{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T18:03:52Z","timestamp":1784829832782,"version":"3.55.0"},"reference-count":112,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T00:00:00Z","timestamp":1784764800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100016958","name":"Office of Research Infrastructure Programs","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100016958","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    While the non-obese diabetic (NOD) mouse is the most widely used animal model of type 1 diabetes (T1D), it suffers from poor reproducibility in disease incidence often attributed to variables in the environment, including the gut microbiota (GM). Prior research suggests a protective effect of segmented filamentous bacteria (SFB) on disease incidence, but it is unclear whether other pathobiont organisms or resident GM affect disease incidence. The objectives of the current study were to determine the effect of supplier-origin GMs and three different microbial challenges (SFB,\n                    <jats:italic>Helicobacter hepaticus<\/jats:italic>\n                    , and Mouse Hepatitis Virus [MHV]) on early-stage insulitis and lifelong disease incidence in NOD mice. The fecal microbiome was assessed pre- and post-disease onset to identify shifts in composition and predicted function of the GM. Results show that all three microbes influence T1D incidence and insulitis severity. Overall, SFB, MHV, and a high-richness microbiome were associated with lower disease incidence, while\n                    <jats:italic>H. hepaticus<\/jats:italic>\n                    and a low-richness microbiome were associated with higher disease incidence.\n                    <jats:italic>H. hepaticus<\/jats:italic>\n                    , but not SFB or MHV, was associated with significant changes in beta-diversity of the GM. While immune outcomes were not included, these findings provide guidance on microbes affecting disease incidence in NOD mice and evidence that such microbes may contribute to poor reproducibility in NOD mice or other mouse models.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1844128","type":"journal-article","created":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T17:10:19Z","timestamp":1784826619000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Gut microbiota and pathobiont exposure influences disease incidence in non-obese diabetic mice"],"prefix":"10.3389","volume":"17","author":[{"given":"Amber L.","family":"Russell","sequence":"first","affiliation":[{"name":"Department of Pathobiology and Integrative Biomedical Sciences, College of Veterinary Medicine, University of Missouri","place":["Columbia, MO, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Olthoff","sequence":"additional","affiliation":[{"name":"Comparative Medicine Program, University of Missouri","place":["Columbia, MO, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunye","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Pathobiology and Integrative Biomedical Sciences, College of Veterinary Medicine, University of Missouri","place":["Columbia, MO, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cat","family":"Lutz","sequence":"additional","affiliation":[{"name":"The Jackson Laboratory","place":["Bar Harbor, ME, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Craig L.","family":"Franklin","sequence":"additional","affiliation":[{"name":"Department of Pathobiology and Integrative Biomedical Sciences, College of Veterinary Medicine, University of Missouri","place":["Columbia, MO, United States"]},{"name":"Comparative Medicine Program, University of Missouri","place":["Columbia, MO, United States"]},{"name":"University of Missouri Mutant Mouse Resource and Research Center (MU MMRRC), University of Missouri","place":["Columbia, MO, United States"]},{"name":"University of Missouri Metagenomics Center (MUMC), University of Missouri","place":["Columbia, MO, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aaron C.","family":"Ericsson","sequence":"additional","affiliation":[{"name":"Department of Pathobiology and Integrative Biomedical Sciences, College of Veterinary Medicine, University of Missouri","place":["Columbia, MO, United States"]},{"name":"Comparative Medicine Program, University of Missouri","place":["Columbia, MO, United States"]},{"name":"University of Missouri Mutant Mouse Resource and Research Center (MU MMRRC), University of Missouri","place":["Columbia, MO, United