Dynamic immunoglobulin responses to gut bacteria during inflammatory bowel disease

References

• Maloy KJ, Powrie F. Intestinal homeostasis and its breakdown in inflammatory bowel disease. Nature. 2011;474(7351):298–306. doi:10.1038/nature10208.
   Google Scholar
• Alexander KL, Targan SR; Elson 3rd CO. Microbiota activation and regulation of innate and adaptive immunity. Immunol Rev. 2014;260(1):206–220. doi:10.1111/imr.12180.
   Google Scholar
• Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. A human gut microbial gene catalogue established by metagenomic sequencing : article : nature. Nature. 2010;464(7285):59–65. doi:10.1038/nature08821.
   Google Scholar
• Macpherson A, Khoo UY, Forgacs I, Philpott-Howard J, Bjarnason I. Mucosal antibodies in inflammatory bowel disease are directed against intestinal bacteria. Gut. 1996;38(3):365–375. doi:10.1136/gut.38.3.365.
   Google Scholar
• van der Waaij LA, Kroese FGM, Visser A, Nelis GF, Westerveld BD, Jansen PLM, Hunter JO. Immunoglobulin coating of faecal bacteria in inflammatory bowel disease. Eur J Gastroenterol Hepatol. 2004;16(7):669–674. doi:10.1097/01.meg.0000108346.41221.19.
   Google Scholar
• Peterson DA, McNulty NP, Guruge JL, Gordon JI. IgA response to symbiotic bacteria as a mediator of gut homeostasis. Cell Host Microbe. 2007;2(5):328–339. doi:10.1016/j.chom.2007.09.013.
   Google Scholar
• Palm NW, de Zoete MR, Cullen TW, Barry NA, Stefanowski J, Hao L, Degnan PH, Hu J, Peter I, Zhang W, et al. Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell. 2014;158(5):1000–1010. doi:10.1016/j.cell.2014.08.006.
   Google Scholar
• Kau AL, Planer JD, Liu J, Rao S, Yatsunenko T, Trehan I, Manary MJ, Liu T-C, Stappenbeck TS, Maleta KM, et al. Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy. Sci Transl Med. 2015;7(276):276ra24. doi:10.1126/scitranslmed.aaa4877.
   Google Scholar
• Bunker JJ, Flynn TM, Koval JC, Shaw DG, Meisel M, McDonald BD, Ishizuka IE, Dent AL, Wilson PC, Jabri B, et al. Innate and adaptive humoral responses coat distinct commensal bacteria with immunoglobulin A. Immunity. 2015;43(3):541–553. doi:10.1016/j.immuni.2015.08.007.
   Google Scholar
• Jansen A, Mandić AD, Bennek E, Frehn L, Verdier J, Tebrügge I, Lutz H, Streetz K, Trautwein C, Sellge G. Anti-food and anti-microbial IgG subclass antibodies in inflammatory bowel disease. Scand J Gastroenterol. 2016;5521:(August):1–9. doi:10.1080/00365521.2016.1205130.
   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):13780–13785. doi:10.1073/pnas.0706625104.
   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):179–184. doi:10.1002/ibd.21339.
   Google Scholar
• Gevers D, Kugathasan S, Denson LA, zquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Sj S, Yassour M, et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe. 2014;15(3):382–392. doi:10.1016/j.chom.2014.02.005.
   Google Scholar
• Bunker JJ, Erickson SA, Flynn TM, Henry C, Koval JC, Meisel M, Jabri B, Antonopoulos DA, Wilson PC, Bendelac A. Natural polyreactive IgA antibodies coat the intestinal microbiota. Science. 2017;358(6361):eaan6619. doi:10.1126/science.aan6619.
   Google Scholar
• Kubinak JL, Petersen C, Stephens WZ, Soto R, Bake E, O’Connell RM, Round JL. MyD88 signaling in T cells directs IgA-mediated control of the microbiota to promote health. Cell Host Microbe. 2015;17(2):153–163. doi:10.1016/j.chom.2014.12.009.
   Google Scholar
• Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12(6):R60. doi:10.1186/gb-2011-12-6-r60.
   Google Scholar
• Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. doi:10.1186/s13059-014-0550-8.
   Google Scholar
• McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217. doi:10.1371/JOURNAL.PONE.0061217.
   Google Scholar
• Planer JD, Peng Y, Kau AL, Blanton LV, Ndao IM, Tarr PI, Warner BB, Gordon JI. Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice. Nature. 2016;534(7606):263–266. doi:10.1038/nature17940.
   Google Scholar
• Brito F, Zaltman C, Carvalho ATP, Fischer RG, Persson R, Gustafsson A, Figueredo CMS. Subgingival microflora in inflammatory bowel disease patients with untreated periodontitis. Eur J Gastroenterol Hepatol. 2013;25(2):239–245. doi:10.1097/MEG.0b013e32835a2b70.
