Martindale J, Shukla R, Goodacre J. The impact of ankylosing spondylitis/axial spondyloarthritis on work productivity. Best Pract Res Clin Rheumatol. 2015;29(3):512–23.
Article
PubMed
Google Scholar
Loftus CG, Loftus EV Jr, Harmsen WS, Zinsmeister AR, Tremaine WJ, Melton LJ 3rd, Sandborn WJ. Update on the incidence and prevalence of Crohn's disease and ulcerative colitis in Olmsted County, Minnesota, 1940-2000. Inflamm Bowel Dis. 2007;13(3):254–61.
Article
PubMed
Google Scholar
Ranganathan V, Gracey E, Brown MA, Inman RD, Haroon N. Pathogenesis of ankylosing spondylitis - recent advances and future directions. Nat Rev Rheumatol. 2017;13(6):359–67.
Article
PubMed
CAS
Google Scholar
Turkcapar N, Toruner M, Soykan I, Aydintug OT, Cetinkaya H, Duzgun N, Ozden A, Duman M. The prevalence of extraintestinal manifestations and HLA association in patients with inflammatory bowel disease. Rheumatol Int. 2006;26(7):663–8.
Article
PubMed
Google Scholar
Faustini F, Zoli A, Ferraccioli GF. Immunologic and genetic links between spondylarthropathies and inflammatory bowel diseases. Eur Rev Med Pharmacol Sci. 2009;13(Suppl 1):1–9.
PubMed
Google Scholar
Jacques P, Elewaut D. Joint expedition: linking gut inflammation to arthritis. Mucosal Immunol. 2008;1(5):364–71.
Article
PubMed
CAS
Google Scholar
Wright PB, McEntegart A, McCarey D, McInnes IB, Siebert S, Milling SW. Ankylosing spondylitis patients display altered dendritic cell and T cell populations that implicate pathogenic roles for the IL-23 cytokine axis and intestinal inflammation. Rheumatology (Oxford). 2016;55(1):120–32.
Article
CAS
Google Scholar
Catana CS, Berindan Neagoe I, Cozma V, Magdas C, Tabaran F, Dumitrascu DL. Contribution of the IL-17/IL-23 axis to the pathogenesis of inflammatory bowel disease. World J Gastroenterol. 2015;21(19):5823–30.
Article
PubMed
PubMed Central
CAS
Google Scholar
Tito RY, Cypers H, Joossens M, Varkas G, Van Praet L, Glorieus E, Van den Bosch F, De Vos M, Raes J, Elewaut D. Brief report: dialister as a microbial marker of disease activity in spondyloarthritis. Arthritis Rheumatol. 2017;69(1):114–21.
Article
PubMed
CAS
Google Scholar
Breban M, Tap J, Leboime A, Said-Nahal R, Langella P, Chiocchia G, Furet JP, Sokol H. Faecal microbiota study reveals specific dysbiosis in spondyloarthritis. Ann Rheum Dis. 2017;76(9):1614–22.
Article
PubMed
Google Scholar
Costello ME, Ciccia F, Willner D, Warrington N, Robinson PC, Gardiner B, Marshall M, Kenna TJ, Triolo G, Brown MA. Intestinal dysbiosis in ankylosing spondylitis. Arthritis Rheumatol. 2015;67(3):686–91.
Article
PubMed
Google Scholar
Frank DN, Robertson CE, Hamm CM, Kpadeh Z, Zhang T, Chen H, Zhu W, Sartor RB, Boedeker EC, Harpaz N, et al. Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Inflamm Bowel Dis. 2011;17(1):179–84.
Article
PubMed
Google Scholar
Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A. 2007;104(34):13780–5.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe. 2014;15(3):382–92.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kuhn KA, Schulz HM, Regner EH, Severs EL, Hendrickson JD, Mehta G, Whitney AK, Ir D, Ohri N, Robertson CE, et al. Bacteroidales recruit IL-6-producing intraepithelial lymphocytes in the colon to promote barrier integrity. Arthritis Rheumatol. 2017;2018. https://doi.org/10.1002/art.40490. [Epub ahead of print].