States"]},{"name":"University of Missouri Metagenomics Center (MUMC), University of Missouri","place":["Columbia, MO, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,7,23]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1398","DOI":"10.1007\/s00125-011-2097-5","article-title":"Effects of a germ-free environment on gut immune regulation and diabetes progression in non-obese diabetic (NOD) mice","volume":"54","author":"Alam","year":"2011","journal-title":"Diabetologia"},{"key":"B2","doi-asserted-by":"publisher","first-page":"229","DOI":"10.30802\/AALAS-JAALAS-22-000097","article-title":"Pathogen prevalence estimates and diagnostic methodology trends in laboratory mice and rats from 2003 to 2020","volume":"62","author":"Albers","year":"2023","journal-title":"J Am. Assoc. Lab. Anim. Sci"},{"key":"B3","doi-asserted-by":"publisher","first-page":"1591","DOI":"10.1016\/j.intimp.2011.05.020","article-title":"Autoimmune hepatitis-like disease in C57BL\/6 mice infected with mouse hepatitis virus A59","volume":"11","author":"Aparicio","year":"2011","journal-title":"Int. Immunopharmacol"},{"key":"B4","doi-asserted-by":"publisher","first-page":"5369","DOI":"10.4049\/jimmunol.168.10.5369","article-title":"Molecular mechanisms for gender differences in susceptibility to T cell-mediated autoimmune diabetes in nonobese diabetic mice","volume":"168","author":"Bao","year":"2002","journal-title":"J. Immunol"},{"key":"B5","first-page":"133","article-title":"Duration of mouse hepatitis virus infection: studies in immunocompetent and chemically immunosuppressed mice","volume":"40","author":"Barthold","year":"1990","journal-title":"Lab. Anim. Sci"},{"key":"B6","first-page":"782","article-title":"Influence of rack design and disease prevalence on detection of rodent pathogens in exhaust debris samples from individually ventilated caging systems","volume":"55","author":"Bauer","year":"2016","journal-title":"J. Am. Assoc. Lab. Anim. Sci"},{"key":"B7","doi-asserted-by":"publisher","first-page":"61","DOI":"10.3109\/08916939108997125","article-title":"High and low diabetes incidence nonobese diabetic (NOD) mice: origins and characterisation","volume":"9","author":"Baxter","year":"1991","journal-title":"Autoimmunity"},{"key":"B8","doi-asserted-by":"publisher","first-page":"e0198305","DOI":"10.1371\/journal.pone.0198305","article-title":"Effects of water decontamination methods and bedding material on the gut microbiota","volume":"13","author":"Bidot","year":"2018","journal-title":"PLoS ONE"},{"key":"B9","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol"},{"key":"B10","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1038\/ismej.2015.114","article-title":"Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice","volume":"10","author":"Brown","year":"2016","journal-title":"ISME J"},{"key":"B11","doi-asserted-by":"publisher","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":"B12","doi-asserted-by":"publisher","first-page":"e0125448","DOI":"10.1371\/journal.pone.0125448","article-title":"Antibiotics in early life alter the gut microbiome and increase disease incidence in a spontaneous mouse model of autoimmune insulin-dependent diabetes","volume":"10","author":"Candon","year":"2015","journal-title":"PLoS ONE"},{"key":"B13","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1038\/s41575-022-00631-9","article-title":"Akkermansia muciniphila: paradigm for next-generation beneficial microorganisms","volume":"19","author":"Cani","year":"2022","journal-title":"Nat. Rev. Gastroenterol. Hepatol"},{"key":"B14","doi-asserted-by":"publisher","first-page":"4516","DOI":"10.1073\/pnas.1000080107","article-title":"Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci","volume":"108","author":"Caporaso","year":"2011","journal-title":"USA"},{"key":"B15","first-page":"245","article-title":"The use of animal models in the study of diabetes mellitus","volume":"23","author":"Chatzigeorgiou","year":"2009","journal-title":"In Vivo"},{"key":"B16","doi-asserted-by":"publisher","first-page":"1403","DOI":"10.3389\/fmicb.2018.01403","article-title":"Presence of segmented filamentous bacteria in human children and its potential role in the modulation of human gut immunity","volume":"9","author":"Chen","year":"2018","journal-title":"Front. Microbiol"},{"key":"B17","doi-asserted-by":"publisher","first-page":"51","DOI":"10.3389\/fendo.2018.00051","article-title":"The role of NOD mice in type 1 diabetes research: lessons from the past and recommendations for the future","volume":"9","author":"Chen","year":"2018","journal-title":"Front. Endocrinol."