1. Ayabe, T.; Satchell, D.P.; Wilson, C.L.; Parks, W.C.; Selsted, M.E.; Ouellette, A.J. Secretion of microbicidal alpha-defensins by intestinal Paneth cells in response to bacteria. Nat. Immunol. 2000, 1, 113–118.
2. Masuda, K.; Sakai, N.; Nakamura, K.; Yoshioka, S.; Ayabe, T. Bactericidal activity of mouse alpha- defensin cryptdin-4 predominantly affects noncommensal bacteria. J. Innate Immun. 2011, 3, 315– 326.
3. Salzman, N.H.; Hung, K.; Haribhai, D.; Chu, H.; Karlsson-Sjoberg, J.; Amir, E.; Teggatz, P.; Barman, M.; Hayward, M.; Eastwood, D. Stoel, M.; Zhou, Y.; Sodergren, E.; Weinstock, G.M.; Bevins, C.L.; Williams, C.B.; Bos, N.A. Enteric defensins are essential regulators of intestinal microbial ecology. Nat. Immunol. 2010, 11, 76-83.
4. Mastroianni, J.R.; Ouellette, A.J. Alpha-defensins in enteric innate immunity: functional Paneth cell alpha-defensins in mouse colonic lumen. J. Biol. Chem. 2009, 284, 27848–27856.
5. Mastroianni, J.R.; Costales, J.K.; Zaksheske, J.; Selsted, M.E.; Salzman, N.H.; Ouellette, A.J. Alternative luminal activation mechanisms for Paneth cell alpha-defensins. J. Biol. Chem. 2012, 287, 11205–11212.
6. Salzman, N.H.; Bevins, C.L. Dysbiosis--a consequence of Paneth cell dysfunction. Semin. Immunol. 2013, 25, 334–341.
7. Sartor, R.B. Microbial influences in inflammatory bowel diseases. Gastroenterology 2008, 134, 577–594.
8. Boulange, C.L.; Neves, A.L.; Chilloux, J.; Nicholson, J.K.; Dumas, M.E. Impact of the gut microbiota on inflammation, obesity, and metabolic disease. Genome Med 2016, 8, 42.
9. Ley, R.E.; Turnbaugh, P.J.; Klein, S.; Gordon, J.I. Microbial ecology: human gut microbes associated with obesity. Nature 2006, 444, 1022-1023.
10. Smith, M.I.; Yatsunenko, T.; Manary, M.J.; Trehan, I.; Mkakosya, R.; Cheng, J.; Kau, A.L.; Rich, S.S.; Concannon, P.; Mychaleckyj, J.C., et al. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science 2013, 339, 548-554.
11. Sato, T.; van Es, J.H.; Snippert, H.J.; Stange, D.E.; Vries, R.G.; van den Born, M.; Barker, N.; Shroyer, N.F.; van de Wetering, M.; Clevers, H. Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts. Nature 2011, 469, 415–418.
12. Yilmaz, O.H.; Katajisto, P.; Lamming, D.W.; Gultekin, Y.; Bauer-Rowe, K.E.; Sengupta, S.; Birsoy, K.; Dursun, A.; Yilmaz, V.O.; Selig, M., Nielsen,G.P.; Mino-Kenudson, M.; Zukerberg, L.R.; Bhan, A.K.; Deshpande, V.; Sabatini, D.M. mTORC1 in the Paneth cell niche couples intestinal stem- cell function to calorie intake. Nature 2012, 486, 490–495.
13. Nakamura, K.; Sakuragi, N.; Takakuwa, A.; Ayabe, T. Paneth cell alpha-defensins and enteric microbiota in health and disease. Biosci. Microbiota Food Health 2016, 35, 57–67.
14. Salminen, S.; Bouley, C.; Boutron-Ruault, M.C.; Cummings, J.H.; Franck, A.; Gibson, G.R.; Isolauri, E.; Moreau, M.C.; Roberfroid, M.; Rowland, I. Functional food science and gastrointestinal physiology and function. Br J Nutr 1998, 80 Suppl 1, S147-171.
15. Gibson, G.R.; Roberfroid, M.B. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. The Journal of nutrition 1995, 125, 1401-1412.
16. Hardy, H.; Harris, J.; Lyon, E.; Beal, J.; Foey, A.D. Probiotics, prebiotics and immunomodulation of gut mucosal defences: homeostasis and immunopathology. Nutrients 2013, 5, 1869-1912.