Cheroutre H, Lambolez F, Mucida D. The light and dark sides of intestinal intraepithelial lymphocytes. Nat Rev Immunol. 2011;11(7):445–56.
Article
PubMed
PubMed Central
CAS
Google Scholar
Najarian RM, Hait EJ, Leichtner AM, Glickman JN, Antonioli DA, Goldsmith JD. Clinical significance of colonic intraepithelial lymphocytosis in a pediatric population. Mod Pathol. 2009;22(1):13–20.
Article
PubMed
Google Scholar
Torrente F, Barabino A, Bellini T, Murch SH. Intraepithelial lymphocyte eotaxin-2 expression and perineural mast cell degranulation differentiate allergic/eosinophilic colitis from classic IBD. J Pediatr Gastroenterol Nutr. 2014;59(3):300–7.
Article
PubMed
CAS
Google Scholar
Dalton HR, Dipaolo MC, Sachdev GK, Crotty B, Hoang P, Jewell DP. Human colonic intraepithelial lymphocytes from patients with inflammatory bowel disease fail to down-regulate proliferative responses of primed allogeneic peripheral blood mononuclear cells after rechallenge with antigens. Clin Exp Immunol. 1993;93(1):97–102.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ahn JY, Lee KH, Choi CH, Kim JW, Lee HW, Kim JW, Kim MK, Kwon GY, Han S, Kim SE, et al. Colonic mucosal immune activity in irritable bowel syndrome: comparison with healthy controls and patients with ulcerative colitis. Dig Dis Sci. 2014;59(5):1001–11.
Article
PubMed
CAS
Google Scholar
Rudwaleit M, van der Heijde D, Landewe R, Listing J, Akkoc N, Brandt J, Braun J, Chou CT, Collantes-Estevez E, Dougados M, et al. The development of assessment of SpondyloArthritis International Society classification criteria for axial spondyloarthritis (part II): validation and final selection. Ann Rheum Dis. 2009;68(6):777–83.
Article
PubMed
CAS
Google Scholar
Brumbaugh DE, Arruda J, Robbins K, Ir D, Santorico SA, Robertson CE, Frank DN. Mode of delivery determines neonatal pharyngeal bacterial composition and early intestinal colonization. J Pediatr Gastroenterol Nutr. 2016;63(3):320–8.
Article
PubMed
Google Scholar
Lemas DJ, Young BE, Baker PR 2nd, Tomczik AC, Soderborg TK, Hernandez TL, de la Houssaye BA, Robertson CE, Rudolph MC, Ir D, et al. Alterations in human milk leptin and insulin are associated with early changes in the infant intestinal microbiome. Am J Clin Nutr. 2016;103(5):1291–300.
Article
PubMed
PubMed Central
CAS
Google Scholar
Markle JG, Frank DN, Mortin-Toth S, Robertson CE, Feazel LM, Rolle-Kampczyk U, von Bergen M, McCoy KD, Macpherson AJ, Danska JS. Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science. 2013;339(6123):1084–8.
Article
PubMed
CAS
Google Scholar
Pandrea I, Xu C, Stock JL, Frank DN, Ma D, Policicchio BB, He T, Kristoff J, Cornell E, Haret-Richter GS, et al. Antibiotic and antiinflammatory therapy transiently reduces inflammation and hypercoagulation in acutely SIV-infected pigtailed macaques. PLoS Pathog. 2016;12(1):e1005384.
Article
PubMed
PubMed Central
CAS
Google Scholar
Frank DN. BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. BMC Bioinformatics. 2009;10:362.
Article
PubMed
PubMed Central
CAS
Google Scholar
iGenomes [http://support.illumina.com/sequencing/sequencing_software/igenome.html]. Accessed 8 Dec 2014.
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998;8(3):186–94.
Article
PubMed
CAS
Google Scholar
Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998;8(3):175–85.
Article
PubMed
CAS
Google Scholar
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27(16):2194–200.
Article
PubMed
PubMed Central
CAS
Google Scholar
Schloss PD, Westcott SL. Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. 2011;77(10):3219–26.
