title":"Nat. Biotechnol."},{"key":"8679_CR59","doi-asserted-by":"publisher","first-page":"e0116955","DOI":"10.1371\/journal.pone.0116955","volume":"10","author":"L Sinclair","year":"2015","unstructured":"Sinclair, L., Osman, O. A., Bertilsson, S. & Eiler, A. Microbial community composition and diversity via 16S rRNA gene amplicons: evaluating the illumina platform. PLoS One 10, e0116955 (2015).","journal-title":"PLoS One"},{"key":"8679_CR60","doi-asserted-by":"publisher","first-page":"6275","DOI":"10.4238\/2013.December.4.15","volume":"12","author":"W He","year":"2013","unstructured":"He, W. et al. ReSeqTools: an integrated toolkit for large-scale next-generation sequencing based resequencing analysis. Genet. Mol. Res. 12, 6275\u20136283 (2013).","journal-title":"Genet. Mol. Res."},{"key":"8679_CR61","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1038\/nmeth.2604","volume":"10","author":"RC Edgar","year":"2013","unstructured":"Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996\u2013998 (2013).","journal-title":"Nat. Methods"},{"key":"8679_CR62","first-page":"555630","volume":"30","author":"M Thapa","year":"2023","unstructured":"Thapa, M. et al. Translocation of gut commensal bacteria to the brain. bioRxiv 30, 555630 (2023).","journal-title":"bioRxiv"},{"key":"8679_CR63","doi-asserted-by":"crossref","unstructured":"Anderson, M. J. Permutational multivariate analysis of variance (PERMANOVA). In Wiley StatsRef: statistics reference online, 1\u201315 (Wiley, 2017).","DOI":"10.1002\/9781118445112.stat07841"}],"container-title":["Communications Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-08679-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-08679-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-08679-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,9]],"date-time":"2025-09-09T05:08:44Z","timestamp":1757394524000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-08679-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,14]]},"references-count":63,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["8679"],"URL":"https:\/\/doi.org\/10.1038\/s42003-025-08679-4","relation":{},"ISSN":["2399-3642"],"issn-type":[{"value":"2399-3642","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,8,14]]},"assertion":[{"value":"14 November 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 August 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 August 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"1222"}}