1. Sender, R., Fuchs, S. & Milo, R. Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans. Cell 164, 337–340 (2016).
2. Nishijima, S. et al. The gut microbiome of healthy Japanese and its microbial and functional uniqueness. DNA Research 23, 125–133 (2016).
3. Bäckhed, F. et al. The gut microbiota as an environmental factor that regulates fat storage. Proceedings of the National Academy of Sciences 101, 15718–15723 (2004).
4. Atarashi, K. et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 500, 232–236 (2013).
5. Ma, Q. et al. Impact of microbiota on central nervous system and neurological diseases: the gutbrain axis. Journal of Neuroinflammation 16, 53 (2019).
6. Kho, Z. Y. & Lal, S. K. The Human Gut Microbiome - A Potential Controller of Wellness and Disease. Frontiers in Microbiology 9, 1835 (2018).
7. Selsted, M. E. & Ouellette, A. J. Mammalian defensins in the antimicrobial immune response. Nature Immunology 6, 551–557 (2005).
8. Ouellette, A. J. et al. Developmental regulation of cryptdin, a corticostatin/defensin precursor mRNA in mouse small intestinal crypt epithelium. The Journal of Cell Biology 108, 1687–1695 (1989).
9. Jones, D. E. & Bevins, C. L. Defensin-6 mRNA in human Paneth cells: implications for antimicrobial peptides in host defense of the human bowel. FEBS Letters 315, 187–192 (1993).
10. Porter, E. M., Liu, L., Oren, A., Anton, P. A. & Ganz, T. Localization of human intestinal defensin 5 in Paneth cell granules. Infection and Immunity 65, 2389–2395 (1997).
11. Wilson, C. L. et al. Regulation of intestinal alpha-defensin activation by the metalloproteinase matrilysin in innate host defense. Science 286, 113–117 (1999).
12. Ayabe, T. et al. Secretion of microbicidal a-defensins by intestinal Paneth cells in response to bacteria. Nature Immunology 1, 113–118 (2000).
13. Salzman, N. H., Ghosh, D., Huttner, K. M., Paterson, Y. & Bevins, C. L. Protection against enteric salmonellosis in transgenic mice expressing a human intestinal defensin. Nature 422, 522–526 (2003).
14. Salzman, N. H. et al. Enteric defensins are essential regulators of intestinal microbial ecology. Nature Immunology 11, 76–83 (2010).
15. Hayase, E. et al. R-Spondin1 expands Paneth cells and prevents dysbiosis induced by graft-versushost disease. The Journal of Experimental Medicine 214, 3507–3518 (2017).
16. Eriguchi, Y. et al. Graft-versus-host disease disrupts intestinal microbial ecology by inhibiting Paneth cell production of α-defensins. Blood 120, 223–231 (2012).
17. Nakamura, K., Sakuragi, N., Takakuwa, A. & Ayabe, T. Paneth cell α-defensins and enteric microbiota in health and disease. Bioscience of Microbiota, Food and Health 35, 57–67 (2016).
18. Eriguchi, Y. et al. Essential role of IFN-γ in T cell-associated intestinal inflammation. JCI Insight 3, e121886 (2018).
19. Zuo, T. & Ng, S. C. The Gut Microbiota in the Pathogenesis and Therapeutics of Inflammatory Bowel Disease. Frontiers in Microbiology 9, 2247 (2018).
20. Torres, J., Mehandru, S., Colombel, J.-F. & Peyrin-Biroulet, L. Crohn’s disease. Lancet 389, 1741– 1755 (2017).
21. Burisch, J., Jess, T., Martinato, M., Lakatos, P. L. & ECCO-EpiCom. The burden of inflammatory bowel disease in Europe. Journal of Crohn’s and Colitis 7, 322–337 (2013).
22. Brusaferro, A. et al. Gut dysbiosis and paediatric Crohn’s disease. The Journal of Infection 78, 1– 7 (2019).
23. Jostins, L. et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 491, 119–124 (2012).
24. Shaw, S. Y., Blanchard, J. F. & Bernstein, C. N. Association Between the Use of Antibiotics and New Diagnoses of Crohnʼs Disease and Ulcerative Colitis. American Journal of Gastroenterology 106, 2133–2142 (2011).
25. Hou, J. K., Abraham, B. & El-Serag, H. Dietary Intake and Risk of Developing Inflammatory Bowel Disease: A Systematic Review of the Literature. The American Journal of Gastroenterology 106, 563–573 (2011).
