{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,27]],"date-time":"2026-10-27T02:14:06Z","timestamp":1793067246573,"version":"4.5.0"},"reference-count":187,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2019,3,1]],"date-time":"2019-03-01T00:00:00Z","timestamp":1551398400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2019,3,1]],"date-time":"2019-03-01T00:00:00Z","timestamp":1551398400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2019,1,9]],"date-time":"2019-01-09T00:00:00Z","timestamp":1546992000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Autoimmunity"],"published-print":{"date-parts":[[2019,3]]},"DOI":"10.1016\/j.jaut.2019.01.001","type":"journal-article","created":{"date-parts":[[2019,1,9]],"date-time":"2019-01-09T09:02:24Z","timestamp":1547024544000},"page":"1-12","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":49,"special_numbering":"C","title":["Gut microbiota in children and altered profiles in juvenile idiopathic arthritis"],"prefix":"10.1016","volume":"98","author":[{"given":"Carlotta","family":"De Filippo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monica","family":"Di Paola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Teresa","family":"Giani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Tirelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rolando","family":"Cimaz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jaut.2019.01.001_bib1","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/j.resmic.2007.12.007","article-title":"Is meconium from healthy newborns actually sterile?","volume":"159","author":"Jimenez","year":"2008","journal-title":"Res. Microbiol."},{"key":"10.1016\/j.jaut.2019.01.001_bib2","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1111\/cea.12063","article-title":"Meconium microbiota types dominated by lactic acid or enteric bacteria are differentially associated with maternal eczema and respiratory problems in infants","volume":"43","author":"Gosalbes","year":"2013","journal-title":"Clin. Exp. Allergy: J. British Soc. Allergy Clin. Immunol."},{"key":"10.1016\/j.jaut.2019.01.001_bib3","doi-asserted-by":"crossref","first-page":"1614","DOI":"10.1136\/gutjnl-2018-315988","article-title":"Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus","volume":"67","author":"Wang","year":"2018","journal-title":"Gut"},{"key":"10.1016\/j.jaut.2019.01.001_bib4","doi-asserted-by":"crossref","first-page":"e177","DOI":"10.1371\/journal.pbio.0050177","article-title":"Development of the human infant intestinal microbiota","volume":"5","author":"Palmer","year":"2007","journal-title":"PLoS Biol."},{"key":"10.1016\/j.jaut.2019.01.001_bib5","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","author":"Human Microbiome Project","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.jaut.2019.01.001_bib6","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1126\/science.1110591","article-title":"Diversity of the human intestinal microbial flora","volume":"308","author":"Eckburg","year":"2005","journal-title":"Science"},{"key":"10.1016\/j.jaut.2019.01.001_bib7","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature08821","article-title":"A human gut microbial gene catalogue established by metagenomic sequencing","volume":"464","author":"Qin","year":"2010","journal-title":"Nature"},{"key":"10.1016\/j.jaut.2019.01.001_bib8","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1126\/science.1104816","article-title":"Host-bacterial mutualism in the human intestine","volume":"307","author":"Backhed","year":"2005","journal-title":"Science"},{"key":"10.1016\/j.jaut.2019.01.001_bib9","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1111\/j.1651-2227.2008.01060.x","article-title":"Establishment of the gut microbiota in Western infants","volume":"98","author":"Adlerberth","year":"2009","journal-title":"Acta Paediatr."},{"key":"10.1016\/j.jaut.2019.01.001_bib10","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/j.copbio.2010.03.020","article-title":"Programming infant gut microbiota: influence of dietary and environmental factors","volume":"21","author":"Marques","year":"2010","journal-title":"Curr. Opin. Biotechnol."},{"issue":"Suppl 1","key":"10.1016\/j.jaut.2019.01.001_bib11","doi-asserted-by":"crossref","first-page":"4578","DOI":"10.1073\/pnas.1000081107","article-title":"Succession of microbial consortia in the developing infant gut microbiome","volume":"108","author":"Koenig","year":"2011","journal-title":"Proceed. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jaut.2019.01.001_bib12","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1038\/nature11053","article-title":"Human gut microbiome viewed across age and geography","volume":"486","author":"Yatsunenko","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.jaut.2019.01.001_bib13","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1111\/j.1574-6941.2011.01120.x","article-title":"Distal gut microbiota of adolescent children is different from that of adults","volume":"77","author":"Agans","year":"2011","journal-title":"FEMS Microbiol. Ecol."},{"key":"10.1016\/j.jaut.2019.01.001_bib14","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0064315","article-title":"Intestinal microbiota in healthy U.S. young children and adults--a high throughput microarray analysis","volume":"8","author":"Ringel-Kulka","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.jaut.2019.01.001_bib15","first-page":"323","article-title":"Contribution of the intestinal microbiota to human health: from birth to 100 years of age","volume":"358","author":"Cheng","year":"2013","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"10.1016\/j.jaut.2019.01.001_bib16","doi-asserted-by":"crossref","DOI":"10.1371\/annotation\/df45912f-d15c-44ab-8312-e7ec0607604d","article-title":"Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians","volume":"5","author":"Biagi","year":"2010","journal-title":"PLoS One"},{"key":"10.1016\/j.jaut.2019.01.001_bib17","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1038\/nature11550","article-title":"Diversity, stability and resilience of the human gut microbiota","volume":"489","author":"Lozupone","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.jaut.2019.01.001_bib18","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1053\/j.gastro.2014.02.009","article-title":"The microbiome in inflammatory bowel disease: current status and the future ahead","volume":"146","author":"Kostic","year":"2014","journal-title":"Gastroenterology"},{"key":"10.1016\/j.jaut.2019.01.001_bib19","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1126\/science.1155725","article-title":"Evolution of mammals and their gut microbes","volume":"320","author":"Ley","year":"2008","journal-title":"Science"},{"key":"10.1016\/j.jaut.2019.01.001_bib20","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/nature12480","article-title":"Dietary intervention impact on gut microbial gene richness","volume":"500","author":"Cotillard","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.jaut.2019.01.001_bib21","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":"Le