17. Mack, D.R.; Michail, S.; Wei, S.; McDougall, L.; Hollingsworth, M.A. Probiotics inhibit enteropathogenic E. coliadherence in vitro by inducing intestinal mucin gene expression. American Journal of Physiology-Gastrointestinal and Liver Physiology 1999, 276, G941-G950.
18. Mucida, D.; Park, Y.; Kim, G.; Turovskaya, O.; Scott, I.; Kronenberg, M.; Cheroutre, H. Reciprocal TH17 and regulatory T cell differentiation mediated by retinoic acid. Science 2007, 317, 256-260.
19. Singh, N.; Gurav, A.; Sivaprakasam, S.; Brady, E.; Padia, R.; Shi, H.; Thangaraju, M.; Prasad, P.D.; Manicassamy, S.; Munn, D.H., et al. Activation of Gpr109a, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis. Immunity 2014, 40, 128-139.
20. Yasuda, S.; Miyazaki, T.; Munechika, K.; Yamashita, M.; Ikeda, Y.; Kamizono, A. Isolation of Zn2+ as an endogenous agonist of GPR39 from fetal bovine serum. J Recept Signal Transduct Res 2007, 27, 235-246.
21. Ohashi, W.; Kimura, S.; Iwanaga, T.; Furusawa, Y.; Irie, T.; Izumi, H.; Watanabe, T.; Hijikata, A.; Hara, T.; Ohara, O., et al. Zinc Transporter SLC39A7/ZIP7 Promotes Intestinal Epithelial Self- Renewal by Resolving ER Stress. PLoS Genet 2016, 12, e1006349.
22. Zelante, T.; Iannitti, R.G.; Cunha, C.; De Luca, A.; Giovannini, G.; Pieraccini, G.; Zecchi, R.; D'Angelo, C.; Massi-Benedetti, C.; Fallarino, F., et al. Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity 2013, 39, 372- 385.
23. Wrong O.M. Definitions and history. Physiological and clinical aspects of short-chain fatty acids, 1st pbk.ed.; Cummings, J.H.; Rombeau, J.L.; Sakata, T., Eds.; Cambridge University Press: Cambridge, UK, 2004; pp. 1–14.
24. Furusawa, Y.; Obata, Y.; Fukuda, S.; Endo, T.A.; Nakato, G.; Takahashi, D.; Nakanishi, Y.; Uetake, C.; Kato, K.; Kato, T.; Takahashi, M.; Fukuda, N.N.; Murakami, S.; Miyauchi, E.; Hino, S.; Atarashi, K.; Onawa, S.; Fujimura, Y.; Lockett, T.; Kikuchi, J.; Honda, K.; Hase, K.; Ohno, H. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 2013, 504, 446–450.
25. Becerril, A.; Castillo-Robles, G.; Gonzalez-Hernandez, M.; Villanueva, I. Influence of high- calorie (cafeteria) diets on the population of Paneth cells in the small intestine of the rat. Eur. J. Morphol. 2005, 42, 201–207.
26. Nakamura, K.; Sakuragi, N.; Ayabe, T. A monoclonal antibody-based sandwich enzyme-linked immunosorbent assay for detection of secreted alpha-defensin. Anal. Biochem. 2013, 443, 124–131.
27. Yokoi, Y.; Nakamura, K.; Yoneda, T.; Kikuchi, M.; Sugimoto, R.; Shimizu, Y.; Ayabe, T. Paneth cell granule dynamics on secretory responses to bacterial stimuli in enteroids. Scientific reports 2019, 9, 2710.
28. Sakata, T. Stimulatory effect of short-chain fatty acids on epithelial cell proliferation in the rat intestine: a possible explanation for trophic effects of fermentable fibre, gut microbes and luminal trophic factors. Br J Nutr 1987.
29. Brown, A.J.; Goldsworthy, S.M.; Barnes, A.A.; Eilert, M.M.; Tcheang, L.; Daniels, D.; Muir, A.I.; Wigglesworth, M.J.; Kinghorn, I.; Fraser, N.J.; et al. The Orphan G protein-coupled receptors GPR41 and GPR43 are activated by propionate and other short chain carboxylic acids. J. Biol. Chem. 2003, 278, 11312–11319.
