{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T05:00:32Z","timestamp":1790312432829,"version":"4.1.0"},"reference-count":67,"publisher":"Elsevier BV","issue":"6","license":[{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T00:00:00Z","timestamp":1778630400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006338","name":"Flemish Interuniversity Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006338","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007601","name":"Horizon 2020","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014989","name":"The Chan Zuckerberg Initiative","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014989","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013326","name":"Universitaire Stichting","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013326","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003761","name":"Universitair Medisch Centrum Utrecht","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003761","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100018707","name":"European Commission Reforming and enhancing the European Research and Innovation system","doi-asserted-by":"publisher","award":["851752-CELLULO-EPI"],"award-info":[{"award-number":["851752-CELLULO-EPI"]}],"id":[{"id":"10.13039\/100018707","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003130","name":"Research Foundation Flanders","doi-asserted-by":"publisher","award":["G0C9620N"],"award-info":[{"award-number":["G0C9620N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003130","name":"Research Foundation Flanders","doi-asserted-by":"publisher","award":["G031222N"],"award-info":[{"award-number":["G031222N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003130","name":"Research Foundation Flanders","doi-asserted-by":"publisher","award":["1861219N"],"award-info":[{"award-number":["1861219N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003130","name":"Research Foundation Flanders","doi-asserted-by":"publisher","award":["1SH3924N"],"award-info":[{"award-number":["1SH3924N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001826","name":"ZonMw","doi-asserted-by":"publisher","award":["09150182010023"],"award-info":[{"award-number":["09150182010023"]}],"id":[{"id":"10.13039\/501100001826","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports"],"published-print":{"date-parts":[[2026,6]]},"DOI":"10.1016\/j.celrep.2026.117479","type":"journal-article","created":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T00:46:02Z","timestamp":1780101962000},"page":"117479","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["AIRRWAS integrates TCR-microbiome data to reveal how the gut microbiome shapes the circulating and mucosal T cell repertoire"],"prefix":"10.1016","volume":"45","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2694-5251","authenticated-orcid":false,"given":"Romi","family":"Vandoren","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"My","family":"Ha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincent M.L.","family":"Van Deuren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naomi","family":"De Roeck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting","family":"Pu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eelco C.","family":"Brand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Kuznetsova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hajar","family":"Besbassi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esther","family":"Bartholomeus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabio","family":"Affaticati","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilke","family":"De Boeck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thies","family":"Gehrmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Lebeer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bas","family":"Oldenburg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Femke","family":"van Wijk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Delputte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Verbandt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabine","family":"Tejpar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kris","family":"Laukens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benson","family":"Ogunjimi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pieter","family":"Meysman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.celrep.2026.117479_bib1","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1016\/j.immuni.2017.04.008","article-title":"Homeostatic Immunity and the Microbiota","volume":"46","author":"Belkaid","year":"2017","journal-title":"Immunity"},{"key":"10.1016\/j.celrep.2026.117479_bib2","first-page":"781","article-title":"Intestinal mucosal tolerance and impact of gut microbiota to mucosal tolerance","volume":"5","author":"Chistiakov","year":"2014","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.celrep.2026.117479_bib3","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1038\/s41385-022-00539-2","article-title":"Long-distance relationships - regulation of systemic host defense against infections by the gut microbiota","volume":"15","author":"Schlechte","year":"2022","journal-title":"Mucosal Immunol."