Chatelier","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.jaut.2019.01.001_bib22","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":"Turnbaugh","year":"2009","journal-title":"Nature"},{"key":"10.1016\/j.jaut.2019.01.001_bib23","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1126\/science.aad2602","article-title":"The ecology of the microbiome: networks, competition, and stability","volume":"350","author":"Coyte","year":"2015","journal-title":"Science"},{"key":"10.1016\/j.jaut.2019.01.001_bib24","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1126\/science.1241165","article-title":"The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis","volume":"341","author":"Smith","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.jaut.2019.01.001_bib25","doi-asserted-by":"crossref","first-page":"11450","DOI":"10.1038\/s41598-017-11734-8","article-title":"Butyrate-producing bacteria supplemented in vitro to Crohn's disease patient microbiota increased butyrate production and enhanced intestinal epithelial barrier integrity","volume":"7","author":"Geirnaert","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.jaut.2019.01.001_bib26","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1016\/j.cell.2016.10.020","article-title":"Linking the human gut microbiome to inflammatory cytokine production capacity","volume":"167","author":"Schirmer","year":"2016","journal-title":"Cell"},{"key":"10.1016\/j.jaut.2019.01.001_bib27","doi-asserted-by":"crossref","first-page":"2474","DOI":"10.1016\/j.celrep.2016.10.053","article-title":"Differential effects of environmental and genetic factors on T and B cell immune traits","volume":"17","author":"Aguirre-Gamboa","year":"2016","journal-title":"Cell Rep."},{"key":"10.1016\/j.jaut.2019.01.001_bib28","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1016\/j.cell.2016.10.017","article-title":"A functional genomics approach to understand variation in cytokine production in humans","volume":"167","author":"Li","year":"2016","journal-title":"Cell"},{"key":"10.1016\/j.jaut.2019.01.001_bib29","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1016\/j.cell.2016.10.018","article-title":"Host and environmental factors influencing individual human cytokine responses","volume":"167","author":"Ter Horst","year":"2016","journal-title":"Cell"},{"key":"10.1016\/j.jaut.2019.01.001_bib30","doi-asserted-by":"crossref","first-page":"7806","DOI":"10.1038\/ncomms8806","article-title":"Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model","volume":"6","author":"Brown","year":"2015","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jaut.2019.01.001_bib31","doi-asserted-by":"crossref","first-page":"1350","DOI":"10.1111\/eci.12548","article-title":"Immune dysregulation in the functional gastrointestinal disorders","volume":"45","author":"Keely","year":"2015","journal-title":"Eur. J. Clin. Investig."},{"key":"10.1016\/j.jaut.2019.01.001_bib32","doi-asserted-by":"crossref","first-page":"1659","DOI":"10.1038\/ajg.2016.227","article-title":"No change in the mucosal gut microbiome is associated with celiac disease-specific microbiome alteration in adult patients","volume":"111","author":"D'Argenio","year":"2016","journal-title":"Am. J. Gastroenterol."},{"key":"10.1016\/j.jaut.2019.01.001_bib33","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1016\/j.tim.2016.02.001","article-title":"Involvement of bacteria other than Clostridium difficile in antibiotic-associated diarrhoea","volume":"24","author":"Larcombe","year":"2016","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.jaut.2019.01.001_bib34","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1007\/s11064-014-1266-6","article-title":"Chronic functional bowel syndrome enhances gut-brain axis dysfunction, neuroinflammation, cognitive impairment, and vulnerability to dementia","volume":"39","author":"Daulatzai","year":"2014","journal-title":"Neurochem. Res."},{"key":"10.1016\/j.jaut.2019.01.001_bib35","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1136\/gutjnl-2015-309897","article-title":"Periodontitis induced by Porphyromonas gingivalis drives periodontal microbiota dysbiosis and insulin resistance via an impaired adaptive immune response","volume":"66","author":"Blasco-Baque","year":"2017","journal-title":"Gut"},{"key":"10.1016\/j.jaut.2019.01.001_bib36","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1586\/1744666X.2016.1139452","article-title":"Allergies and asthma: do atopic disorders result from inadequate immune homeostasis arising from infant gut dysbiosis?","volume":"12","author":"Johnson","year":"2016","journal-title":"Expert Rev. Clin. Immunol."},{"key":"10.1016\/j.jaut.2019.01.001_bib37","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s40168-017-0242-1","article-title":"New evidences on the altered gut microbiota in autism spectrum disorders","volume":"5","author":"Strati","year":"2017","journal-title":"Microbiome"},{"key":"10.1016\/j.jaut.2019.01.001_bib38","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1093\/intimm\/dxs094","article-title":"Regulation of intestinal homeostasis by innate and adaptive immunity","volume":"24","author":"Kayama","year":"2012","journal-title":"Int. Immunol."},{"key":"10.1016\/j.jaut.2019.01.001_bib39","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1038\/nature11319","article-title":"Gut microbiota composition correlates with diet and health in the elderly","volume":"488","author":"Claesson","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.jaut.2019.01.001_bib40","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/nri2515","article-title":"The gut microbiota shapes intestinal immune responses during health and disease","volume":"9","author":"Round","year":"2009","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.jaut.2019.01.001_bib41","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1097\/00130832-200310000-00003","article-title":"Innate immune responses to mycobacteria and the downregulation of atopic responses","volume":"3","author":"Rook","year":"2003","journal-title":"Curr. Opin. Allergy Clin. Immunol."},{"issue":"Suppl 1","key":"10.1016\/j.jaut.2019.01.001_bib42","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1136\/thorax.55.suppl_1.S2","article-title":"Family size, infection and atopy: the first decade of the \u201chygiene hypothesis\u201d","volume":"55","author":"Strachan","year":"2000","journal-title":"Thorax"},{"key":"10.1016\/j.jaut.2019.01.001_bib43","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1093\/emph\/eot004","article-title":"Microbial \u2018Old Friends\u2019, immunoregulation and stress resilience","volume":"2013","author":"Rook","year":"2013","journal-title":"Evol., Med., Publ. Health"},{"key":"10.1016\/j.jaut.2019.01.001_bib44","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1136\/gut.2004.053785","article-title":"Microbes, immunoregulation, and the gut","volume":"54","author":"Rook","year":"2005","journal-title":"Gut"},{"key":"10.1016\/j.jaut.2019.01.001_bib45","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1111\/j.1365-2222.2005.02112.x","article-title":"Old friends for breakfast","volume":"35","author":"Rook","year":"2005","journal-title":"Clin. Exp. Allergy: J. British Soc. Allergy Clin. Immunol."