   Google Scholar
• Said HS, Suda W, Nakagome S, Chinen H, Oshima K, Kim S, Kimura R, Iraha A, Ishida H, Fujita J, et al. Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkers. DNA Res. 2014;21(1):15–25. doi:10.1093/dnares/dst037.
   Google Scholar
• Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–583. doi:10.1038/nmeth.3869.
   Google Scholar
• Tsuruta T, Inoue R, Nojima I, Tsukahara T, Hara H, Yajima T. The amount of secreted IgA may not determine the secretory IgA coating ratio of gastrointestinal bacteria. FEMS Immunol Med Microbiol. 2009;56(2):185–189. doi:10.1111/j.1574-695X.2009.00568.x.
   Google Scholar
• Santoru ML, Piras C, Murgia A, Palmas V, Camboni T, Liggi S, Ibba I, Lai MA, Orrù S, Blois S, et al. Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients. Sci Rep. 2017;7(1):9523. doi:10.1038/s41598-017-10034-5.
   Google Scholar
• Fyderek K, Strus M, Kowalska-Duplaga K, Gosiewski T, Wedrychowicz A, Jedynak-Wasowicz U, Sładek M, Pieczarkowski S, Adamski P, Kochan P, et al. Mucosal bacterial microflora and mucus layer thickness in adolescents with inflammatory bowel disease. World J Gastroenterol. 2009;15(42):5287–5294. doi:10.3748/wjg.15.919.
   Google Scholar
• Reuken PA, Kruis W, Maaser C, Teich N, Büning J, Preiß JC, Schmelz R, Bruns T, Fichtner-Feigl S, Stallmach A. Microbial spectrum of intra-abdominal abscesses in perforating crohn’s disease: results from a prospective German registry. J Crohn’s Colitis. 2018;12(6):695–701. doi:10.1093/ecco-jcc/jjy017.
   Google Scholar
• Atarashi K, Suda W, Luo C, Kawaguchi T, Motoo I, Narushima S, Kiguchi Y, Yasuma K, Watanabe E, Tanoue T, et al. Ectopic colonization of oral bacteria in the intestine drives T H 1 cell induction and inflammation. Science. 2017;358(6361):359–365. doi:10.1126/science.aan4526.
   Google Scholar
• Del Carmen S, de Moreno de LeBlanc A, Martin R, Chain F, Langella P, Lg B-H, Jg L. Genetically engineered immunomodulatory Streptococcus thermophilus strains producing antioxidant enzymes exhibit enhanced anti-inflammatory activities. Appl Environ Microbiol. 2014;80(3):869–877. doi:10.1128/AEM.03296-13.
   Google Scholar
• Nguyen TLA, Vieira-Silva S, Liston A, Raes J. How informative is the mouse for human gut microbiota research? Dis Model Mech. 2015;8(1):1–16. doi:10.1242/dmm.017400.
   Google Scholar
• Chung H, Sj P, Ja H, Nk S, Sm E, Eb T, Nc R, Ej V, Wang S, Jr M, et al. Gut immune maturation depends on colonization with a host-specific microbiota. Cell. 2012;149(7):1578–1593. doi:10.1016/j.cell.2012.04.037.
   Google Scholar
• Bates D, Mächler M, Bolker B, Walker S. Fitting linear mixed-effects models using lme4. J Stat Softw. 2015;67(1):1–48. doi:10.18637/jss.v067.i01.
   Google Scholar
• Nakagawa S, Schielzeth H. A general and simple method for obtaining R2 from generalized linear mixed-effects models. Methods Ecol Evol. 2013;4(2):133–142. doi:10.1111/j.2041-210x.2012.00261.x.
   Google Scholar
• Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. Isme J. 2012;6(8):1621–1624. doi:10.1038/ismej.2012.8.
   Google Scholar
• Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10(10):996–998. doi:10.1038/nmeth.2604.
   Google Scholar
• Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73(16):5261–5267. doi:10.1128/AEM.00062-07.
   Google Scholar
• Jari Oksanen F, Blanchet G, Friendly M, Kindt R, Legendre P, Dan McGlinn PR, Minchin RB, O’Hara GL, Simpson PS, Henry M, et al. vegan: community ecology package 2017; (R package version 2.4-3).
   Google Scholar
• Kuhn M caret: classification and regression training 2017;(R package version 6.0-76).
   Google Scholar
• Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez J-C MM. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics. 2011;12(1):77. doi:10.1186/1471-2105-12-77.
   Google Scholar
• Afgan E, Baker D, Batut B, van Den Beek M, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Grüning BA, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 2018;46(W1):W537–44. doi:10.1093/nar/gky379.
   Google Scholar
• R Core Team. R: A language and environment for statistical computing. R Found Stat Comput. 2016. Vienna, Austria. http://www.R-project.org/.
   Google Scholar
• Wickham H. ggplot2: elegant graphics for data analysis. New York (NY): Springer-Verlag; 2009.
   Google Scholar