},{"key":"10.1016\/j.celrep.2026.117479_bib4","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/s41392-024-02043-4","article-title":"Mucosal immune response in biology, disease prevention and treatment","volume":"10","author":"Zhou","year":"2025","journal-title":"Signal Transduct. Target. Ther."},{"key":"10.1016\/j.celrep.2026.117479_bib5","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1186\/s12967-025-06433-2","article-title":"The intricate interplay among microbiota, mucosal immunity, and viral infection in the respiratory tract","volume":"23","author":"Li","year":"2025","journal-title":"J. Transl. Med."},{"key":"10.1016\/j.celrep.2026.117479_bib6","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1038\/s41585-020-0350-8","article-title":"The immune response to infection in the bladder","volume":"17","author":"Lacerda Mariano","year":"2020","journal-title":"Nat. Rev. Urol."},{"key":"10.1016\/j.celrep.2026.117479_bib7","doi-asserted-by":"crossref","DOI":"10.37349\/etat.2025.1002329","article-title":"Dysbiosis and colorectal cancer: conducive factors, biological and molecular role, and therapeutic prospectives","volume":"6","author":"Singh","year":"2025","journal-title":"Explor Target Antitumor Ther."},{"key":"10.1016\/j.celrep.2026.117479_bib8","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2020.615056","article-title":"The Intestinal Microbiota and Colorectal Cancer","volume":"11","author":"Cheng","year":"2020","journal-title":"Front. Immunol."},{"key":"10.1016\/j.celrep.2026.117479_bib9","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.7150\/ijbs.79430","article-title":"The role of gut microbiota in T cell immunity and immune mediated disorders","volume":"19","author":"Shim","year":"2023","journal-title":"Int. J. Biol. Sci."},{"key":"10.1016\/j.celrep.2026.117479_bib10","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1146\/annurev-immunol-101320-011829","article-title":"T Cell Responses to the Microbiota","volume":"40","author":"Ivanov","year":"2022","journal-title":"Annu. Rev. Immunol."},{"key":"10.1016\/j.celrep.2026.117479_bib11","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1038\/s41422-020-0332-7","article-title":"Interaction between microbiota and immunity in health and disease","volume":"30","author":"Zheng","year":"2020","journal-title":"Cell Res."},{"key":"10.1016\/j.celrep.2026.117479_bib12","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2022.1004339","article-title":"Regulation of T cell repertoires by commensal microbiota","volume":"12","author":"Kim","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"10.1016\/j.celrep.2026.117479_bib13","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1038\/s41423-019-0208-2","article-title":"T lymphocytes in the intestinal mucosa: defense and tolerance","volume":"16","author":"Ma","year":"2019","journal-title":"Cell. Mol. Immunol."},{"key":"10.1016\/j.celrep.2026.117479_bib14","doi-asserted-by":"crossref","first-page":"1320","DOI":"10.1053\/j.gastro.2017.07.047","article-title":"Circulating and Tissue-Resident CD4(+) T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function Is Altered During Inflammation","volume":"153","author":"Hegazy","year":"2017","journal-title":"Gastroenterology"},{"key":"10.1016\/j.celrep.2026.117479_bib15","doi-asserted-by":"crossref","first-page":"2602","DOI":"10.1038\/s41591-023-02556-5","article-title":"Selection of cross-reactive T cells by commensal and food-derived yeasts drives cytotoxic T(H)1 cell responses in Crohn's disease","volume":"29","author":"Martini","year":"2023","journal-title":"Nat. Med."},{"key":"10.1016\/j.celrep.2026.117479_bib16","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1046\/j.1365-3083.1996.d01-273.x","article-title":"Bacteria-specific T-cell clones are selective in their reactivity towards different enterobacteria or H. pylori and increased in inflammatory bowel disease","volume":"44","author":"Duchmann","year":"1996","journal-title":"Scand. J. Immunol."},{"key":"10.1016\/j.celrep.2026.117479_bib17","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1016\/j.chom.2022.03.002","article-title":"Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden","volume":"30","author":"Olsson","year":"2022","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.celrep.2026.117479_bib18","doi-asserted-by":"crossref","DOI":"10.1016\/j.smim.2023.101810","article-title":"Numbers and odds: TCR repertoire size and its age changes impacting on T cell functions","volume":"69","author":"Weng","year":"2023","journal-title":"Semin. Immunol."},{"key":"10.1016\/j.celrep.2026.117479_bib19","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1186\/s12866-025-04106-0","article-title":"[1]The human gut microbiota in IBD, characterizing hubs, the core microbiota and terminal nodes: a network-based approach","volume":"25","author":"Geese","year":"2025","journal-title":"BMC Microbiol."