Article
PubMed
PubMed Central
CAS
Google Scholar
Pruesse E, Peplies J, Glockner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics. 2012;28(14):1823–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(Database issue):D590–6.
PubMed
CAS
Google Scholar
Robertson CE, Harris JK, Wagner BD, Granger D, Browne K, Tatem B, Feazel LM, Park K, Pace NR, Frank DN. Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data. Bioinformatics. 2013;29(23):3100–1.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gorfu G, Rivera-Nieves J, Ley K. Role of beta7 integrins in intestinal lymphocyte homing and retention. Curr Mol Med. 2009;9(7):836–50.
Article
PubMed
PubMed Central
CAS
Google Scholar
Qiu Y, Yang H. Effects of intraepithelial lymphocyte-derived cytokines on intestinal mucosal barrier function. J Interf Cytokine Res. 2013;33(10):551–62.
Article
CAS
Google Scholar
Fantini MC, Pallone F, Monteleone G. Common immunologic mechanisms in inflammatory bowel disease and spondylarthropathies. World J Gastroenterol. 2009;15(20):2472–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kabeerdoss J, Sandhya P, Danda D. Gut inflammation and microbiome in spondyloarthritis. Rheumatol Int. 2016;36(4):457–68.
Article
PubMed
CAS
Google Scholar
Casini-Raggi V, Kam L, Chong YJ, Fiocchi C, Pizarro TT, Cominelli F. Mucosal imbalance of IL-1 and IL-1 receptor antagonist in inflammatory bowel disease. A novel mechanism of chronic intestinal inflammation. J Immunol. 1995;154(5):2434–40.
PubMed
CAS
Google Scholar
Olsen T, Rismo R, Cui G, Goll R, Christiansen I, Florholmen J. TH1 and TH17 interactions in untreated inflamed mucosa of inflammatory bowel disease, and their potential to mediate the inflammation. Cytokine. 2011;56(3):633–40.
Article
PubMed
CAS
Google Scholar
Sun YP, Wang HH, He Q, Cho CH. Effect of passive cigarette smoking on colonic alpha7-nicotinic acetylcholine receptors in TNBS-induced colitis in rats. Digestion. 2007;76(3–4):181–7.
Article
PubMed
CAS
Google Scholar
Gill T, Asquith M, Rosenbaum JT, Colbert RA. The intestinal microbiome in spondyloarthritis. Curr Opin Rheumatol. 2015;27(4):319–25.
Article
PubMed
PubMed Central
CAS
Google Scholar
Stebbings S, Munro K, Simon MA, Tannock G, Highton J, Harmsen H, Welling G, Seksik P, Dore J, Grame G, et al. Comparison of the faecal microflora of patients with ankylosing spondylitis and controls using molecular methods of analysis. Rheumatology (Oxford). 2002;41(12):1395–401.
Article
CAS
Google Scholar
Santoru ML, Piras C, Murgia A, Palmas V, Camboni T, Liggi S, Ibba I, Lai MA, Orru S, Loizedda AL, et al. Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients. Sci Rep. 2017;7(1):9523.
Article
PubMed
PubMed Central
CAS
Google Scholar
Forbes JD, Van Domselaar G, Bernstein CN. Microbiome survey of the inflamed and noninflamed gut at different compartments within the gastrointestinal tract of inflammatory bowel disease patients. Inflamm Bowel Dis. 2016;22(4):817–25.
Article
PubMed
Google Scholar
Wen C, Zheng Z, Shao T, Liu L, Xie Z, Le Chatelier E, He Z, Zhong W, Fan Y, Zhang L, et al. Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis. Genome Biol. 2017;18(1):142.
Article
PubMed
PubMed Central
Google Scholar
Araujo-Perez F, McCoy AN, Okechukwu C, Carroll IM, Smith KM, Jeremiah K, Sandler RS, Asher GN, Keku TO. Differences in microbial signatures between rectal mucosal biopsies and rectal swabs. Gut Microbes. 2012;3(6):530–5.
Article
PubMed
PubMed Central
Google Scholar