},{"key":"B18","doi-asserted-by":"publisher","first-page":"7767","DOI":"10.1128\/AEM.01477-07","article-title":"Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly","volume":"73","author":"Collado","year":"2007","journal-title":"Appl. Environ. Microbiol"},{"key":"B19","doi-asserted-by":"publisher","first-page":"3263","DOI":"10.1093\/bioinformatics\/btaa070","article-title":"Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data","volume":"36","author":"Czech","year":"2020","journal-title":"Bioinformatics"},{"key":"B20","doi-asserted-by":"publisher","first-page":"1569","DOI":"10.1007\/s00125-014-3274-0","article-title":"Aberrant gut microbiota composition at the onset of type 1 diabetes in young children","volume":"57","author":"de Goffau","year":"2014","journal-title":"Diabetologia"},{"key":"B21","doi-asserted-by":"publisher","first-page":"e0181964","DOI":"10.1371\/journal.pone.0181964","article-title":"Regulation of type 1 diabetes development and B-cell activation in nonobese diabetic mice by early life exposure to a diabetogenic environment","volume":"12","author":"De Riva","year":"2017","journal-title":"PLoS ONE"},{"key":"B22","doi-asserted-by":"publisher","first-page":"1646","DOI":"10.1128\/AEM.01226-07","article-title":"The Mucin degrader Akkermansia muciniphila is an abundant resident of the human intestinal tract","volume":"74","author":"Derrien","year":"2008","journal-title":"Appl. Environ. Microbiol"},{"key":"B23","doi-asserted-by":"publisher","first-page":"1890","DOI":"10.2337\/db06-0089","article-title":"The variable number of tandem repeats upstream of the insulin gene is a susceptibility locus for latent autoimmune diabetes in adults","volume":"55","author":"Desai","year":"2006","journal-title":"Diabetes"},{"key":"B24","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1038\/s41587-020-0548-6","article-title":"PICRUSt2 for prediction of metagenome functions","volume":"38","author":"Douglas","year":"2020","journal-title":"Nat. Biotechnol"},{"key":"B25","first-page":"347","article-title":"Detection of rodent Helicobacter spp. by use of fluorogenic nuclease polymerase chain reaction assays","volume":"52","author":"Drazenovich","year":"2002","journal-title":"Comp. Med"},{"key":"B26","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1152\/physiolgenomics.00010.2015","article-title":"Exoelectrogenic capacity of host microbiota predicts lymphocyte recruitment to the gut","volume":"47","author":"Ericsson","year":"2015","journal-title":"Physiol. Genom."},{"key":"B27","doi-asserted-by":"publisher","first-page":"e0111225","DOI":"10.1128\/msystems.01112-25","article-title":"Dominant effects of the immediate environment on the gut microbiome of mice used in biomedical research","volume":"10","author":"Ericsson","year":"2025","journal-title":"mSystems"},{"key":"B28","first-page":"335","article-title":"Antibiotic-associated manipulation of the gut microbiota and phenotypic restoration in NOD mice","volume":"67","author":"Fahey","year":"2017","journal-title":"Comp. Med"},{"key":"B29","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1128\/iai.59.3.852-856.1991","article-title":"Mouse hepatitis virus strain UAB infection enhances resistance to Salmonella typhimurium in mice by inducing suppression of bacterial growth","volume":"59","author":"Fallon","year":"1991","journal-title":"Infect. Immun"},{"key":"B30","doi-asserted-by":"publisher","first-page":"1425235","DOI":"10.3389\/fendo.2024.1425235","article-title":"The protective effect of the intestinal microbiota in type-1 diabetes in NOD mice is limited to a time window in early life","volume":"15","author":"Fernandez Trigo","year":"2024","journal-title":"Front. Endocrinol"},{"key":"B31","doi-asserted-by":"publisher","first-page":"2863","DOI":"10.2337\/db07-1023","article-title":"Viral trigger for type 1 diabetes: pros and cons","volume":"57","author":"Filippi","year":"2008","journal-title":"Diabetes"},{"key":"B32","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1136\/gut.50.2.273","article-title":"The non-H pylori helicobacters: their expanding role in gastrointestinal and systemic diseases","volume":"50","author":"Fox","year":"2002","journal-title":"Gut"},{"key":"B33","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1002\/(SICI)1520-7560(199909\/10)15:5<323::AID-DMRR53>3.0.CO;2-P","article-title":"Gluten-free diet prevents diabetes in NOD