26. Somineni, H. K. & Kugathasan, S. The Microbiome in Patients With Inflammatory Diseases. Clinical Gastroenterology and Hepatology 17, 243–255 (2019).
27. Hosomi, S., Kaser, A. & Blumberg, R. S. Role of endoplasmic reticulum stress and autophagy as interlinking pathways in the pathogenesis of inflammatory bowel disease. Current Opinion in Gastroenterology 31, 81–88 (2015).
28. Bernales, S., Papa, F. R. & Walter, P. Intracellular Signaling by the Unfolded Protein Response. Annual Review of Cell and Developmental Biology 22, 487–508 (2006).
29. Kaser, A. et al. XBP1 links ER stress to intestinal inflammation and confers genetic risk for human inflammatory bowel disease. Cell 134, 743–756 (2008).
30. Zhao, F. et al. Disruption of Paneth and goblet cell homeostasis and increased endoplasmic reticulum stress in Agr2-/- mice. Developmental Biology 338, 270–279 (2010).
31. Cadwell, K. et al. A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells. Nature 456, 259–263 (2008).
32. Liu, B. et al. Irgm1-deficient mice exhibit Paneth cell abnormalities and increased susceptibility to acute intestinal inflammation. American Journal of Physiology Gastrointestinal and Liver Physiology 305, G573-84 (2013).
33. Zhang, Q. et al. Commensal bacteria direct selective cargo sorting to promote symbiosis. Nature Immunology 16, 918–926 (2015).
34. Liu, T. C. et al. Paneth cell defects in Crohn’s disease patients promote dysbiosis. JCI Insight 1, e86907 (2016).
35. Deuring, J. J. et al. Genomic ATG16L1 risk allele-restricted Paneth cell ER stress in quiescent Crohn’s disease. Gut 63, 1081–1091 (2014).
36. Hamdan, N., Kritsiligkou, P. & Grant, C. M. ER stress causes widespread protein aggregation and prion formation. The Journal of Cell Biology 216, 2295–2304 (2017).
37. Tsuchiya, Y. et al. IRE1-XBP1 pathway regulates oxidative proinsulin folding in pancreatic β cells. The Journal of Cell Biology 217, 1287–1301 (2018).
38. Cook, K. M. & Hogg, P. J. Post-Translational Control of Protein Function by Disulfide Bond Cleavage. Antioxidant & Redox Signaling 18, 1987–2015 (2013).
39. Masuda, K., Sakai, N., Nakamura, K., Yoshioka, S. & Ayabe, T. Bactericidal activity of mouse αdefensin cryptdin-4 predominantly affects noncommensal bacteria. Journal of Innate Immunity 3, 315–326 (2011).
40. Tanabe, H. et al. Denatured human alpha-defensin attenuates the bactericidal activity and the stability against enzymatic digestion. Biochemical and Biophysical Research Communications 358, 349–355 (2007).
41. Rivera-Nieves, J. et al. Emergence of perianal fistulizing disease in the SAMP1/YitFc mouse, a spontaneous model of chronic ileitis. Gastroenterology 124, 972–982 (2003).
42. Pizarro, T. T. et al. SAMP1/YitFc mouse strain: a spontaneous model of Crohn’s disease-like ileitis. Inflammatory Bowel Diseases 17, 2566–2584 (2011).
43. Cominelli, F., Arseneau, K. O., Rodriguez-Palacios, A. & Pizarro, T. T. Uncovering Pathogenic Mechanisms of Inflammatory Bowel Disease Using Mouse Models of Crohn’s Disease-Like Ileitis: What is the Right Model? Cellular and Molecular Gastroenterology and Hepatology 4, 19–32 (2017).
44. Rath, H. C. et al. Normal luminal bacteria, especially Bacteroides species, mediate chronic colitis, gastritis, and arthritis in HLA-B27/human beta2 microglobulin transgenic rats. The Journal of Clinical Investigation 98, 945–953 (1996).
45. Yokoi, Y. et al. Paneth cell granule dynamics on secretory responses to bacterial stimuli in enteroids. Scientific Reports 9, 2710 (2019).
46. Selsted, M. E. Investigational approaches for studying the structures and biological functions of myeloid antimicrobial peptides. Genetic Engineering 15, 131–147 (1993).