30. Le Poul, E.; Loison, C.; Struyf, S.; Springael, J.Y.; Lannoy, V.; Decobecq, M.E.; Brezillon, S.; Dupriez, V.; Vassart, G.; Van Damme, J.; et al. Functional characterization of human receptors for short chain fatty acids and their role in polymorphonuclear cell activation. J. Biol. Chem. 2003, 278, 25481–25489.
31. Bakdash, G.; Vogelpoel, L.T.; van Capel, T.M.; Kapsenberg, M.L.; de Jong, E.C. Retinoic acid primes human dendritic cells to induce gut-homing, IL-10-producing regulatory T cells. Mucosal Immunol 2015, 8, 265-278 .
32. Takahashi, K.; Nishida, A.; Fujimoto, T.; Fujii, M.; Shioya, M.; Imaeda, H.; Inatomi, O.; Bamba, S.; Sugimoto, M.; Andoh, A. Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn's Disease. Digestion 2016, 93, 59-65.
33. Zhang, Y.G.; Wu, S.; Yi, J.; Xia, Y.; Jin, D.; Zhou, J.; Sun, J. Target intestinal microbiota to alleviate disease progression in amyotrophic lateral sclerosis. Clin. Ther. 2017, 39, 322–336.
34. Sugi, Y.; Takahashi, K.; Kurihara, K.; Nakano, K.; Kobayakawa, T.; Nakata, K.; Tsuda, M.; Hanazawa, S.; Hosono, A.; Kaminogawa, S. alpha-Defensin 5 gene expression is regulated by gut microbial metabolites. Biosci. Biotechnol. Biochem. 2017, 81, 242–248.
35. Joint WHO/FAO/UNU Expert Consultation. Protein and Amino Acid Requirements in Human Nutrition; World Health Organ Technical Report Series; WHO: Geneva, 2007; Volume 935, pp. 1- 265.
36. Newsholme, P.; Procopio, J.; Lima, M.M.; Pithon-Curi, T.C.; Curi, R. Glutamine and glutamate-- their central role in cell metabolism and function. Cell Biochem Funct 2003.
37. Reeds, P.J.; Burrin, D.G.; Stoll, B.; Jahoor, F. Intestinal glutamate metabolism. J Nutr 2000, 130, 978s-982s.
38. Andou, A.; Hisamatsu, T.; Okamoto, S.; Chinen, H.; Kamada, N.; Kobayashi, T.; Hashimoto, M.; Okutsu, T.; Shimbo, K.; Takeda, T., et al. Dietary histidine ameliorates murine colitis by inhibition of proinflammatory cytokine production from macrophages. Gastroenterology 2009, 136, 564-574 e562.
39. Omata, J.; Pierre, J.F.; Heneghan, A.F.; Tsao, F.H.; Sano, Y.; Jonker, M.A.; Kudsk, K.A. Parenteral nutrition suppresses the bactericidal response of the small intestine. Surgery 2013, 153, 17– 24.
40. Heneghan, A.F.; Pierre, J.F.; Tandee, K.; Shanmuganayagam, D.; Wang, X.; Reed, J.D.; Steele, J.L.; Kudsk, K.A. Parenteral nutrition decreases paneth cell function and intestinal bactericidal activity while increasing susceptibility to bacterial enteroinvasion. JPEN J. Parenter. Enteral. Nutr. 2014, 38, 817–824.
41. Sun, M.; Wu, W.; Liu, Z.; Cong, Y. Microbiota metabolite short chain fatty acids, GPCR, and inflammatory bowel diseases. Journal of Gastroenterology 2017, 52, 1-8.
42. Ahmed, K.; Tunaru, S.; Offermanns, S. GPR109A, GPR109B and GPR81, a family of hydroxy- carboxylic acid receptors. Trends Pharmacol Sci 2009, 30, 557-562.
43. Kimura, I.; Inoue, D.; Maeda, T.; Hara, T.; Ichimura, A.; Miyauchi, S.; Kobayashi, M.; Hirasawa, A.; Tsujimoto, G. Short-chain fatty acids and ketones directly regulate sympathetic nervous system via G protein-coupled receptor 41 (GPR41). Proc. Natl. Acad. Sci. U S A 2011, 108, 8030–8035.