mice","volume":"15","author":"Funda","year":"1999","journal-title":"Diabetes Metab. Res. Rev"},{"key":"B34","doi-asserted-by":"publisher","first-page":"6541","DOI":"10.1128\/jvi.69.10.6541-6547.1995","article-title":"Thymus involution induced by mouse hepatitis virus A59 in BALB\/c mice","volume":"69","author":"Godfraind","year":"1995","journal-title":"J. Virol"},{"key":"B35","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1016\/j.immuni.2014.03.005","article-title":"Segmented filamentous bacteria antigens presented by intestinal dendritic cells drive mucosal Th17 cell differentiation","volume":"40","author":"Goto","year":"2014","journal-title":"Immunity"},{"key":"B36","doi-asserted-by":"publisher","first-page":"1062","DOI":"10.1002\/eji.202048984","article-title":"Insights into coronavirus immunity taught by the murine coronavirus","volume":"51","author":"Grabherr","year":"2021","journal-title":"Eur. J. Immunol"},{"key":"B37","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1016\/S2213-8587(22)00218-2","article-title":"Global incidence, prevalence, and mortality of type 1 diabetes in 2021 with projection to 2040: a modelling study","volume":"10","author":"Gregory","year":"2022","journal-title":"Lancet Diabetes Endocrinol"},{"key":"B38","doi-asserted-by":"publisher","first-page":"1445","DOI":"10.1136\/gutjnl-2017-314508","article-title":"Akkermansia muciniphila induces gut microbiota remodelling and controls islet autoimmunity in NOD mice","volume":"67","author":"Hanninen","year":"2018","journal-title":"Gut"},{"key":"B39","doi-asserted-by":"publisher","first-page":"792","DOI":"10.3389\/fmicb.2017.00792","article-title":"Differing complex microbiota alter disease severity of the IL-10-\/- mouse model of inflammatory bowel disease","volume":"8","author":"Hart","year":"2017","journal-title":"Front. Microbiol"},{"key":"B40","doi-asserted-by":"publisher","first-page":"10107","DOI":"10.1038\/s41598-018-28448-0","article-title":"Development of outbred CD1 mouse colonies with distinct standardized gut microbiota profiles for use in complex microbiota targeted studies","volume":"8","author":"Hart","year":"2018","journal-title":"Sci. Rep"},{"key":"B41","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1007\/s00430-021-00702-9","article-title":"The human symbiont Mucispirillum schaedleri: causality in health and disease","volume":"210","author":"Herp","year":"2021","journal-title":"Med. Microbiol. Immunol"},{"key":"B42","doi-asserted-by":"publisher","first-page":"544","DOI":"10.1007\/s00335-011-9343-5","article-title":"Quantitative trait loci in a bacterially induced model of inflammatory bowel disease","volume":"22","author":"Hillhouse","year":"2011","journal-title":"Mamm. Genome"},{"key":"B43","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1258\/002367797780600189","article-title":"Enterotropic mouse hepatitis virus","volume":"31","author":"Homberger","year":"1997","journal-title":"Lab. Anim"},{"key":"B44","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1007\/BF01309682","article-title":"Passively acquired challenge immunity to enterotropic coronavirus in mice","volume":"126","author":"Homberger","year":"1992","journal-title":"Arch. Virol"},{"key":"B45","first-page":"347","article-title":"Duration and strain-specificity of immunity to enterotropic mouse hepatitis virus","volume":"42","author":"Homberger","year":"1992","journal-title":"Lab. Anim. Sci"},{"key":"B46","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1016\/j.cell.2009.09.033","article-title":"Induction of intestinal Th17 cells by segmented filamentous bacteria","volume":"139","author":"Ivanov","year":"2009","journal-title":"Cell"},{"key":"B47","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1084\/jem.20071878","article-title":"Innocuous IFNgamma induced by adjuvant-free antigen restores normoglycemia in NOD mice through inhibition of IL-17 production","volume":"205","author":"Jain","year":"2008","journal-title":"J. Exp. Med"},{"key":"B48","doi-asserted-by":"publisher","first-page":"3424691","DOI":"10.1155\/2018\/3424691","article-title":"Long-term provision of acidified drinking water fails to influence autoimmune diabetes and encephalomyelitis","volume":"2018","author":"Jayaraman","year":"2018","journal-title":"J. Diabetes Res"},{"key":"B49","doi-asserted-by":"publisher","first-page":"1602","DOI":"10.1016\/j.micinf.2006.01.019","article-title":"Induction of differential immune reactivity to members of the flora of gnotobiotic mice