},{"key":"10.1016\/j.jaut.2019.01.001_bib46","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1016\/j.tim.2006.03.001","article-title":"The Neolithic revolution of bacterial genomes","volume":"14","author":"Mira","year":"2006","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.jaut.2019.01.001_bib47","doi-asserted-by":"crossref","DOI":"10.1126\/science.aaf1098","article-title":"Trained immunity: a program of innate immune memory in health and disease","volume":"352","author":"Netea","year":"2016","journal-title":"Science"},{"key":"10.1016\/j.jaut.2019.01.001_bib48","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1099\/00222615-15-2-189","article-title":"The microbial ecology of the large bowel of breast-fed and formula-fed infants during the first year of life","volume":"15","author":"Stark","year":"1982","journal-title":"J. Med. Microbiol."},{"key":"10.1016\/j.jaut.2019.01.001_bib49","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1542\/peds.72.3.317","article-title":"Development and differences of intestinal flora in the neonatal period in breast-fed and bottle-fed infants","volume":"72","author":"Yoshioka","year":"1983","journal-title":"Pediatrics"},{"key":"10.1016\/j.jaut.2019.01.001_bib50","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1542\/peds.2005-2824","article-title":"Factors influencing the composition of the intestinal microbiota in early infancy","volume":"118","author":"Penders","year":"2006","journal-title":"Pediatrics"},{"key":"10.1016\/j.jaut.2019.01.001_bib51","doi-asserted-by":"crossref","first-page":"1685","DOI":"10.1136\/adc.64.12.1685","article-title":"Diet and faecal flora in the newborn: lactoferrin","volume":"64","author":"Balmer","year":"1989","journal-title":"Arch. Dis. Child."},{"key":"10.1016\/j.jaut.2019.01.001_bib52","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1017\/S0954422410000065","article-title":"Breast- v. formula-feeding: impacts on the digestive tract and immediate and long-term health effects","volume":"23","author":"Le Huerou-Luron","year":"2010","journal-title":"Nutr. Res. Rev."},{"key":"10.1016\/j.jaut.2019.01.001_bib53","first-page":"17","article-title":"Human milk vs. cow's milk and the evolution of infant formulas","volume":"vol. 67","author":"Hernell","year":"2011"},{"key":"10.1016\/j.jaut.2019.01.001_bib54","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1136\/gut.47.5.646","article-title":"Bifidobacterium strains from resident infant human gastrointestinal microflora exert antimicrobial activity","volume":"47","author":"Lievin","year":"2000","journal-title":"Gut"},{"issue":"Suppl 1","key":"10.1016\/j.jaut.2019.01.001_bib55","first-page":"I32","article-title":"The role of the intestinal microflora for the development of the immune system in early childhood","volume":"41","author":"Ouwehand","year":"2002","journal-title":"Eur. J. Nutr."},{"key":"10.1016\/j.jaut.2019.01.001_bib56","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1038\/nature09646","article-title":"Bifidobacteria can protect from enteropathogenic infection through production of acetate","volume":"469","author":"Fukuda","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.jaut.2019.01.001_bib57","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1038\/ismej.2010.118","article-title":"Dominant and diet-responsive groups of bacteria within the human colonic microbiota","volume":"5","author":"Walker","year":"2011","journal-title":"ISME J."},{"key":"10.1016\/j.jaut.2019.01.001_bib58","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1111\/j.1462-2920.2006.01186.x","article-title":"Selective colonization of insoluble substrates by human faecal bacteria","volume":"9","author":"Leitch","year":"2007","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.jaut.2019.01.001_bib59","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/nrmicro2746","article-title":"How glycan metabolism shapes the human gut microbiota","volume":"10","author":"Koropatkin","year":"2012","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.jaut.2019.01.001_bib60","doi-asserted-by":"crossref","first-page":"14691","DOI":"10.1073\/pnas.1005963107","article-title":"Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa","volume":"107","author":"De Filippo","year":"2010","journal-title":"Proceed. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jaut.2019.01.001_bib61","doi-asserted-by":"crossref","first-page":"1979","DOI":"10.3389\/fmicb.2017.01979","article-title":"Diet, environments, and gut microbiota. A preliminary investigation in children living in rural and urban Burkina Faso and Italy","volume":"8","author":"De Filippo","year":"2017","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.jaut.2019.01.001_bib62","doi-asserted-by":"crossref","first-page":"3654","DOI":"10.1038\/ncomms4654","article-title":"Gut microbiome of the Hadza hunter-gatherers","volume":"5","author":"Schnorr","year":"2014","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jaut.2019.01.001_bib63","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1016\/j.celrep.2015.03.049","article-title":"The gut microbiota of rural papua new guineans: composition, diversity patterns, and ecological processes","volume":"11","author":"Martinez","year":"2015","journal-title":"Cell Rep."},{"key":"10.1016\/j.jaut.2019.01.001_bib64","doi-asserted-by":"crossref","first-page":"2142","DOI":"10.1016\/j.celrep.2016.02.013","article-title":"Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns","volume":"14","author":"Gomez","year":"2016","journal-title":"Cell Rep."},{"key":"10.1016\/j.jaut.2019.01.001_bib65","article-title":"Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States","volume":"8","author":"Lin","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.jaut.2019.01.001_bib66","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":"David","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.jaut.2019.01.001_bib67","doi-asserted-by":"crossref","first-page":"R60","DOI":"10.1186\/gb-2012-13-7-r60","article-title":"A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples","volume":"13","author":"Dollive","year":"2012","journal-title":"Genome Biol."},{"key":"10.1016\/j.jaut.2019.01.001_bib68","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0066019","article-title":"Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents","volume":"8","author":"Hoffmann","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.jaut.2019.01.001_bib69","doi-asserted-by":"crossref","first-page":"10011","DOI":"10.1073\/pnas.0602187103","article-title":"A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism","volume":"103","author":"Samuel","year":"2006","journal-title":"Proceed. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jaut.2019.01.001_bib70","doi-asserted-by":"crossref","first-page":"1306","DOI":"10.1111\/j.1572-0241.1998.00415.x","article-title":"Anti-Saccharomyces cerevisiae mannan antibodies in familial Crohn's disease","volume":"93","author":"Sendid","year":"1998","journal-title":"Am. J. Gastroenterol."