},{"key":"10.1016\/j.celrep.2026.117479_bib20","doi-asserted-by":"crossref","DOI":"10.3390\/ijms25136831","article-title":"Association between Circulating T Cells and the Gut Microbiome in Healthy Individuals: Findings from a Pilot Study","volume":"25","author":"Vivek","year":"2024","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.celrep.2026.117479_bib21","doi-asserted-by":"crossref","DOI":"10.1080\/19490976.2023.2263934","article-title":"Colorectal cancer-associated T cell receptor repertoire abnormalities are linked to gut microbiome shifts and somatic cell mutations","volume":"15","author":"Cao","year":"2023","journal-title":"Gut Microbes"},{"key":"10.1016\/j.celrep.2026.117479_bib22","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1007\/s12672-025-02486-3","article-title":"Gut microbiota influences colorectal cancer through immune cell interactions: a Mendelian randomization study","volume":"16","author":"Zheng","year":"2025","journal-title":"Discov. Oncol."},{"key":"10.1016\/j.celrep.2026.117479_bib23","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2020.03.035","article-title":"Gut Microbiota Modulate CD8 T Cell Responses to Influence Colitis-Associated Tumorigenesis","volume":"31","author":"Yu","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2026.117479_bib24","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1038\/s41586-023-06431-8","article-title":"Mapping the T cell repertoire to a complex gut bacterial community","volume":"621","author":"Nagashima","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2026.117479_bib25","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1016\/j.immuni.2018.12.015","article-title":"Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORgammat(+) Regulatory T Cells and Exacerbate Colitis in Mice","volume":"50","author":"Britton","year":"2019","journal-title":"Immunity"},{"key":"10.1016\/j.celrep.2026.117479_bib26","article-title":"Multimodal immune cell phenotyping in GI biopsies reveals microbiome-related T cell modulations in human GvHD","volume":"4","author":"Jarosch","year":"2023","journal-title":"Cell Rep. Med."},{"key":"10.1016\/j.celrep.2026.117479_bib27","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.jcmgh.2023.09.003","article-title":"T Cell Repertoire Homogeneity and Blood-Gut Overlap in Patients With Inflammatory Bowel Disease","volume":"17","author":"Williams","year":"2024","journal-title":"Cell. Mol. Gastroenterol. Hepatol."},{"key":"10.1016\/j.celrep.2026.117479_bib28","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1038\/s41590-023-01575-1","article-title":"Single-cell analysis of human MAIT cell transcriptional, functional and clonal diversity","volume":"24","author":"Garner","year":"2023","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.celrep.2026.117479_bib29","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2024.1414000","article-title":"Temporal dynamics and species-level complexity of Prevotella spp. in the human gut microbiota: implications for enterotypes and health","volume":"15","author":"Han","year":"2024","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.celrep.2026.117479_bib30","doi-asserted-by":"crossref","DOI":"10.3390\/microorganisms8040573","article-title":"The Controversial Role of Human Gut Lachnospiraceae","volume":"8","author":"Vacca","year":"2020","journal-title":"Microorganisms"},{"key":"10.1016\/j.celrep.2026.117479_bib31","doi-asserted-by":"crossref","DOI":"10.1016\/j.ijbiomac.2025.142815","article-title":"Gut commensal Lachnospiraceae bacteria contribute to anti-colitis effects of Lactiplantibacillus plantarum exopolysaccharides","volume":"309","author":"Yang","year":"2025","journal-title":"Int. J. Biol. Macromol."},{"key":"10.1016\/j.celrep.2026.117479_bib32","doi-asserted-by":"crossref","first-page":"84","DOI":"10.3389\/fcimb.2015.00084","article-title":"Insights into the Role of Erysipelotrichaceae in the Human Host","volume":"5","author":"Kaakoush","year":"2015","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"10.1016\/j.celrep.2026.117479_bib33","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2020.575455","article-title":"Novel Odoribacter splanchnicus Strain and Its Outer Membrane Vesicles Exert Immunoregulatory Effects in vitro","volume":"11","author":"Hiippala","year":"2020","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.celrep.2026.117479_bib34","doi-asserted-by":"crossref","DOI":"10.1016\/j.biopha.2022.113518","article-title":"Collinsella is associated with cumulative inflammatory burden in an established rheumatoid arthritis cohort","volume":"153","author":"Ruiz-Lim\u00f3n","year":"2022","journal-title":"Biomed. Pharmacother."},{"key":"10.1016\/j.celrep.2026.117479_bib35","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.3389\/fimmu.2017.01540","article-title":"Mucosal-Associated Invariant T Cells: New Insights into Antigen Recognition and Activation","volume":"8","author":"Xiao","year":"2017","journal-title":"Front. Immunol."