47. Nakamura, K., Sakuragi, N. & Ayabe, T. A monoclonal antibody-based sandwich enzyme-linked immunosorbent assay for detection of secreted α-defensin. Analytical Biochemistry 443, 124–131 (2013).
48. Takakuwa, A. et al. Butyric Acid and Leucine Induce α-Defensin Secretion from Small Intestinal Paneth Cells. Nutrients 11, (2019).
49. Schägger, H. & Jagow, G. von. Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Analytical Biochemistry 166, 368– 379 (1987).
50. Herlemann, D. P. et al. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME Journal 5, 1571–1579 (2011).
51. Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7, 335–336 (2010).
52. Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).
53. Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).
54. Reikvam, D. H. et al. Depletion of murine intestinal microbiota: effects on gut mucosa and epithelial gene expression. PLoS ONE 6, e17996 (2011).
55. Vidrich, A. et al. Altered epithelial cell lineage allocation and global expansion of the crypt epithelial stem cell population are associated with ileitis in SAMP1/YitFc mice. The American Journal of Pathology 166, 1055–1067 (2005).
56. Batlle, E. et al. Beta-catenin and TCF mediate cell positioning in the intestinal epithelium by controlling the expression of EphB/ephrinB. Cell 111, 251–263 (2002).
57. Dekaney, C. M., King, S., Sheahan, B. & Cortes, J. E. Mist1 Expression Is Required for Paneth Cell Maturation. Cellular and Molecular Gastroenterology and Hepatology 8, 549–560 (2019).
58. Ouellette, A. J. et al. Mouse Paneth cell defensins: primary structures and antibacterial activities of numerous cryptdin isoforms. Infection and Immunity 62, 5040–5047 (1994).
59. Maemoto, A. et al. Functional analysis of the alpha-defensin disulfide array in mouse cryptdin-4. The Journal of Biological Chemistry 279, 44188–44196 (2004).
60. Walker, A. W. et al. High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiology 11, 7 (2011).
61. Manichanh, C. et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 55, 205–211 (2006).
62. Nishino, K. et al. Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease. Journal of Gastroenterology 53, 95–106 (2017).
63. Frank, D. N. et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proceedings of the National Academy of Sciences 104, 13780–13785 (2007).
64. Gophna, U., Sommerfeld, K., Gophna, S., Doolittle, W. F. & Zanten, S. J. O. V. van. Differences between tissue-associated intestinal microfloras of patients with Crohn’s disease and ulcerative colitis. Journal of Clinical Microbiology 44, 4136–4141 (2006).
65. Marini, M. et al. TNF-alpha neutralization ameliorates the severity of murine Crohn’s-like ileitis by abrogation of intestinal epithelial cell apoptosis. Proceedings of the National Academy of Sciences 100, 8366–8371 (2003).
66. Odashima, M. et al. Activation of A2A Adenosine Receptor Attenuates Intestinal Inflammation in Animal Models of Inflammatory Bowel Disease. Gastroenterology 129, 26–33 (2005).
67. Million, M. et al. New insights in gut microbiota and mucosal immunity of the small intestine. Human Microbiome Journal 7–8, 23–32 (2018).
68. Wexler, H. M. Bacteroides: the good, the bad, and the nitty-gritty. Clinical Microbiology Reviews 20, 593–621 (2007).
69. Walker, A. et al. Sulfonolipids as novel metabolite markers of Alistipes and Odoribacter affected by high-fat diets. Scientific Reports 7, 1–10 (2017).
70. Ferguson, L. R., Laing, B., Marlow, G. & Bishop, K. The role of vitamin D in reducing gastrointestinal disease risk and assessment of individual dietary intake needs: Focus on genetic and genomic technologies. Molecular Nutrition & Food Research 60, 119–133 (2015).
71. Gombart, A. F., Borregaard, N. & Koeffler, H. P. Human cathelicidin antimicrobial peptide (CAMP) gene is a direct target of the vitamin D receptor and is strongly up-regulated in myeloid cells by 1,25-dihydroxyvitamin D3. FASEB Journal 19, 1067–1077 (2005).
72. Su, D. et al. Vitamin D Signaling through Induction of Paneth Cell Defensins Maintains Gut Microbiota and Improves Metabolic Disorders and Hepatic Steatosis in Animal Models. Frontiers in Physiology 7, 471–18 (2016).