},{"key":"10.1016\/j.jaut.2019.01.001_bib71","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.1126\/science.1221789","article-title":"Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis","volume":"336","author":"Iliev","year":"2012","journal-title":"Science"},{"key":"10.1016\/j.jaut.2019.01.001_bib72","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1136\/gutjnl-2015-310746","article-title":"Fungal microbiota dysbiosis in IBD","volume":"66","author":"Sokol","year":"2016","journal-title":"Gut"},{"key":"10.1016\/j.jaut.2019.01.001_bib73","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1038\/nature09944","article-title":"Enterotypes of the human gut microbiome","volume":"473","author":"Arumugam","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.jaut.2019.01.001_bib74","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1126\/science.1208344","article-title":"Linking long-term dietary patterns with gut microbial enterotypes","volume":"334","author":"Wu","year":"2011","journal-title":"Science"},{"key":"10.1016\/j.jaut.2019.01.001_bib75","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1002863","article-title":"A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets","volume":"9","author":"Koren","year":"2013","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.jaut.2019.01.001_bib76","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1002606","article-title":"Microbial co-occurrence relationships in the human microbiome","volume":"8","author":"Faust","year":"2012","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.jaut.2019.01.001_bib77","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature18846","article-title":"Diet-microbiota interactions as moderators of human metabolism","volume":"535","author":"Sonnenburg","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.jaut.2019.01.001_bib78","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1007\/s10096-012-1787-3","article-title":"The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics","volume":"32","author":"Dubourg","year":"2013","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis. : Off. Publ. Eur. Soc. Clin. Microbiol."},{"key":"10.1016\/j.jaut.2019.01.001_bib79","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0009836","article-title":"Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome","volume":"5","author":"Jakobsson","year":"2010","journal-title":"PLoS One"},{"key":"10.1016\/j.jaut.2019.01.001_bib80","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.0060280","article-title":"The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing","volume":"6","author":"Dethlefsen","year":"2008","journal-title":"PLoS Biol."},{"key":"10.1016\/j.jaut.2019.01.001_bib81","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0095476","article-title":"Short-term effect of antibiotics on human gut microbiota","volume":"9","author":"Panda","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.jaut.2019.01.001_bib82","doi-asserted-by":"crossref","first-page":"5811","DOI":"10.1128\/AAC.00789-12","article-title":"High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin","volume":"56","author":"Fouhy","year":"2012","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jaut.2019.01.001_bib83","doi-asserted-by":"crossref","first-page":"5537","DOI":"10.1007\/s00253-016-7410-2","article-title":"Evaluation of the effects of intrapartum antibiotic prophylaxis on newborn intestinal microbiota using a sequencing approach targeted to multi hypervariable 16S rDNA regions","volume":"100","author":"Aloisio","year":"2016","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"10.1016\/j.jaut.2019.01.001_bib84","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1186\/s40168-018-0567-4","article-title":"Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants","volume":"6","author":"Korpela","year":"2018","journal-title":"Microbiome"},{"key":"10.1016\/j.jaut.2019.01.001_bib85","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1038\/s42003-018-0140-5","article-title":"Antibiotic treatment of rat dams affects bacterial colonization and causes decreased weight gain in pups","volume":"1","author":"Tulstrup","year":"2018","journal-title":"Commun. Biol."},{"issue":"Suppl 1","key":"10.1016\/j.jaut.2019.01.001_bib86","doi-asserted-by":"crossref","first-page":"4554","DOI":"10.1073\/pnas.1000087107","article-title":"Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation","volume":"108","author":"Dethlefsen","year":"2011","journal-title":"Proceed. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jaut.2019.01.001_bib87","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/ismej.2007.3","article-title":"Long-term ecological impacts of antibiotic administration on the human intestinal microbiota","volume":"1","author":"Jernberg","year":"2007","journal-title":"ISME J."},{"key":"10.1016\/j.jaut.2019.01.001_bib88","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/s12969-016-0104-6","article-title":"Gut microbiota-host interactions and juvenile idiopathic arthritis","volume":"14","author":"Arvonen","year":"2016","journal-title":"Pediatric Rheumatol. Online J."},{"key":"10.1016\/j.jaut.2019.01.001_bib89","doi-asserted-by":"crossref","first-page":"1768","DOI":"10.1126\/science.1195568","article-title":"Has the microbiota played a critical role in the evolution of the adaptive immune system?","volume":"330","author":"Lee","year":"2010","journal-title":"Science"},{"key":"10.1016\/j.jaut.2019.01.001_bib90","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0033387","article-title":"Proof of concept of microbiome-metabolome analysis and delayed gluten exposure on celiac disease autoimmunity in genetically at-risk infants","volume":"7","author":"Sellitto","year":"2012","journal-title":"PLoS One"},{"key":"10.1016\/j.jaut.2019.01.001_bib91","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1038\/nature07336","article-title":"Innate immunity and intestinal microbiota in the development of Type 1 diabetes","volume":"455","author":"Wen","year":"2008","journal-title":"Nature"},{"key":"10.1016\/j.jaut.2019.01.001_bib92","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1038\/ismej.2010.92","article-title":"Toward defining the autoimmune microbiome for type 1 diabetes","volume":"5","author":"Giongo","year":"2011","journal-title":"ISME J."},{"key":"10.1016\/j.jaut.2019.01.001_bib93","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1016\/j.patbio.2007.09.008","article-title":"Role of gut microflora in the development of obesity and insulin resistance following high-fat diet feeding","volume":"56","author":"Cani","year":"2008","journal-title":"Pathol. Biol."},{"key":"10.1016\/j.jaut.2019.01.001_bib94","first-page":"1543","article-title":"Antibiotics and the human gut microbiome: dysbioses and accumulation of resistances","volume":"6","author":"Francino","year":"2015","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.jaut.2019.01.001_bib95","doi-asserted-by":"crossref","first-page":"769","DOI":"10.3390\/pathogens3030769","article-title":"Early development of the gut microbiota and immune health","volume":"3","author":"Francino","year":"2014","journal-title":"Pathogens"},{"key":"10.1016\/j.jaut.2019.01.001_bib96","doi-asserted-by":"crossref","first-page":"e333","DOI":"10.1542\/peds.2015-0036","article-title":"Antibiotic exposure and juvenile idiopathic arthritis: a case-control study","volume":"136","author":"Horton","year":"2015","journal-title":"Pediatrics"},{"key":"10.1016\/j.jaut.2019.01.001_bib97","doi-asserted-by":"crossref","first-page":"521","DOI":"10.3899\/jrheum.140348","article-title":"Repeated exposure to antibiotics in infancy: a predisposing factor for juvenile idiopathic arthritis or a sign of this group's greater susceptibility to infections?","volume":"42","author":"Arvonen","year":"2015","journal-title":"J. Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib98","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1136\/gut.2010.219683","article-title":"Antibiotic use and inflammatory bowel diseases in childhood","volume":"60","author":"Hviid","year":"2011","journal-title":"Gut"},{"key":"10.1016\/j.jaut.2019.01.001_bib99","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.3000322","article-title":"The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice","volume":"1","author":"Turnbaugh","year":"2009","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.jaut.2019.01.001_bib100","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1038\/nri3112","article-title":"The impact of perinatal immune development on mucosal homeostasis and chronic inflammation","volume":"12","author":"Renz","year":"2011","journal-title":"Nat. Rev. Immunol."},{"issue":"Suppl 2","key":"10.1016\/j.jaut.2019.01.001_bib101","doi-asserted-by":"crossref","first-page":"17281","DOI":"10.1073\/pnas.1202244109","article-title":"Early environments and the ecology of inflammation","volume":"109","author":"McDade","year":"2012","journal-title":"Proceed. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jaut.2019.01.001_bib102","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1111\/apm.12023","article-title":"The \u2018Hygiene hypothesis\u2019 and the sharp gradient in the incidence of autoimmune and allergic diseases between Russian Karelia and Finland","volume":"121","author":"Kondrashova","year":"2013","journal-title":"APMIS: Acta Pathol. Microbiol. Immunol. Scand."},{"key":"10.1016\/j.jaut.2019.01.001_bib103","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1111\/cea.12332","article-title":"The gut microbiota and its role in the development of allergic disease: a wider perspective","volume":"45","author":"West","year":"2015","journal-title":"Clin. Exp. Allergy : J. British Soc. Allergy Clin. Immunol."},{"key":"10.1016\/j.jaut.2019.01.001_bib104","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1038\/s41575-018-0003-z","article-title":"Urbanization and the gut microbiota in health and inflammatory bowel disease","volume":"15","author":"Zuo","year":"2018","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib105","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1038\/nrmicro2245","article-title":"What are the consequences of the disappearing human microbiota?","volume":"7","author":"Blaser","year":"2009","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.jaut.2019.01.001_bib106","doi-asserted-by":"crossref","DOI":"10.1155\/2017\/8201672","article-title":"New frontiers in genetics, gut microbiota, and immunity: a Rosetta stone for the pathogenesis of inflammatory bowel disease","volume":"2017","author":"Zhou","year":"2017","journal-title":"BioMed Res. Int."},{"key":"10.1016\/j.jaut.2019.01.001_bib107","doi-asserted-by":"crossref","first-page":"4","DOI":"10.4161\/gmic.19320","article-title":"The role of gut microbiota in immune homeostasis and autoimmunity","volume":"3","author":"Wu","year":"2012","journal-title":"Gut Microb."},{"key":"10.1016\/j.jaut.2019.01.001_bib108","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1136\/gutjnl-2016-313235","article-title":"A microbial signature for Crohn's disease","volume":"66","author":"Pascal","year":"2017","journal-title":"Gut"},{"key":"10.1016\/j.jaut.2019.01.001_bib109","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1111\/apt.14384","article-title":"Review article: the gut microbiome in inflammatory bowel disease-avenues for microbial management","volume":"47","author":"McIlroy","year":"2018","journal-title":"Aliment. Pharmacol. Ther."},{"key":"10.1016\/j.jaut.2019.01.001_bib110","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1136\/annrheumdis-2015-208187","article-title":"Patients with ankylosing spondylitis have been breast fed less often than healthy controls: a case-control retrospective study","volume":"75","author":"Montoya","year":"2016","journal-title":"Ann. Rheum. Dis."},{"key":"10.1016\/j.jaut.2019.01.001_bib111","first-page":"1166","article-title":"Breast feeding and the development of juvenile rheumatoid arthritis","volume":"22","author":"Mason","year":"1995","journal-title":"J. Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib112","first-page":"1080","article-title":"Evaluation of associations between breast feeding and subsequent development of juvenile rheumatoid arthritis","volume":"23","author":"Rosenberg","year":"1996","journal-title":"J. Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib113","first-page":"2286","article-title":"Does breast feeding prevent the development of juvenile rheumatoid arthritis?","volume":"25","author":"Kasapcopur","year":"1998","journal-title":"J. Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib114","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1016\/j.coi.2010.06.008","article-title":"Microbiota-stimulated immune mechanisms to maintain gut homeostasis","volume":"22","author":"Chung","year":"2010","journal-title":"Curr. Opin. Immunol."},{"key":"10.1016\/j.jaut.2019.01.001_bib115","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1186\/s13075-014-0486-0","article-title":"Altered microbiota associated with abnormal humoral immune responses to commensal organisms in enthesitis-related arthritis","volume":"16","author":"Stoll","year":"2014","journal-title":"Arthritis Res. Ther."},{"key":"10.1016\/j.jaut.2019.01.001_bib116","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1016\/j.immuni.2010.06.001","article-title":"Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells","volume":"32","author":"Wu","year":"2010","journal-title":"Immunity"},{"key":"10.1016\/j.jaut.2019.01.001_bib117","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1186\/s13075-017-1398-6","article-title":"The impact of age and gut microbiota on Th17 and Tfh cells in K\/BxN autoimmune arthritis","volume":"19","author":"Teng","year":"2017","journal-title":"Arthritis Res. Ther."},{"key":"10.1016\/j.jaut.2019.01.001_bib118","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1038\/mi.2009.132","article-title":"Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis","volume":"3","author":"Hill","year":"2010","journal-title":"Mucosal Immunol."},{"key":"10.1016\/j.jaut.2019.01.001_bib119","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1080\/19490976.2015.1127463","article-title":"Antibiotic-treated versus germ-free rodents for microbiota transplantation studies","volume":"7","author":"Lundberg","year":"2016","journal-title":"Gut Microb."},{"key":"10.1016\/j.jaut.2019.01.001_bib120","article-title":"Akkermansia muciniphila is permissive to arthritis in the K\/BxN mouse model of arthritis","author":"Stoll","year":"2018","journal-title":"Genes Immun."},{"key":"10.1016\/j.jaut.2019.01.001_bib121","doi-asserted-by":"crossref","first-page":"2359","DOI":"10.1084\/jem.180.6.2359","article-title":"The germfree state prevents development of gut and joint inflammatory disease in HLA-B27 transgenic rats","volume":"180","author":"Taurog","year":"1994","journal-title":"J. Exp. Med."