following colonization with Helicobacter bilis or Brachyspira hyodysenteriae","volume":"8","author":"Jergens","year":"2006","journal-title":"Microbes Infect"},{"key":"B50","doi-asserted-by":"publisher","first-page":"934","DOI":"10.1136\/gut.2006.099242","article-title":"Helicobacter bilis triggers persistent immune reactivity to antigens derived from the commensal bacteria in gnotobiotic C3H\/HeN mice","volume":"56","author":"Jergens","year":"2007","journal-title":"Gut"},{"key":"B51","doi-asserted-by":"publisher","first-page":"3611","DOI":"10.1128\/IAI.69.6.3611-3617.2001","article-title":"Timing, localization, and persistence of colonization by segmented filamentous bacteria in the neonatal mouse gut depend on immune status of mothers and pups","volume":"69","author":"Jiang","year":"2001","journal-title":"Infect. Immun"},{"key":"B52","doi-asserted-by":"publisher","first-page":"4643","DOI":"10.1038\/s41467-019-12669-6","article-title":"Species abundance information improves sequence taxonomy classification accuracy","volume":"10","author":"Kaehler","year":"2019","journal-title":"Nat. Commun"},{"key":"B53","author":"Kassambara","year":"2021","journal-title":"rstatix: Pipe-Friendly Framework for Basic Statistical Tests"},{"key":"B54","doi-asserted-by":"publisher","first-page":"9258","DOI":"10.1128\/JVI.00355-09","article-title":"Protective and pathologic roles of the immune response to mouse hepatitis virus type 1: implications for severe acute respiratory syndrome","volume":"83","author":"Khanolkar","year":"2009","journal-title":"J. Virol"},{"key":"B55","doi-asserted-by":"publisher","first-page":"880","DOI":"10.3390\/v12080880","article-title":"Of mice and men: the coronavirus MHV and mouse models as a translational approach to understand SARS-CoV-2","volume":"12","author":"K\u00f6rner","year":"2020","journal-title":"Viruses"},{"key":"B56","doi-asserted-by":"publisher","first-page":"11548","DOI":"10.1073\/pnas.1108924108","article-title":"Naturally transmitted segmented filamentous bacteria segregate with diabetes protection in nonobese diabetic mice","volume":"108","author":"Kriegel","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"key":"B57","doi-asserted-by":"publisher","first-page":"6952","DOI":"10.1128\/IAI.73.10.6852-6961.2005","article-title":"Colonization of the cecal mucosa by Helicobacter hepaticus impacts the diversity of the indigenous microbiota","volume":"73","author":"Kuehl","year":"2005","journal-title":"Infect. Immun"},{"key":"B58","doi-asserted-by":"publisher","first-page":"15830","DOI":"10.1073\/pnas.2534546100","article-title":"Induction of colitis by a CD4+ T cell clone specific for a bacterial epitope","volume":"100","author":"Kullberg","year":"2003","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"B59","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1292\/jvms.58.431","article-title":"Characterization of T cells expanded in vivo during primary mouse hepatitis virus infection in mice","volume":"58","author":"Kyuwa","year":"1996","journal-title":"J. Vet. Med. Sci"},{"key":"B60","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1016\/j.immuni.2014.03.009","article-title":"Segmented filamentous bacterium uses secondary and tertiary lymphoid tissues to induce gut IgA and specific T helper 17 cell responses","volume":"40","author":"L\u00e9cuyer","year":"2014","journal-title":"Immunity"},{"key":"B61","doi-asserted-by":"publisher","first-page":"879","DOI":"10.1292\/jvms.56.879","article-title":"Apoptotic changes in the thymus of mice infected with mouse hepatitis virus, MHV-2","volume":"56","author":"Lee","year":"1994","journal-title":"J. Vet. Med. Sci"},{"key":"B62","author":"Lenth","year":"2022","journal-title":"emmeans: Estimated Marginal Means, aka Least-Squares Means"},{"key":"B63","doi-asserted-by":"publisher","first-page":"1053","DOI":"10.1093\/bioinformatics\/btx701","article-title":"Efficient comparative phylogenetics on large trees","volume":"34","author":"Louca","year":"2018","journal-title":"Bioinformatics"},{"key":"B64","doi-asserted-by":"publisher","first-page":"D800","DOI":"10.1093\/nar\/gkl856","article-title":"probeBase\u2013an online resource for rRNA-targeted oligonucleotide probes: new features 2007","volume":"35","author":"Loy","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"B65","doi-asserted-by":"publisher","first-page":"4916","DOI":"10.1021\/pr300429x","article-title":"Serum metabolomics in a Helicobacter hepaticus mouse model of inflammatory bowel disease