{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T04:47:11Z","timestamp":1784868431622,"version":"3.55.0"},"reference-count":50,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2015,7,24]],"date-time":"2015-07-24T00:00:00Z","timestamp":1437696000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0133804","type":"journal-article","created":{"date-parts":[[2015,7,24]],"date-time":"2015-07-24T18:06:36Z","timestamp":1437761196000},"page":"e0133804","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":37,"title":["The Influence of the Autoimmunity-Associated Ancestral HLA Haplotype AH8.1 on the Human Gut Microbiota: A Cross-Sectional Study"],"prefix":"10.1371","volume":"10","author":[{"given":"Johannes R.","family":"Hov","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huanzi","family":"Zhong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bingcai","family":"Qin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jarl Andreas","family":"Anmarkrud","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristian","family":"Holm","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andre","family":"Franke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benedicte A.","family":"Lie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tom H.","family":"Karlsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2015,7,24]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1038\/nrg1489","article-title":"Gene map of the extended human MHC","volume":"5","author":"R Horton","year":"2004","journal-title":"Nat Rev Genet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1126\/science.1143767","article-title":"A whole-genome association study of major determinants for host control of HIV-1","volume":"317","author":"J Fellay","year":"2007","journal-title":"Science"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/j.trim.2005.03.021","article-title":"HLA associated genetic predisposition to autoimmune diseases: Genes involved and possible mechanisms","volume":"14","author":"E Thorsby","year":"2005","journal-title":"Transpl Immunol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1111\/j.1744-313X.2008.00765.x","article-title":"Human MHC architecture and evolution: implications for disease association studies","volume":"35","author":"JA Traherne","year":"2008","journal-title":"Int J Immunogenet"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00251-007-0262-2","article-title":"Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project","volume":"60","author":"R Horton","year":"2008","journal-title":"Immunogenetics"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/S1568-9972(01)00004-0","article-title":"Pathogenesis of autoimmune diseases associated with 8.1 ancestral haplotype: effect of multiple gene interactions","volume":"1","author":"G Candore","year":"2002","journal-title":"Autoimmun Rev"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1111\/j.1600-065X.1999.tb01398.x","article-title":"The genetic basis for the association of the 8.1 ancestral haplotype (A1, B8, DR3) with multiple immunopathological diseases","volume":"167","author":"P Price","year":"1999","journal-title":"Immunol Rev"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1016\/j.ajhg.2012.08.026","article-title":"Unraveling multiple MHC gene associations with systemic lupus erythematosus: model choice indicates a role for HLA alleles and non-HLA genes in Europeans","volume":"91","author":"DL Morris","year":"2012","journal-title":"Am J Hum Genet"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"e114486","DOI":"10.1371\/journal.pone.0114486","article-title":"Refinement of the MHC risk map in a scandinavian primary sclerosing cholangitis population","volume":"9","author":"S Naess","year":"2014","journal-title":"PLoS One"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"e01202","DOI":"10.7554\/eLife.01202","article-title":"Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis","volume":"2","author":"JU Scher","year":"2013","journal-title":"Elife"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1844","DOI":"10.1053\/j.gastro.2010.08.049","article-title":"A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes","volume":"139","author":"BP Willing","year":"2010","journal-title":"Gastroenterology"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1053\/j.gastro.2012.06.031","article-title":"Transfer of Intestinal Microbiota From Lean Donors Increases Insulin Sensitivity in Subjects With Metabolic Syndrome","volume":"143","author":"A Vrieze","year":"2012","journal-title":"Gastroenterology"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1038\/nature12820","article-title":"Diet rapidly and reproducibly alters the human gut microbiome","volume":"505","author":"LA David","year":"2014","journal-title":"Nature"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1016\/j.cell.2014.09.053","article-title":"Human genetics shape the gut microbiome","volume":"159","author":"JK Goodrich","year":"2014","journal-title":"Cell"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1038\/nrmicro2540","article-title":"Unravelling the effects of the environment and host genotype on the gut microbiome","volume":"9","author":"A Spor","year":"2011","journal-title":"Nature reviews Microbiology"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1038\/ni.1825","article-title":"Enteric defensins are essential regulators of intestinal microbial ecology","volume":"11","author":"NH Salzman","year":"2010","journal-title":"Nat Immunol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1981","DOI":"10.1073\/pnas.0307317101","article-title":"Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut","volume":"101","author":"K Suzuki","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref18","article-title":"NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer","author":"A Couturier-Maillard","year":"2013","journal-title":"J Clin Invest"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1354","DOI":"10.1136\/gut.2010.216259","article-title":"Nod2 is essential for temporal development of intestinal microbial communities","volume":"60","author":"A Rehman","year":"2011","journal-title":"Gut"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"19030","DOI":"10.1073\/pnas.1106408108","article-title":"Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype","volume":"108","author":"P Rausch","year":"2011","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"2372","DOI":"10.1128\/IAI.69.4.2372-2377.2001","article-title":"Influence of major histocompatibility complex on bacterial composition of fecal flora","volume":"69","author":"P Toivanen","year":"2001","journal-title":"Infection and Immunity"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"e36095","DOI":"10.1371\/journal.pone.0036095","article-title":"Loss of sex and age driven