},{"key":"10.1016\/j.jaut.2019.01.001_bib122","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1172\/JCI118878","article-title":"Normal luminal bacteria, especially Bacteroides species, mediate chronic colitis, gastritis, and arthritis in HLA-B27\/human beta2 microglobulin transgenic rats","volume":"98","author":"Rath","year":"1996","journal-title":"J. Clin. Invest."},{"key":"10.1016\/j.jaut.2019.01.001_bib123","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1097\/BOR.0000000000000190","article-title":"The functional impact of the intestinal microbiome on mucosal immunity and systemic autoimmunity","volume":"27","author":"Longman","year":"2015","journal-title":"Curr. Opin. Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib124","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1111\/1756-185X.12728","article-title":"Does the buck stop with the bugs?: an overview of microbial dysbiosis in rheumatoid arthritis","volume":"19","author":"Sandhya","year":"2016","journal-title":"Int. J. Rheum. Dis."},{"key":"10.1016\/j.jaut.2019.01.001_bib125","doi-asserted-by":"crossref","first-page":"2295","DOI":"10.1128\/iai.63.6.2295-2301.1995","article-title":"Reactivation of arthritis induced by small bowel bacterial overgrowth in rats: role of cytokines, bacteria, and bacterial polymers","volume":"63","author":"Lichtman","year":"1995","journal-title":"Infect. Immun."},{"key":"10.1016\/j.jaut.2019.01.001_bib126","doi-asserted-by":"crossref","first-page":"1402","DOI":"10.1002\/art.1780281213","article-title":"Reactivation of streptococcal cell wall-induced arthritis by homologous and heterologous cell wall polymers","volume":"28","author":"Esser","year":"1985","journal-title":"Arthritis Rheum."},{"key":"10.1016\/j.jaut.2019.01.001_bib127","doi-asserted-by":"crossref","first-page":"1688","DOI":"10.1084\/jem.165.6.1688","article-title":"Lipopolysaccharide induces recurrence of arthritis in rat joints previously injured by peptidoglycan-polysaccharide","volume":"165","author":"Stimpson","year":"1987","journal-title":"J. Exp. Med."},{"key":"10.1016\/j.jaut.2019.01.001_bib128","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1056\/NEJM198901263200404","article-title":"Yersinia antigens in synovial-fluid cells from patients with reactive arthritis","volume":"320","author":"Granfors","year":"1989","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.jaut.2019.01.001_bib129","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1016\/0140-6736(90)90804-E","article-title":"Salmonella lipopolysaccharide in synovial cells from patients with reactive arthritis","volume":"335","author":"Granfors","year":"1990","journal-title":"Lancet"},{"key":"10.1016\/j.jaut.2019.01.001_bib130","doi-asserted-by":"crossref","first-page":"3753","DOI":"10.1002\/art.24127","article-title":"Shift from toll-like receptor 2 (TLR-2) toward TLR-4 dependency in the erosive stage of chronic streptococcal cell wall arthritis coincident with TLR-4-mediated interleukin-17 production","volume":"58","author":"Abdollahi-Roodsaz","year":"2008","journal-title":"Arthritis Rheum."},{"key":"10.1016\/j.jaut.2019.01.001_bib131","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1016\/j.humimm.2008.08.296","article-title":"Commensal intestinal bacterial strains trigger ankylosing enthesopathy of the ankle in inbred B10.BR (H-2(k)) male mice","volume":"69","author":"Sinkorova","year":"2008","journal-title":"Hum. Immunol."},{"key":"10.1016\/j.jaut.2019.01.001_bib132","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.01202","article-title":"Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis","volume":"2","author":"Scher","year":"2013","journal-title":"eLife"},{"key":"10.1016\/j.jaut.2019.01.001_bib133","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1097\/BOR.0000000000000008","article-title":"Microbiome and mucosal inflammation as extra-articular triggers for rheumatoid arthritis and autoimmunity","volume":"26","author":"Brusca","year":"2014","journal-title":"Curr. Opin. Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib134","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1002\/art.38967","article-title":"Brief Report: Intestinal dysbiosis in ankylosing spondylitis","volume":"67","author":"Costello","year":"2015","journal-title":"Arthritis Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib135","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1128\/IAI.01197-12","article-title":"Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization","volume":"81","author":"Ubeda","year":"2013","journal-title":"Infect. Immun."},{"key":"10.1016\/j.jaut.2019.01.001_bib136","doi-asserted-by":"crossref","first-page":"81","DOI":"10.3389\/fgene.2015.00081","article-title":"Mucin glycan foraging in the human gut microbiome","volume":"6","author":"Tailford","year":"2015","journal-title":"Front. Genet."},{"key":"10.1016\/j.jaut.2019.01.001_bib137","doi-asserted-by":"crossref","first-page":"1429","DOI":"10.1053\/gast.1996.v110.pm8613048","article-title":"Bacteroides fragilis enterotoxin modulates epithelial permeability and bacterial internalization by HT-29 enterocytes","volume":"110","author":"Wells","year":"1996","journal-title":"Gastroenterology"},{"key":"10.1016\/j.jaut.2019.01.001_bib138","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1099\/ijs.0.02873-0","article-title":"Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium","volume":"54","author":"Derrien","year":"2004","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"10.1016\/j.jaut.2019.01.001_bib139","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1093\/rheumatology\/33.7.644","article-title":"Intestinal permeability in patients with ankylosing spondylitis and their healthy relatives","volume":"33","author":"Martinez-Gonzalez","year":"1994","journal-title":"Br. J. Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib140","doi-asserted-by":"crossref","first-page":"2151","DOI":"10.1002\/art.39681","article-title":"Perturbed mucosal immunity and dysbiosis accompany clinical disease in a rat model of spondyloarthritis","volume":"68","author":"Asquith","year":"2016","journal-title":"Arthritis Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib141","first-page":"1538","article-title":"Evidence of subclinical intestinal inflammation by 99m technetium leukocyte scintigraphy in patients with HLA-B27 positive juvenile onset active spondyloarthropathy","volume":"27","author":"Lionetti","year":"2000","journal-title":"J. Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib142","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1007\/s11926-012-0314-y","article-title":"The role of the microbiome in rheumatic diseases","volume":"15","author":"Yeoh","year":"2013","journal-title":"Curr. Rheumatol. Rep."},{"key":"10.1016\/j.jaut.2019.01.001_bib143","doi-asserted-by":"crossref","first-page":"167","DOI":"10.14740\/gr641w","article-title":"Coeliac disease with rheumatoid arthritis: an unusual association","volume":"8","author":"Warjri","year":"2015","journal-title":"Gastroenterol. Res."