An insight into the fecal microbiota composition in Romanian patients with ankylosing spondylitis using high-throughput 16S rRNA gene amplicon sequencing

1. Zhu W, He X, Cheng K, Zhang L, Chen D, Wang X, et al. Ankylosing spondylitis: etiology, pathogenesis, and treatments. Bone Res. 2019 7(22). DOI: 10.1038/s41413-019-0057-810.1038/s41413-019-0057-8680488231666997Search in Google Scholar

2. Wang R, Ward MM. Epidemiology of axial spondyloarthritis: un update. Curr Opin Rheumatol. 2018 March;30(2):137-43. DOI: 10.1097/BOR.000000000000047510.1097/BOR.0000000000000475581120329227352Search in Google Scholar

3. Ranganathan V, Gracey E, Brown MA, Inman RD, Haroon N. Pathogenesis of ankylosing spondylitis - recent advances and future directions. Nat Rev Rheumatol. 2017 Jun;13(6):359-67. DOI: 10.1038/nrrheum.2017.5610.1038/nrrheum.2017.5628446810Search in Google Scholar

4. Costello ME, Ciccia F, Willner D, Warrington N, Robinson PC, et al. Brief Report: Intestinal Dysbiosis in Ankylosing Spondylitis. Arthritis Rheumatol. 2015 Mar;67(3):686-91. DOI: 10.1002/art.3896710.1002/art.3896725417597Search in Google Scholar

5. Tito RY, Cypers H, Joossens M, Varkas G, Van Praet L, Glorieu E, et al. Brief Report: Dialister as a Microbial Marker of Disease Activity in Spondyloarthritis. Arthritis Rheumatol. 2017 69(1):114-21. DOI: 10.1002/art.3980210.1002/art.3980227390077Search in Google Scholar

6. Browne HP, Forster SC, Anonye BO, Kumar N, Neville BA, Stares MD, et al. Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation. Nature. 2016 May;533(7604):543-546. DOI: 10.1038/nature1764510.1038/nature17645489068127144353Search in Google Scholar

7. Cullen CM, Aneja KK, Beyhan S, Cho CE, Woloszynek S, Convertino M, et al. Emerging Priorities for Microbiome Research. Front Microbiol. 2020 Feb;19(11):136. DOI: 10.3389/fmicb.2020.0013610.3389/fmicb.2020.00136704232232140140Search in Google Scholar

8. van der Linden S, Valkenburg HA, Cats A. Evaluation of diagnostic criteria for ankylosing spondylitis. A proposal for modification of the New York criteria. Arthritis Rheum. 1984 27:361-8. DOI: 10.1002/art.178027040110.1002/art.17802704016231933Search in Google Scholar

9. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biol. 2011 Jun;12(6):R60. DOI: 10.1186/gb-2011-12-6-r6010.1186/gb-2011-12-6-r60321884821702898Search in Google Scholar

10. Kashyap PC, Chia N, Nelson H, Segal E, Elinav E. Microbiome at the Frontier of Personalized Medicine. Mayo Clin Proc. 2017 Dec;92(12):1855-64. DOI: 10.1016/j.mayocp.2017.10.00410.1016/j.mayocp.2017.10.004573033729202942Search in Google Scholar

11. Cardoneanu A, Cozma S, Rezus C, Petrariu F, Burlui AM, Rezus E. Characteristics of the intestinal micro-biome in ankylosing spondylitis. Exp Ther Med. 2021 Jul;22(1):676. DOI: 10.3892/etm.2021.1010810.3892/etm.2021.10108811212933986841Search in Google Scholar

12. Pollock J, Glendinning L, Wisedchanwet T, Watson M. The madness of microbiome: attempting to find consensus “best practice” for 16S microbiome studies. Appl Environ Microbiol. 2018 84(7):e02627-17. DOI: 10.1128/AEM.02627-1710.1128/AEM.02627-17586182129427429Search in Google Scholar

13. Bharti R, Grimm DG. Current challenges and best-practice protocols for microbiome analysis. Brief Bioin-form. 2021 22(1):178-93. DOI: 10.1093/bib/bbz15510.1093/bib/bbz155782083931848574Search in Google Scholar

14. Allali I, Arnold JW, Roach J, Cadenas MB, Butz N, Hassan HM, et al. A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome. BMC Microbiol. 2017 Sep;17(1):194. DOI: 10.1186/s12866-017-1101-810.1186/s12866-017-1101-8559803928903732Search in Google Scholar

15. Salipante SJ, Kawashima T, Rosenthal C, Hoogestraat DR, Cummings LA, Sengupta DJ, et al. Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling. Appl Environ Microbiol. 2014 Dec;80(24):7583-91. DOI: 10.1128/AEM.02206-1410.1128/AEM.02206-14424921525261520Search in Google Scholar

16. Mas-Lloret J, Obón-Santacana M, Ibá-ez-Sanz G, Guinó E, Pato ML, Rodriguez-Moranta F, et al. Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample. Sci Data. 2020 Mar;7(1):92. DOI: 10.1038/s41597-020-0427-510.1038/s41597-020-0427-5707595032179734Search in Google Scholar