73. Wu, S. et al. Intestinal epithelial vitamin D receptor deletion leads to defective autophagy in colitis. Gut 64, 1082–1094 (2015).
74. VanDussen, K. L. et al. Genetic variants synthesize to produce Paneth cell phenotypes that define subtypes of Crohn’s disease. Gastroenterology 146, 200–209 (2014).
75. Wehkamp, J. et al. NOD2 (CARD15) mutations in Crohn’s disease are associated with diminished mucosal alpha-defensin expression. Gut 53, 1658–1664 (2004).
76. Williams, A. D. et al. Human alpha defensin 5 is a candidate biomarker to delineate inflammatory bowel disease. PLoS ONE 12, e0179710 (2017).
77. Ananthakrishnan, A. N. et al. Zinc intake and risk of Crohn’s disease and ulcerative colitis: a prospective cohort study. International Journal of Epidemiology 44, 1995–2005 (2015).
78. Guo, X. et al. Rutin and Its Combination With Inulin Attenuate Gut Dysbiosis, the Inflammatory Status and Endoplasmic Reticulum Stress in Paneth Cells of Obese Mice Induced by High-Fat Diet. Frontiers in Microbiology 9, 2651 (2018).
79. Podany, A. B., Wright, J., Lamendella, R., Soybel, D. I. & Kelleher, S. L. ZnT2-Mediated Zinc Import Into Paneth Cell Granules Is Necessary for Coordinated Secretion and Paneth Cell Function in Mice. Cellular and Molecular Gastroenterology and Hepatology 2, 369–383 (2016).
80. Hess, D. A. et al. MIST1 Links Secretion and Stress as both Target and Regulator of the Unfolded Protein Response. Molecular and Cell Biology 36, 2931–2944 (2016).
81. Pin, C. L., Rukstalis, J. M., Johnson, C. & Konieczny, S. F. The bHLH transcription factor Mist1 is required to maintain exocrine pancreas cell organization and acinar cell identity. Journal of Cell Biology 155, 519–530 (2001).
82. Jing, W., Hunter, H. N., Tanabe, H., Ouellette, A. J. & Vogel, H. J. Solution structure of cryptdin4, a mouse Paneth cell a-defensin. Biochemistry 43, 15759–15766 (2004).
83. Szyk, A. et al. Crystal structures of human alpha-defensins HNP4, HD5, and HD6. Protein Science 15, 2749–2760 (2006).
84. Hadjicharalambous, C. et al. Mechanisms of alpha-defensin bactericidal action: comparative membrane disruption by Cryptdin-4 and its disulfide-null analogue. Biochemistry 47, 12626–12634 (2008).
85. Zhang, Y., Cougnon, F. B. L., Wanniarachchi, Y. A., Hayden, J. A. & Nolan, E. M. Reduction of human defensin 5 affords a high-affinity zinc-chelating peptide. ACS chemical biology 8, 1907– 1911 (2013).
86. Meyers, S. et al. Fecal alpha 1-antitrypsin measurement: an indicator of Crohn’s disease activity. Gastroenterology 89, 13–18 (1985).
87. Wanniarachchi, Y. A., Kaczmarek, P., Wan, A. & Nolan, E. M. Human defensin 5 disulfide array mutants: disulfide bond deletion attenuates antibacterial activity against Staphylococcus aureus. Biochemistry 50, 8005–8017 (2011).
88. Schroeder, B. O. et al. Paneth cell α-defensin 6 (HD-6) is an antimicrobial peptide. Mucosal Immunology 8, 661–671 (2015).
89. Wang, C. et al. Reduction Impairs the Antibacterial Activity but Benefits the LPS Neutralization Ability of Human Enteric Defensin 5. Scientific Reports 6, 22875 (2016).
90. Hodin, C. M. et al. Reduced Paneth cell antimicrobial protein levels correlate with activation of the unfolded protein response in the gut of obese individuals. The Journal of pathology 225, 276– 284 (2011).
91. Grootjans, J. et al. Level of activation of the unfolded protein response correlates with Paneth cell apoptosis in human small intestine exposed to ischemia/reperfusion. Gastroenterology 140, 529- 539.e3 (2011).
92. Gyongyosi, B. et al. Alcohol-induced IL-17A production in Paneth cells amplifies endoplasmic reticulum stress, apoptosis, and inflammasome-IL-18 activation in the proximal small intestine in mice. Mucosal Immunology 12, 930–944 (2019)