},{"key":"10.1016\/j.jaut.2019.01.001_bib144","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1002\/acr.22932","article-title":"Impact of obesity on remission and disease activity in rheumatoid arthritis: a systematic review and meta-analysis","volume":"69","author":"Liu","year":"2017","journal-title":"Arthritis Care Res."},{"key":"10.1016\/j.jaut.2019.01.001_bib145","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.semarthrit.2005.05.001","article-title":"Diet and rheumatoid arthritis: a review of the literature","volume":"35","author":"Stamp","year":"2005","journal-title":"Semin. Arthritis Rheum."},{"key":"10.1016\/j.jaut.2019.01.001_bib146","doi-asserted-by":"crossref","first-page":"19","DOI":"10.2174\/1874312901812010019","article-title":"Role of diet in influencing rheumatoid arthritis disease activity","volume":"12","author":"Badsha","year":"2018","journal-title":"Open Rheumatol. J."},{"key":"10.1016\/j.jaut.2019.01.001_bib147","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1111\/odi.12472","article-title":"The microbiome-systemic diseases connection","volume":"22","author":"van der Meulen","year":"2016","journal-title":"Oral Dis."},{"key":"10.1016\/j.jaut.2019.01.001_bib148","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.rdc.2010.11.006","article-title":"Role of diet in rheumatic disease","volume":"37","author":"Li","year":"2011","journal-title":"Rheum. Dis. Clin. N. Am."},{"key":"10.1016\/j.jaut.2019.01.001_bib149","doi-asserted-by":"crossref","first-page":"355","DOI":"10.3899\/jrheum.150036","article-title":"Intestinal dysbiosis and potential consequences of microbiome-altering antibiotic use in the pathogenesis of human rheumatic disease","volume":"42","author":"Scher","year":"2015","journal-title":"J. Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib150","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1038\/nrrheum.2016.85","article-title":"How the microbiota shapes rheumatic diseases","volume":"12","author":"Van de Wiele","year":"2016","journal-title":"Nat. Rev. Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib151","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.chom.2008.05.001","article-title":"Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases","volume":"3","author":"Peterson","year":"2008","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.jaut.2019.01.001_bib152","doi-asserted-by":"crossref","first-page":"1799","DOI":"10.1002\/ibd.22860","article-title":"Alterations in the gut microbiome of children with severe ulcerative colitis","volume":"18","author":"Michail","year":"2012","journal-title":"Inflamm. Bowel Dis."},{"key":"10.1016\/j.jaut.2019.01.001_bib153","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/1741-7015-11-46","article-title":"Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study","volume":"11","author":"Murri","year":"2013","journal-title":"BMC Med."},{"key":"10.1016\/j.jaut.2019.01.001_bib154","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1093\/rheumatology\/41.12.1395","article-title":"Comparison of the faecal microflora of patients with ankylosing spondylitis and controls using molecular methods of analysis","volume":"41","author":"Stebbings","year":"2002","journal-title":"Rheumatology"},{"key":"10.1016\/j.jaut.2019.01.001_bib155","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1016\/S0140-6736(07)60363-8","article-title":"Juvenile idiopathic arthritis","volume":"369","author":"Ravelli","year":"2007","journal-title":"Lancet"},{"key":"10.1016\/j.jaut.2019.01.001_bib156","first-page":"390","article-title":"International League of Associations for Rheumatology classification of juvenile idiopathic arthritis: second revision, Edmonton, 2001","volume":"31","author":"Petty","year":"2004","journal-title":"J. Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib157","first-page":"773","article-title":"Increased gut permeability in juvenile chronic arthritides. A multivariate analysis of the diagnostic parameters","volume":"18","author":"Picco","year":"2000","journal-title":"Clin. Exp. Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib158","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.clim.2015.05.001","article-title":"Gut microbes, immunity, and spondyloarthritis","volume":"159","author":"Stoll","year":"2015","journal-title":"Clin. Immunol."},{"key":"10.1016\/j.jaut.2019.01.001_bib159","doi-asserted-by":"crossref","DOI":"10.1155\/2013\/636785","article-title":"Dominant fecal microbiota in newly diagnosed untreated inflammatory bowel disease patients","volume":"2013","author":"Thorkildsen","year":"2013","journal-title":"Gastroenterol. Res. Pract."},{"key":"10.1016\/j.jaut.2019.01.001_bib160","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1128\/JCM.01500-13","article-title":"Increased proportions of Bifidobacterium and the Lactobacillus group and loss of butyrate-producing bacteria in inflammatory bowel disease","volume":"52","author":"Wang","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.jaut.2019.01.001_bib161","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/s13075-018-1510-6","article-title":"Age and fecal microbial strain-specific differences in patients with spondyloarthritis","volume":"20","author":"Stoll","year":"2018","journal-title":"Arthritis Res. Ther."},{"key":"10.1016\/j.jaut.2019.01.001_bib162","doi-asserted-by":"crossref","first-page":"4320","DOI":"10.1128\/AEM.69.7.4320-4324.2003","article-title":"Oligonucleotide probes that detect quantitatively significant groups of butyrate-producing bacteria in human feces","volume":"69","author":"Hold","year":"2003","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.jaut.2019.01.001_bib163","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1111\/cei.12900","article-title":"Gut microbiome in children with enthesitis-related arthritis in a developing country and the effect of probiotic administration","volume":"187","author":"Aggarwal","year":"2017","journal-title":"Clin. Exp. Immunol."},{"key":"10.1016\/j.jaut.2019.01.001_bib164","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.1016\/j.cell.2016.05.056","article-title":"Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans","volume":"165","author":"Vatanen","year":"2016","journal-title":"Cell"},{"key":"10.1016\/j.jaut.2019.01.001_bib165","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1136\/ard.41.1.15","article-title":"A sequential study of the relationship between faecal Klebsiella aerogenes and the common clinical manifestations of ankylosing spondylitis","volume":"41","author":"Eastmond","year":"1982","journal-title":"Ann. Rheum. Dis."},{"key":"10.1016\/j.jaut.2019.01.001_bib166","doi-asserted-by":"crossref","first-page":"2253","DOI":"10.1016\/S0002-9440(10)61172-8","article-title":"Enterococcus faecalis induces inflammatory bowel disease in interleukin-10 knockout mice","volume":"160","author":"Balish","year":"2002","journal-title":"Am. J. Pathol."},{"key":"10.1016\/j.jaut.2019.01.001_bib167","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1007\/s10096-015-2548-x","article-title":"Faecal microbiome in new-onset juvenile idiopathic arthritis","volume":"35","author":"Tejesvi","year":"2015","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis. : Off. Publ. Eur. Soc. Clin. Microbiol."