44. Inoue, D.; Kimura, I.; Wakabayashi, M.; Tsumoto, H.; Ozawa, K.; Hara, T.; Takei, Y.; Hirasawa, A.; Ishihama, Y.; Tsujimoto, G. Short-chain fatty acid receptor GPR41-mediated activation of sympathetic neurons involves synapsin 2b phosphorylation. FEBS Lett 2012, 586, 1547-1554.
45. Bröer, S. Amino acid transport across mammalian intestinal and renal epithelia. Physiol Rev 2008, 88, 249-286.
46. Bröer, S. Apical transporters for neutral amino acids: physiology and pathophysiology. Physiology (Bethesda) 2008, 23, 95-103.
47. Bröer, S.; Bröer, A. Amino acid homeostasis and signalling in mammalian cells and organisms. Biochemical Journal 2017, 474, 1935-1963.
48. Beyaz, S.; Mana, M.D.; Roper, J.; Kedrin, D.; Saadatpour, A.; Hong, S.-J.; Bauer-Rowe, K.E.; Xifaras, M.E.; Akkad, A.; Arias, E., et al. High-fat diet enhances stemness and tumorigenicity of intestinal progenitors. Nature.
49. Kim, C.S.; Cho, S.H.; Chun, H.S.; Lee, S.Y.; Endou, H.; Kanai, Y.; Kim, D.K. BCH, an inhibitor of system L amino acid transporters, induces apoptosis in cancer cells. Biol. Pharm. Bull. 2008, 31, 1096–1100.
50. Offermanns, S. Free fatty acid (FFA) and hydroxy carboxylic acid (HCA) receptors. Annu. Rev. Pharmacol. Toxicol. 2014, 54, 407–434.
51. Wolfson, R.L.; Chantranupong, L.; Saxton, R.A.; Shen, K.; Scaria, S.M.; Cantor, J.R.; Sabatini, D.M. Sestrin2 is a leucine sensor for the mTORC1 pathway. Science 2016, 351, 43-48.
52. Marc Rhoads, J.; Wu, G. Glutamine, arginine, and leucine signaling in the intestine. Amino Acids 2009, 37, 111-122.
53. Hashimoto, T.; Perlot, T.; Rehman, A.; Trichereau, J.; Ishiguro, H.; Paolino, M.; Sigl, V.; Hanada, T.; Hanada, R.; Lipinski, S., et al. ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation. Nature 2012, 487, 477-481.
54. Ravindran, R.; Loebbermann, J.; Nakaya, H.I.; Khan, N.; Ma, H.; Gama, L.; Machiah, D.K.; Lawson, B.; Hakimpour, P.; Wang, Y.C., et al. The amino acid sensor GCN2 controls gut inflammation by inhibiting inflammasome activation. Nature 2016, 531, 523-527.
55. Tan, G.; Zeng, B.; Zhi, F.C. Regulation of human enteric alpha-defensins by NOD2 in the Paneth cell lineage. Eur. J. Cell Biol. 2015, 94, 60–66.
56. Hodin, C.M.; Verdam, F.J.; Grootjans, J.; Rensen, S.S.; Verheyen, F.K.; Dejong, C.H.; Buurman, W.A.; Greve, J.W.; Lenaerts, K. Reduced Paneth cell antimicrobial protein levels correlate with activation of the unfolded protein response in the gut of obese individuals. J. Pathol. 2011, 225, 276– 284.
57. Eriguchi, Y.; Takashima, S.; Oka, H.; Shimoji, S.; Nakamura, K.; Uryu, H.; Shimoda, S.; Iwasaki, H.; Shimono, N.; Ayabe, T., et al. Graft-versus-host disease disrupts intestinal microbial ecology by inhibiting Paneth cell production of alpha-defensins. Blood 2012, 120, 223-231.
58. Eriguchi, Y.; Nakamura, K.; Hashimoto, D.; Shimoda, S.; Shimono, N.; Akashi, K.; Ayabe, T.; Teshima, T. Decreased secretion of Paneth cell alpha-defensins in graft-versus-host disease. Transpl Infect Dis 2015, 17, 702-706.
59. Hayase, E.; Hashimoto, D.; Nakamura, K.; Noizat, C.; Ogasawara, R.; Takahashi, S.; Ohigashi, H.; Yokoi, Y.; Sugimoto, R.; Matsuoka, S.; et al. R-Spondin1 expands Paneth cells and prevents dysbiosis induced by graft-versus-host disease. J. Exp. Med. 2017, 214, 3507–3518.