differences in the gut microbiome characterize arthritis-susceptible 0401 mice but not arthritis-resistant 0402 mice","volume":"7","author":"A Gomez","year":"2012","journal-title":"PloS one"},{"key":"ref23","first-page":"1","article-title":"Interplay between human leukocyte antigen genes and the microbial colonization process of the newborn intestine","volume":"12","author":"G De Palma","year":"2010","journal-title":"Curr Issues Mol Biol"},{"key":"ref24","doi-asserted-by":"crossref","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":"MA Kriegel","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1186\/1471-230X-13-109","article-title":"Antibiotic exposure and the development of coeliac disease: a nationwide case-control study","volume":"13","author":"K Marild","year":"2013","journal-title":"BMC Gastroenterol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"609","DOI":"10.7326\/0003-4819-108-4-609","article-title":"A stool collection device: the first step in occult blood testing","volume":"108","author":"DA Ahlquist","year":"1988","journal-title":"Annals of Internal Medicine"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1186\/1471-2180-10-206","article-title":"Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags","volume":"10","author":"GD Wu","year":"2010","journal-title":"BMC microbiology"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"e74787","DOI":"10.1371\/journal.pone.0074787","article-title":"Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities","volume":"8","author":"G Henderson","year":"2013","journal-title":"PLoS One"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"e39315","DOI":"10.1371\/journal.pone.0039315","article-title":"Evaluation of 16S rDNA-based community profiling for human microbiome research","volume":"7","year":"2012","journal-title":"PLoS One"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"PD Schloss","year":"2009","journal-title":"Appl Environ Microbiol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/1471-2105-12-38","article-title":"Removing noise from pyrosequenced amplicons","volume":"12","author":"C Quince","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"2194","DOI":"10.1093\/bioinformatics\/btr381","article-title":"UCHIME improves sensitivity and speed of chimera detection","volume":"27","author":"RC Edgar","year":"2011","journal-title":"Bioinformatics"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"JG Caporaso","year":"2010","journal-title":"Nature methods"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1038\/nature09944","article-title":"Enterotypes of the human gut microbiome","volume":"473","author":"M Arumugam","year":"2011","journal-title":"Nature"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/nature11450","article-title":"A metagenome-wide association study of gut microbiota in type 2 diabetes","volume":"490","author":"J Qin","year":"2012","journal-title":"Nature"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","year":"2012","journal-title":"Nature"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1038\/nature13075","article-title":"Addendum: Enterotypes of the human gut microbiome","volume":"506","author":"M Arumugam","year":"2014","journal-title":"Nature"},{"key":"ref38","article-title":"High-density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis","author":"P Goyette","year":"2015","journal-title":"Nat Genet"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"e30791","DOI":"10.1371\/journal.pone.0030791","article-title":"Influence of milk-feeding type and genetic risk of developing coeliac disease on intestinal microbiota of infants: the PROFICEL study","volume":"7","author":"GD Palma","year":"2012","journal-title":"PLoS One"},{"key":"ref40","article-title":"The HLA-DQ2 genotype selects for early intestinal microbiota composition in infants at high risk of developing coeliac disease","author":"M Olivares","year":"2014","journal-title":"Gut"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1704","DOI":"10.1101\/gr.151803.112","article-title":"Meta-analyses of studies of the human microbiota","volume":"23","author":"CA Lozupone","year":"2013","journal-title":"Genome Res"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1038\/ismej.2010.161","article-title":"Spatial organization of intestinal microbiota in the mouse ascending colon","volume":"5","author":"GM Nava","year":"2011","journal-title":"ISME J"},{"key":"ref43","doi-asserted-by":"crossref","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":"II Ivanov","year":"2009","journal-title":"Cell"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1126\/science.1198469","article-title":"Induction of colonic regulatory T cells by indigenous Clostridium species","volume":"331","author":"K Atarashi","year":"2011","journal-title":"Science"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1016\/j.chom.2014.02.005","article-title":"The treatment-naive microbiome in new-onset Crohn's disease","volume":"15","author":"D Gevers","year":"2014","journal-title":"Cell Host Microbe"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"e52078","DOI":"10.1371\/journal.pone.0052078","article-title":"Hypothesis testing and power calculations for taxonomic-based human microbiome data","volume":"7","author":"PS La Rosa","year":"2012","journal-title":"PLoS One"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1038\/nature07540","article-title":"A core gut microbiome in obese and lean twins","volume":"457","author":"PJ Turnbaugh","year":"2009","journal-title":"Nature"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1038\/nature12506","article-title":"Richness of human gut microbiome correlates with metabolic markers","volume":"500","author":"E Le Chatelier","year":"2013","journal-title":"Nature"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1038\/nature12331","article-title":"Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota","volume":"500","author":"K Atarashi","year":"2013","journal-title":"Nature"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1016\/j.humimm.2011.12.012","article-title":"Nature and nurture in Foxp3(+) regulatory T cell development, stability, and function","volume":"73","author":"TL Geiger","year":"2012","journal-title":"Hum Immunol"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0133804","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,20]],"date-time":"2018-10-20T09:50:45Z","timestamp":1540029045000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0133804"}},"subtitle":[],"editor":[{"given":"Brenda A","family":"Wilson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2015,7,24]]},"references-count":50,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2015,7,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0133804","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,7,24]]}}}