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Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease. Science. 2016; 352:1116–1120. [PubMed: 27230380] 23. Scholz M, et al. Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Nat Methods. 2016; 13:435–438. [PubMed: 26999001] 24. Yassour M, et al. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Science Translational Medicine. 2016; 8:343ra81–343ra81. 25. Yasuda K, et al. Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque. Cell Host Microbe. 2015; 17:385–391. [PubMed: 25732063] 26. Lee SM, et al. Bacterial colonization factors control specificity and stability of the gut microbiota. Nature. 2013; 501:426–429. [PubMed: 23955152] 27. Pudlo NA, et al. Symbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans. MBio. 2015; 6doi: 10.1128/mBio.01282-15 28. Martens EC, Roth R, Heuser JE, Gordon JI. Coordinate regulation of glycan degradation and polysaccharide capsule biosynthesis by a prominent human gut symbiont. J Biol Chem. 2009; 284:18445–18457. [PubMed: 19403529] 29. Coyne MJ, Chatzidaki-Livanis M, Paoletti LC, Comstock LE. Role of glycan synthesis in colonization of the mammalian gut by the bacterial symbiont Bacteroides fragilis. Proc Natl Acad Sci USA. 2008; 105:13099–13104. [PubMed: 18723678] 30. Liu CH, Lee SM, Vanlare JM, Kasper DL, Mazmanian SK. Regulation of surface architecture by symbiotic bacteria mediates host colonization. Proc Natl Acad Sci USA. 2008; 105:3951–3956. [PubMed: 18319345] 31. Peterson DA, McNulty NP, Guruge JL, Gordon JI. IgA response to symbiotic bacteria as a mediator of gut homeostasis. Cell Host Microbe. 2007; 2:328–339. [PubMed: 18005754] 32. Zitomersky NL, Coyne MJ, Comstock LE. Longitudinal analysis of the prevalence, maintenance, and IgA response to species of the order Bacteroidales in the human gut. Infect Immun. 2011; 79:2012–2020. [PubMed: 21402766] 33. Moor K, et al. Analysis of bacterial-surface-specific antibodies in body fluids using bacterial flow cytometry. Nat Protoc. 2016; 11:1531–1553. [PubMed: 27466712] 34. Shimoda M, Inoue Y, Azuma N, Kanno C. Natural polyreactive immunoglobulin A antibodies produced in mouse Peyer’s patches. Immunology. 1999; 97:9–17. [PubMed: 10447709] 35. Bunker JJ, et al. Natural polyreactive IgA antibodies coat the intestinal microbiota. Science. 2017; 358:eaan6619. [PubMed: 28971969] 36. Gibbins HL, Proctor GB, Yakubov GE, Wilson S, Carpenter GH. SIgA binding to mucosal surfaces is mediated by mucin-mucin interactions. PLoS ONE. 2015; 10:e0119677. [PubMed: 25793390] 37. Biesbrock AR, Reddy MS, Levine MJ. Interaction of a salivary mucin-secretory immunoglobulin A complex with mucosal pathogens. Infect Immun. 1991; 59:3492–3497. [PubMed: 1910004] 38. Phalipon A, et al. Secretory component: a new role in secretory IgA-mediated immune exclusion in vivo. Immunology. 2002; 17:107–115. 39. Sarikonda G, et al. Transient B-cell depletion with anti-CD20 in combination with proinsulin DNA vaccine or oral insulin: immunologic effects and efficacy in NOD mice. PLoS ONE. 2013; 8:e54712. [PubMed: 23405091] 40. Blutt SE, Miller AD, Salmon SL, Metzger DW, Conner ME. IgA is important for clearance and critical for protection from rotavirus infection. Mucosal Immunol. 2012; 5:712–719. [PubMed: 22739233] 41. Moor K, et al. High-avidity IgA protects the intestine by enchaining growing bacteria. Nature. 2017; 103:3–19. Donaldson et al. Page 7 Science. Author manuscript; available in PMC 2018 November 18. Author Manuscript Author Manuscript Author Manuscript Author Manuscript