},{"key":"10.1016\/j.celrep.2026.117479_bib36","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1189\/jlb.1RU0114-010RR","article-title":"IL-17+Foxp3+ T cells: an intermediate differentiation stage between Th17 cells and regulatory T cells","volume":"96","author":"Du","year":"2014","journal-title":"J. Leukoc. Biol."},{"key":"10.1016\/j.celrep.2026.117479_bib37","doi-asserted-by":"crossref","first-page":"276","DOI":"10.4110\/in.2017.17.5.276","article-title":"IL-17A-Producing Foxp3(+) Regulatory T Cells and Human Diseases","volume":"17","author":"Jung","year":"2017","journal-title":"Immune Netw."},{"key":"10.1016\/j.celrep.2026.117479_bib38","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.68388","article-title":"Preexisting memory CD4 T cells in naive individuals confer robust immunity upon hepatitis B vaccination","volume":"11","author":"Elias","year":"2022","journal-title":"eLife"},{"key":"10.1016\/j.celrep.2026.117479_bib39","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.81952","article-title":"T cell receptor convergence is an indicator of antigen-specific T cell response in cancer immunotherapies","volume":"11","author":"Pan","year":"2022","journal-title":"eLife"},{"key":"10.1016\/j.celrep.2026.117479_bib40","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nature18848","article-title":"The microbiota in adaptive immune homeostasis and disease","volume":"535","author":"Honda","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2026.117479_bib41","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1186\/s12964-024-01909-y","article-title":"Exploring the role of Fusobacterium nucleatum in colorectal cancer: implications for tumor proliferation and chemoresistance","volume":"22","author":"Dadgar-Zankbar","year":"2024","journal-title":"Cell Commun. Signal."},{"key":"10.1016\/j.celrep.2026.117479_bib42","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.chom.2013.07.007","article-title":"Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment","volume":"14","author":"Kostic","year":"2013","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.celrep.2026.117479_bib43","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1016\/j.canlet.2021.10.002","article-title":"Bacteroides fragilis restricts colitis-associated cancer via negative regulation of the NLRP3 axis","volume":"523","author":"Shao","year":"2021","journal-title":"Cancer Lett."},{"key":"10.1016\/j.celrep.2026.117479_bib44","article-title":"Protective effects of a new generation of probiotic Bacteroides fragilis against colitis in vivo and in vitro","volume":"13","author":"He","year":"2023","journal-title":"Sci. Rep."},{"key":"10.1016\/j.celrep.2026.117479_bib45","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.jare.2021.06.012","article-title":"Protective effects of different Bacteroides vulgatus strains against lipopolysaccharide-induced acute intestinal injury, and their underlying functional genes","volume":"36","author":"Wang","year":"2022","journal-title":"J. Adv. Res."},{"key":"10.1016\/j.celrep.2026.117479_bib46","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1126\/science.aaw7479","article-title":"Akkermansia muciniphila induces intestinal adaptive immune responses during homeostasis","volume":"364","author":"Ansaldo","year":"2019","journal-title":"Science"},{"key":"10.1016\/j.celrep.2026.117479_bib47","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2007595118","article-title":"Capsular polysaccharide correlates with immune response to the human gut microbe Ruminococcus gnavus","volume":"118","author":"Henke","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2026.117479_bib48","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1038\/nature12721","article-title":"Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells","volume":"504","author":"Furusawa","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2026.117479_bib49","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1038\/s41423-023-00987-1","article-title":"Complex regulatory effects of gut microbial short-chain fatty acids on immune tolerance and autoimmunity","volume":"20","author":"Kim","year":"2023","journal-title":"Cell. Mol. Immunol."},{"key":"10.1016\/j.celrep.2026.117479_bib50","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1038\/nri.2016.42","article-title":"Gut microbiota, metabolites and host immunity","volume":"16","author":"Rooks","year":"2016","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.celrep.2026.117479_bib51","doi-asserted-by":"crossref","first-page":"12204","DOI":"10.1073\/pnas.0909122107","article-title":"Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota","volume":"107","author":"Round","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2026.117479_bib52","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.adt2926","article-title":"Celluloepidemiology-A paradigm for quantifying infectious disease dynamics on a population level","volume":"11","author":"Ha","year":"2025","journal-title":"Sci. Adv."