},{"key":"10.1016\/j.jaut.2019.01.001_bib168","doi-asserted-by":"crossref","first-page":"1703","DOI":"10.3389\/fmicb.2016.01703","article-title":"Alteration of fecal microbiota profiles in juvenile idiopathic arthritis. Associations with HLA-B27 allele and disease status","volume":"7","author":"Di Paola","year":"2016","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.jaut.2019.01.001_bib169","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1002\/art.38892","article-title":"Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease","volume":"67","author":"Scher","year":"2015","journal-title":"Arthritis Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib170","doi-asserted-by":"crossref","first-page":"2020","DOI":"10.1053\/j.gastro.2005.03.046","article-title":"Antibodies to CBir1 flagellin define a unique response that is associated independently with complicated Crohn's disease","volume":"128","author":"Targan","year":"2005","journal-title":"Gastroenterology"},{"key":"10.1016\/j.jaut.2019.01.001_bib171","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1038\/nature11225","article-title":"Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-\/- mice","volume":"487","author":"Devkota","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.jaut.2019.01.001_bib172","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1111\/j.1574-6941.2002.tb00942.x","article-title":"Sulfate-reducing bacteria in human feces and their association with inflammatory bowel diseases","volume":"40","author":"Loubinoux","year":"2002","journal-title":"FEMS Microbiol. Ecol."},{"key":"10.1016\/j.jaut.2019.01.001_bib173","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1002\/bjs.6454","article-title":"Sulphate-reducing bacteria and hydrogen sulphide in the aetiology of ulcerative colitis","volume":"96","author":"Rowan","year":"2009","journal-title":"Br. J. Surg."},{"key":"10.1016\/j.jaut.2019.01.001_bib174","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1016\/j.jpedsurg.2013.06.026","article-title":"Acute appendicitis in children is associated with an abundance of bacteria from the phylum Fusobacteria","volume":"49","author":"Zhong","year":"2014","journal-title":"J. Pediatr. Surg."},{"key":"10.1016\/j.jaut.2019.01.001_bib175","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0034233","article-title":"Increased gut permeability and microbiota change associate with mesenteric fat inflammation and metabolic dysfunction in diet-induced obese mice","volume":"7","author":"Lam","year":"2012","journal-title":"PLoS One"},{"key":"10.1016\/j.jaut.2019.01.001_bib176","doi-asserted-by":"crossref","first-page":"4498","DOI":"10.1128\/AAC.00538-07","article-title":"Antimicrobial susceptibilities and clinical sources of Dialister species","volume":"51","author":"Morio","year":"2007","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jaut.2019.01.001_bib177","article-title":"Microbiome analytics of the gut microbiota in juvenile idiopathic arthritis patients: an observational, longitudinal cohort study","author":"van Dijkhuizen","year":"2018","journal-title":"Arthritis Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib178","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1038\/gene.2016.38","article-title":"Fecal metabolomics in pediatric spondyloarthritis implicate decreased metabolic diversity and altered tryptophan metabolism as pathogenic factors","volume":"17","author":"Stoll","year":"2016","journal-title":"Genes Immun."},{"key":"10.1016\/j.jaut.2019.01.001_bib179","doi-asserted-by":"crossref","first-page":"2344","DOI":"10.1002\/art.38715","article-title":"Treg cell function in rheumatoid arthritis is compromised by ctla-4 promoter methylation resulting in a failure to activate the indoleamine 2,3-dioxygenase pathway","volume":"66","author":"Cribbs","year":"2014","journal-title":"Arthritis Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib180","doi-asserted-by":"crossref","first-page":"2003","DOI":"10.3899\/jrheum.141505","article-title":"Downregulation of tryptophan-related metabolomic profile in rheumatoid arthritis synovial fluid","volume":"42","author":"Kang","year":"2015","journal-title":"J. Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib181","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1038\/nm.4102","article-title":"CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands","volume":"22","author":"Lamas","year":"2016","journal-title":"Nat. Med."},{"key":"10.1016\/j.jaut.2019.01.001_bib182","doi-asserted-by":"crossref","first-page":"2261","DOI":"10.1002\/ibd.21616","article-title":"GCMS-based metabolomic study in mice with colitis induced by dextran sulfate sodium","volume":"17","author":"Shiomi","year":"2011","journal-title":"Inflamm. Bowel Dis."},{"key":"10.1016\/j.jaut.2019.01.001_bib183","doi-asserted-by":"crossref","first-page":"764","DOI":"10.3899\/jrheum.100996","article-title":"An international consensus survey of diagnostic criteria for macrophage activation syndrome in systemic juvenile idiopathic arthritis","volume":"38","author":"Davi","year":"2011","journal-title":"J. Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib184","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1146\/annurev-med-061813-012806","article-title":"Pathogenesis of macrophage activation syndrome and potential for cytokine- directed therapies","volume":"66","author":"Schulert","year":"2015","journal-title":"Annu. Rev. Med."},{"key":"10.1016\/j.jaut.2019.01.001_bib185","doi-asserted-by":"crossref","first-page":"3160","DOI":"10.1002\/art.38802","article-title":"Clinical features, treatment, and outcome of macrophage activation syndrome complicating systemic juvenile idiopathic arthritis: a multinational, multicenter study of 362 patients","volume":"66","author":"Minoia","year":"2014","journal-title":"Arthritis Rheumatol."},{"key":"10.1016\/j.jaut.2019.01.001_bib186","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1136\/annrheumdis-2015-208982","volume":"75","author":"Ravelli","year":"2016","journal-title":"Ann. Rheum. Dis."},{"key":"10.1016\/j.jaut.2019.01.001_bib187","article-title":"ANCA vasculitis and hemophagocytic Lymphohistiocytosis following a fecal microbiota transplant","volume":"2018","author":"Amlani","year":"2018","journal-title":"Case Rep. Rheumatol."}],"container-title":["Journal of Autoimmunity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0896841118306504?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0896841118306504?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T08:20:17Z","timestamp":1760257217000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0896841118306504"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,3]]},"references-count":187,"alternative-id":["S0896841118306504"],"URL":"https:\/\/doi.org\/10.1016\/j.jaut.2019.01.001","relation":{},"ISSN":["0896-8411"],"issn-type":[{"value":"0896-8411","type":"print"}],"subject":[],"published":{"date-parts":[[2019,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Gut microbiota in children and altered profiles in juvenile idiopathic arthritis","name":"articletitle","label":"Article Title"},{"value":"Journal of Autoimmunity","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jaut.2019.01.001","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2019 The Authors. Published by Elsevier Ltd.","name":"copyright","label":"Copyright"}]}}