reveal important changes in the microbiome, serum peptides, and intermediary metabolism","volume":"11","author":"Lu","year":"2012","journal-title":"J. Proteome Res"},{"key":"B66","doi-asserted-by":"publisher","first-page":"e35445","DOI":"10.1371\/journal.pone.0035445","article-title":"Altered metabolic signature in pre-diabetic NOD mice","volume":"7","author":"Madsen","year":"2012","journal-title":"PLoS ONE"},{"key":"B67","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/s12866-021-02406-9","article-title":"Administration of human derived upper gut commensal prevotella histicola delays the onset of type 1 diabetes in NOD mice","volume":"22","author":"Marietta","year":"2022","journal-title":"BMC Microbiol"},{"key":"B68","doi-asserted-by":"publisher","first-page":"552","DOI":"10.1038\/ni.3713","article-title":"Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes","volume":"18","author":"Mari\u00f1o","year":"2017","journal-title":"Nat. Immunol"},{"key":"B69","doi-asserted-by":"publisher","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","author":"Martin","year":"2011","journal-title":"EMBnet.journal"},{"key":"B70","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1142\/9789814366496_0024","article-title":"SEPP: SAT\u00e9-enabled phylogenetic placement","volume":"2012","author":"Mirarab","year":"2011","journal-title":"Pac. Symp. Biocomput"},{"key":"B71","doi-asserted-by":"publisher","first-page":"1143","DOI":"10.1038\/mi.2013.11","article-title":"Th17-cell plasticity in Helicobacter hepaticus-induced intestinal inflammation","volume":"6","author":"Morrison","year":"2013","journal-title":"Mucosal Immunol"},{"key":"B72","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1007\/s00335-019-09814-3","article-title":"The gut microbiota modulates differential adenoma suppression by B6\/J and B6\/N genetic backgrounds in Apc(Min) mice","volume":"30","author":"Moskowitz","year":"2019","journal-title":"Mamm. Genome"},{"key":"B73","doi-asserted-by":"publisher","first-page":"2102","DOI":"10.1182\/blood-2004-01-0310","article-title":"Exacerbation of autoantibody-mediated thrombocytopenic purpura by infection with mouse viruses","volume":"104","author":"Musaji","year":"2004","journal-title":"Blood"},{"key":"B74","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1016\/j.autrev.2004.11.010","article-title":"Enhancement of autoantibody pathogenicity by viral infections in mouse models of anemia and thrombocytopenia","volume":"4","author":"Musaji","year":"2005","journal-title":"Autoimmun. Rev"},{"key":"B75","doi-asserted-by":"publisher","first-page":"822","DOI":"10.1002\/ibd.20138","article-title":"Characterization of cecal gene expression in a differentially susceptible mouse model of bacterial-induced inflammatory bowel disease","volume":"13","author":"Myles","year":"2007","journal-title":"Inflamm. Bowel Dis"},{"key":"B76","doi-asserted-by":"publisher","first-page":"3885","DOI":"10.1128\/IAI.71.7.3885-3893.2003","article-title":"Analysis of gene expression in ceca of Helicobacter hepaticus-infected A\/JCr mice before and after development of typhlitis","volume":"71","author":"Myles","year":"2003","journal-title":"Infect. Immun"},{"key":"B77","doi-asserted-by":"publisher","first-page":"112277","DOI":"10.1016\/j.diabres.2025.112277","article-title":"Global type 1 diabetes prevalence, incidence, and mortality estimates 2025: results from the International diabetes Federation Atlas, 11th Edition, and the T1D Index Version 3.0","volume":"225","author":"Ogle","year":"2025","journal-title":"Diabetes Res. Clin. Pract"},{"key":"B78","unstructured":"Oksanen\n              J.\n            \n            \n              Simpson\n              G. L.\n            \n            \n              Blanchet\n              F. G.\n            \n            \n              Kindt\n              R.