17. Watts GS, Youens-Clark K, Slepian MJ, Wolk DM, Oshiro MM, Metzger GS, et al. 16S rRNA gene sequencing on a benchtop sequencer: accuracy for identification of clinically important bacteria. J Appl Microbiol. 2017 Dec;123(6):1584-96. DOI: 10.1111/jam.1359010.1111/jam.13590576550528940494Search in Google Scholar

18. Soergel DA, Dey N, Knight R, Brenner SE. Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. ISME J. 2012 Jul;6(7):1440-4. DOI: 10.1038/ismej.2011.20810.1038/ismej.2011.208337964222237546Search in Google Scholar

19. Mizrahi-Man O, Davenport ER, Gilad Y. Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. PLoS One. 2013 8(1):e53608. DOI: 10.1371/journal. pone.0053608Search in Google Scholar

20. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010 May;7(5):335-6. DOI: 10.1038/nmeth.f.30310.1038/nmeth.f.303315657320383131Search in Google Scholar

21. Tang Q, Jin G, Wang G, Liu T, Liu X, Wang B et al. Current Sampling Methods for Gut Microbiota: A Call for More Precise Devices. Front Cell Infect Microbiol. 2020 10:151. DOI: 10.3389/fcimb.2020.0015110.3389/fcimb.2020.00151716108732328469Search in Google Scholar

22. Lavelle A, Lennon G, O’Sullivan O, Docherty N, Balfe A, Maguire A, et al. Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers. Gut. 2015 Oct;64(10):1553-61. DOI: 10.1136/gutjnl-2014-30787310.1136/gutjnl-2014-307873460225225596182Search in Google Scholar

23. Penington JS, Penno MAS, Ngui KM, Ajami NJ, Roth-Schulze AJ, Wilcox SA, et al. Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis. Sci Rep. 2018 Mar;8(1):4386. DOI: 10.1038/s41598-018-22491-710.1038/s41598-018-22491-7584757329531234Search in Google Scholar

24. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science. 2009 Dec;326(5960):1694-7. DOI: 10.1126/science.117748610.1126/science.1177486360244419892944Search in Google Scholar

25. Berg G, Rybakova D, Fischer D, Cernava T, Vergès MC, Charles T, et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome. 2020 Jun;8(1):103. DOI: 10.1186/s40168-020-00875-010.1186/s40168-020-00875-0732952332605663Search in Google Scholar

26. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al. Enterotypes of the human gut microbiome. Nature. 2011 May;473(7346):174-80. DOI: 10.1038/nature0994410.1038/nature09944372864721508958Search in Google Scholar

27. Shin NR, Whon TW, Bae JW. Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends Biotechnol. 2015 Sep;33(9):496-503. DOI: 10.1016/j. tibtech.2015.06.011Search in Google Scholar

28. Baldelli V, Scaldaferri F, Putignani L, Del Chierico F. The Role of Enterobacteriaceae in gut microbiota dysbiosis in inflammatory bowel diseases. Microorganisms. 2021 Mar;9(4):697. DOI: 10.3390/microorganisms904069710.3390/microorganisms9040697806630433801755Search in Google Scholar

29. Chen Z, Qi J, Wei Q, Zheng X, Wu X, Li X, et al. Variations in gut microbial profiles in ankylosing spondylitis: disease phenotype-related dysbiosis. Ann Transl Med. 2019 Oct;7(20):571. DOI: 10.21037/atm.2019.09.4110.21037/atm.2019.09.41686174031807552Search in Google Scholar

30. Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, et al. Population-level analysis of gut micro-biome variation. Science. 2016 Apr;352(6285):560-4. DOI: 10.1126/science.aad350310.1126/science.aad350327126039Search in Google Scholar

31. Aguirre de Cárcer D. The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units. Sci Rep. 2018 Sep;8(1):14069. DOI: 10.1038/s41598-018-32221-810.1038/s41598-018-32221-8614591730232462Search in Google Scholar

32. Zhang L, Han R, Zhang X, Fang G, Chen J, Li J, et al. Fecal microbiota in patients with ankylosing spondylitis: Correlation with dietary factors and disease activity. Clin Chim Acta. 2019 Oct;497:189-96. DOI: 10.1016/j. cca.2019.07.038Search in Google Scholar

33. Hooks KB, O’Malley MA. Dysbiosis and its discontents. mBio. 2017 Oct;8(5):e01492-17. DOI: 10.1128/mBio.01492-1710.1128/mBio.01492-17563569129018121Search in Google Scholar

34. Levy M, Kolodziejczyk AA, Thaiss CA, Elinav E. Dysbiosis and the immune system. Nat Rev Immunol. 2017 Apr;17(4):219-32. DOI: 10.1038/nri.2017.710.1038/nri.2017.728260787Search in Google Scholar

35. Harkins P, Burke E, Swales C, Silman A. ‘All disease begins in the gut’-the role of the intestinal microbiome in ankylosing spondylitis. Rheumatol Adv Pract. 2021 Sep;5(3):rkab063. DOI: 10.1093/rap/rkab06310.1093/rap/rkab063845299934557624Search in Google Scholar