},{"key":"10.1016\/j.celrep.2026.117479_bib53","doi-asserted-by":"crossref","first-page":"117752","DOI":"10.1016\/j.celrep.2026.117752","article-title":"Blood transcriptome bridges orthogonal immunotypes and gut microbiome enterotypes in humans","volume":"45","author":"Affaticati","year":"2026","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2026.117479_bib54","doi-asserted-by":"crossref","first-page":"1970","DOI":"10.1053\/j.gastro.2021.01.030","article-title":"Healthy Cotwins Share Gut Microbiome Signatures With Their Inflammatory Bowel Disease Twins and Unrelated Patients","volume":"160","author":"Brand","year":"2021","journal-title":"Gastroenterology"},{"key":"10.1016\/j.celrep.2026.117479_bib55","article-title":"Clonal overlap and convergent clustering of T-cell receptor signatures in Crohn\u2019s disease in monozygotic twins","author":"Brand","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.celrep.2026.117479_bib56","article-title":"TIRTL-seq: Deep, quantitative, and affordable paired TCR repertoire sequencing","author":"Pogorelyy","year":"2024","journal-title":"bioRxiv"},{"key":"10.1016\/j.celrep.2026.117479_bib57","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1038\/nmeth.3364","article-title":"MiXCR: software for comprehensive adaptive immunity profiling","volume":"12","author":"Bolotin","year":"2015","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2026.117479_bib58","article-title":"Generation of a T cell receptor, cytokine and cell repertoire synovial fluid atlas to define commonalities and dissimilarities between arthritic diseases through systems immunology approaches","author":"Ha","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.celrep.2026.117479_bib59","doi-asserted-by":"crossref","first-page":"4865","DOI":"10.1093\/bioinformatics\/btab446","article-title":"ClusTCR: a python interface for rapid clustering of large sets of CDR3 sequences with unknown antigen specificity","volume":"37","author":"Valkiers","year":"2021","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2026.117479_bib61","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.adr3196","article-title":"T cell receptor-centric perspective to multimodal single-cell data analysis","volume":"10","author":"Mullan","year":"2024","journal-title":"Sci. Adv."},{"key":"10.1016\/j.celrep.2026.117479_bib62","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2026.117479_bib63","doi-asserted-by":"crossref","first-page":"6313","DOI":"10.21105\/joss.06313","article-title":"Tidytacos: An R package for analyses on taxonomic composition of microbial communities","volume":"10","author":"Wittouck","year":"2025","journal-title":"J. Open Source Softw."},{"key":"10.1016\/j.celrep.2026.117479_bib64","doi-asserted-by":"crossref","first-page":"902","DOI":"10.1038\/nmeth.3589","article-title":"MetaPhlAn2 for enhanced metagenomic taxonomic profiling","volume":"12","author":"Truong","year":"2015","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2026.117479_bib65","doi-asserted-by":"crossref","first-page":"22","DOI":"10.3389\/fimmu.2014.00022","article-title":"Immunoglobulin and T Cell Receptor Genes: IMGT((R)) and the Birth and Rise of Immunoinformatics","volume":"5","author":"Lefranc","year":"2014","journal-title":"Front. Immunol."},{"key":"10.1016\/j.celrep.2026.117479_bib66","doi-asserted-by":"crossref","first-page":"1613","DOI":"10.1099\/ijsem.0.001755","article-title":"Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies","volume":"67","author":"Yoon","year":"2017","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"10.1016\/j.celrep.2026.117479_bib67","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1158\/2326-6066.CIR-18-0136","article-title":"Peripheral Blood TCR Repertoire Profiling May Facilitate Patient Stratification for Immunotherapy against Melanoma","volume":"7","author":"Hogan","year":"2019","journal-title":"Cancer Immunol. Res."},{"key":"10.1016\/j.celrep.2026.117479_bib68","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.68605","article-title":"TCR meta-clonotypes for biomarker discovery with tcrdist3 enabled identification of public, HLA-restricted clusters of SARS-CoV-2 TCRs","volume":"10","author":"Mayer-Blackwell","year":"2021","journal-title":"eLife"}],"container-title":["Cell Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124726005577?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124726005577?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T04:38:38Z","timestamp":1790311118000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2211124726005577"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6]]},"references-count":67,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2026,6]]}},"alternative-id":["S2211124726005577"],"URL":"https:\/\/doi.org\/10.1016\/j.celrep.2026.117479","relation":{},"ISSN":["2211-1247"],"issn-type":[{"value":"2211-1247","type":"print"}],"subject":[],"published":{"date-parts":[[2026,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"AIRRWAS integrates TCR-microbiome data to reveal how the gut microbiome shapes the circulating and mucosal T cell repertoire","name":"articletitle","label":"Article Title"},{"value":"Cell Reports","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.celrep.2026.117479","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"117479"}}