\n            \n          \n          vegan: Community Ecology Package\n          \n          2022"},{"key":"B79","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1084\/jem.186.2.299","article-title":"T helper 2 (Th2) T cells induce acute pancreatitis and diabetes in immune-compromised nonobese diabetic (NOD) mice","volume":"186","author":"Pakala","year":"1997","journal-title":"J. Exp. Med"},{"key":"B80","doi-asserted-by":"publisher","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","article-title":"ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R","volume":"35","author":"Paradis","year":"2018","journal-title":"Bioinformatics"},{"key":"B81","first-page":"424","article-title":"Infectious diseases in wild mice (Mus musculus) collected on and around the University of Pennsylvania (Philadelphia) Campus","volume":"59","author":"Parker","year":"2009","journal-title":"Comp. Med"},{"key":"B82","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1016\/j.jaut.2014.03.005","article-title":"Long term effect of gut microbiota transfer on diabetes development","volume":"53","author":"Peng","year":"2014","journal-title":"J Autoimmun"},{"key":"B83","doi-asserted-by":"publisher","first-page":"2331","DOI":"10.1016\/S0140-6736(16)30582-7","article-title":"Genetic risk factors for type 1 diabetes","volume":"387","author":"Pociot","year":"2016","journal-title":"Lancet"},{"key":"B84","doi-asserted-by":"publisher","first-page":"7188","DOI":"10.1093\/nar\/gkm864","article-title":"SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB","volume":"35","author":"Pruesse","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"B85","volume-title":"R: A Language and Environment for Statistical Computing","year":"2022"},{"key":"B86","doi-asserted-by":"publisher","first-page":"2340","DOI":"10.1016\/S0140-6736(16)30507-4","article-title":"Environmental risk factors for type 1 diabetes","volume":"387","author":"Rewers","year":"2016","journal-title":"Lancet"},{"key":"B87","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1111\/j.1523-5378.2012.00984.x","volume":"17","author":"Rossi","year":"2012","journal-title":"H. pylori. Helicobacter"},{"key":"B88","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1136\/gutjnl-2020-323664","article-title":"Gut mucosa alterations and loss of segmented filamentous bacteria in type 1 diabetes are associated with inflammation rather than hyperglycaemia","volume":"71","author":"Rouland","year":"2022","journal-title":"Gut"},{"key":"B89","article-title":"\u201cThe gut microbiota and targeted pathobiont exposure alters type 1 diabetes phenotype in non-obese diabetic mice (Chapter 4),\u201d","volume-title":"Environmental Variability Affects Gut Microbiota and Experimental Outcomes in Mouse Models","author":"Russell","year":"2023"},{"key":"B90","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1016\/j.immuni.2005.08.002","article-title":"A comprehensive review of interventions in the NOD mouse and implications for translation","volume":"23","author":"Shoda","year":"2005","journal-title":"Immunity"},{"key":"B91","first-page":"591","article-title":"Modulation of autoimmune diseases by interleukin (IL)-17 producing regulatory T helper (Th17) cells","volume":"138","author":"Singh","year":"2013","journal-title":"Indian J. Med. Res"},{"key":"B92","unstructured":"Smith\n              R.\n            \n          \n          Phytomosaic\/ecole: ecole: School of Ecology Package\n          \n          2021"},{"key":"B93","doi-asserted-by":"publisher","first-page":"632","DOI":"10.2337\/db13-0981","article-title":"pH of drinking water influences the composition of gut microbiome and type 1 diabetes incidence","volume":"63","author":"Sofi","year":"2014","journal-title":"Diabetes"},{"key":"B94","doi-asserted-by":"publisher","first-page":"943","DOI":"10.1128\/JVI.72.2.943-949.1998","article-title":"Kinetic analysis of the specific host response to a murine gammaherpesvirus","volume":"72","author":"Stevenson","year":"1998","journal-title":"J. Virol"},{"key":"B95","doi-asserted-by":"publisher","first-page":"1520","DOI":"10.3389\/fmicb.2016.01520","article-title":"Functional characteristics of the gut microbiome in C57BL\/6 mice differentially susceptible to Plasmodium yoelii","volume":"7","author":"Stough","year":"2016","journal-title":"Front. Microbiol"},{"key":"B96","doi-asserted-by":"publisher","first-page":"e106764","DOI":"10.1371\/journal.pone.0106764","article-title":"Helicobacter hepaticus infection promotes hepatitis and preneoplastic foci in farnesoid X receptor (FXR) deficient mice","volume":"9","author":"Swennes","year":"2014","journal-title":"PLoS ONE"},{"key":"B97","doi-asserted-by":"publisher","first-page":"1992","DOI":"10.1128\/IAI.67.4.1992-2000.1999","article-title":"Segmented filamentous bacteria are potent stimuli of a physiologically normal state of the murine gut mucosal immune system","volume":"67","author":"Talham","year":"1999","journal-title":"Infect. Immun"},{"key":"B98","doi-asserted-by":"publisher","first-page":"817","DOI":"10.1084\/jem.181.2.817","article-title":"Interleukin 12 administration induces T helper type 1 cells and accelerates autoimmune diabetes in NOD mice","volume":"181","author":"Trembleau","year":"1995","journal-title":"J Exp Med"},{"key":"B99","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1038\/s41586-018-0620-2","article-title":"The human gut microbiome in early-onset type 1 diabetes from the TEDDY study","volume":"562","author":"Vatanen","year":"2018","journal-title":"Nature"},{"key":"B100","doi-asserted-by":"publisher","first-page":"1057","DOI":"10.1038\/s41564-019-0407-8","article-title":"Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection","volume":"4","author":"Velazquez","year":"2019","journal-title":"Nat. Microbiol"},{"key":"B101","doi-asserted-by":"publisher","first-page":"2235","DOI":"10.1073\/pnas.1504887113","article-title":"Composition of the gut microbiota modulates the severity of malaria","volume":"113","author":"Villarino","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"B102","doi-asserted-by":"publisher","first-page":"1159","DOI":"10.1093\/bioinformatics\/btr087","article-title":"PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers","volume":"27","author":"Walters","year":"2011","journal-title":"Bioinformatics"},{"key":"B103","doi-asserted-by":"publisher","first-page":"2750","DOI":"10.3389\/fimmu.2019.02750","article-title":"Induction of intestinal Th17 cells by flagellins from segmented filamentous bacteria","volume":"10","author":"Wang","year":"2019","journal-title":"Front. Immunol"},{"key":"B104","doi-asserted-by":"publisher","first-page":"3142","DOI":"10.1128\/IAI.66.7.3142-3148.1998","article-title":"Chronic active hepatitis induced by Helicobacter hepaticus in the A\/JCr mouse is associated with a Th1 cell-mediated immune response","volume":"66","author":"Whary","year":"1998","journal-title":"Infect. Immun"},{"key":"B105","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-24277-4_9","author":"Wickham","year":"2016","journal-title":"ggplot2: Elegant Graphics for Data Analysis"},{"key":"B106","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1007\/BF00404016","article-title":"Persistent MHV (mouse hepatitis virus) infection reduces the incidence of diabetes mellitus in non-obese diabetic mice","volume":"34","author":"Wilberz","year":"1991","journal-title":"Diabetologia"},{"key":"B107","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1369\/0022155413519650","article-title":"Consumption of acidic water alters the gut microbiome and decreases the risk of diabetes in NOD mice","volume":"62","author":"Wolf","year":"2014","journal-title":"J. Histochem. Cytochem"},{"key":"B108","doi-asserted-by":"publisher","first-page":"e0236595","DOI":"10.1371\/journal.pone.0236595","article-title":"Interactions of segmented filamentous bacteria (Candidatus Savagella) and bacterial drivers in colitis-associated colorectal cancer development","volume":"15","author":"Wolfe","year":"2020","journal-title":"PLoS ONE"},{"key":"B109","doi-asserted-by":"publisher","first-page":"e1000465","DOI":"10.1371\/journal.pcbi.1000465","article-title":"Parsimony approach to biological pathway reconstruction\/inference for genomes and metagenomes","volume":"5","author":"Ye","year":"2009","journal-title":"PLOS Comput. Biol"},{"key":"B110","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1038\/ismej.2012.128","article-title":"Comparative analysis of the distribution of segmented filamentous bacteria in humans, mice and chickens","volume":"7","author":"Yin","year":"2013","journal-title":"ISME J"},{"key":"B111","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1016\/j.immuni.2013.08.013","article-title":"Gender bias in autoimmunity is influenced by microbiota","volume":"39","author":"Yurkovetskiy","year":"2013","journal-title":"Immunity"},{"key":"B112","doi-asserted-by":"publisher","DOI":"10.2337\/db15-0321","article-title":"Comment on Sofi et al. pH of Drinking water influences the composition of gut microbiome and type 1 diabetes incidence. Diabetes. 63, 632\u2013644","author":"Zhao","year":"2014","journal-title":"Diabetes"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1844128\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T17:10:22Z","timestamp":1784826622000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1844128\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,23]]},"references-count":112,"alternative-id":["10.3389\/fmicb.2026.1844128"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1844128","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,23]]},"article-number":"1844128"}}