REFERENCES
1. Karcher N, Nigro E, Punčochář M, et al. Genomic diversity and ecology of human-associated
2. Geerlings SY, Ouwerkerk JP, Koehorst JJ, et al. Genomic convergence between
3. Cani PD, Depommier C, Derrien M, Everard A, de Vos WM.
4. Cani PD, de Vos WM. Next-generation beneficial microbes: the case of
5. Dao MC, Everard A, Aron-Wisnewsky J, et al. MICRO-Obes Consortium.
6. Dehghanbanadaki H, Aazami H, Keshavarz Azizi Raftar S, et al. Global scientific output trend for
7. Fassatoui M, Lopez-Siles M, Díaz-Rizzolo DA, et al. Gut microbiota imbalances in Tunisian participants with type 1 and type 2 diabetes mellitus. Biosci Rep 2019;39:BSR20182348.
8. Rajilić-Stojanović M, Shanahan F, Guarner F, de Vos WM. Phylogenetic analysis of dysbiosis in ulcerative colitis during remission. Inflamm Bowel Dis 2013;19:481-8.
9. Png CW, Lindén SK, Gilshenan KS, et al. Mucolytic bacteria with increased prevalence in IBD mucosa augment
10. Everard A, Belzer C, Geurts L, et al. Cross-talk between
11. Zhang T, Li P, Wu X, et al. Alterations of
12. Pittayanon R, Lau JT, Leontiadis GI, et al. Differences in gut microbiota in patients with vs without inflammatory bowel diseases: a systematic review. Gastroenterology 2020;158:930-946.e1.
13. Demirci M, Tokman HB, Uysal HK, et al. Reduced
14. Plovier H, Everard A, Druart C, et al. A purified membrane protein from
15. Hänninen A, Toivonen R, Pöysti S, et al.
16. Zhai R, Xue X, Zhang L, Yang X, Zhao L, Zhang C. Strain-specific anti-inflammatory properties of two
17. Han Y, Li L, Wang B. Role of
18. Acharya KD, Friedline RH, Ward DV, et al. Differential effects of
19. Li N, Wang X, Sun C, et al. Change of intestinal microbiota in cerebral ischemic stroke patients. BMC Microbiol 2019;19:191.
20. Nishiwaki H, Ito M, Ishida T, et al. Meta-analysis of gut dysbiosis in parkinson’s disease. Mov Disord 2020;35:1626-35.
21. Consortium. Electronic address: [email protected], iMSMS Consortium. Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course. Cell 2022;185:3467-3486.e16.
22. Liu S, Rezende R, Moreira T, et al. Oral administration of miR-30d from feces of MS patients suppresses MS-like symptoms in mice by expanding
23. Gotkine M, Kviatcovsky D, Elinav E. Amyotrophic lateral sclerosis and intestinal microbiota-toward establishing cause and effect. Gut Microbes 2020;11:1833-41.
24. Nath N, Khan M, Paintlia MK, Singh I, Hoda MN, Giri S. Metformin attenuated the autoimmune disease of the central nervous system in animal models of multiple sclerosis. J Immunol 2009;182:8005-14.
25. Rotermund C, Machetanz G, Fitzgerald JC. The therapeutic potential of metformin in neurodegenerative diseases. Front Endocrinol (Lausanne) 2018;9:400.
26. de la Cuesta-Zuluaga J, Mueller NT, Corrales-Agudelo V, et al. Metformin is associated with higher relative abundance of mucin-degrading
27. Routy B, Gopalakrishnan V, Daillère R, Zitvogel L, Wargo JA, Kroemer G. The gut microbiota influences anticancer immunosurveillance and general health. Nat Rev Clin Oncol 2018;15:382-96.
28. Jin Y, Dong H, Xia L, et al. The diversity of gut microbiome is associated with favorable responses to anti-programmed death 1 immunotherapy in Chinese patients with NSCLC. J Thorac Oncol 2019;14:1378-89.
29. Zheng Y, Wang T, Tu X, et al. Gut microbiome affects the response to anti-PD-1 immunotherapy in patients with hepatocellular carcinoma. J Immunother Cancer 2019;7:193.
30. Derosa L, Routy B, Thomas AM, et al. Intestinal
31. Lee KA, Thomas AM, Bolte LA, et al. Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma. Nat Med 2022;28:535-44.
32. Shi L, Sheng J, Chen G, et al. Combining IL-2-based immunotherapy with commensal probiotics produces enhanced antitumor immune response and tumor clearance. J Immunother Cancer 2020;8:e000973.
33. Daisley BA, Chanyi RM, Abdur-Rashid K, et al. Abiraterone acetate preferentially enriches for the gut commensal
34. Terrisse S, Goubet AG, Ueda K, et al. Immune system and intestinal microbiota determine efficacy of androgen deprivation therapy against prostate cancer. J Immunother Cancer 2022;10:e004191.
35. Martel J, Chang SH, Ko YF, Hwang TL, Young JD, Ojcius DM. Gut barrier disruption and chronic disease. Trends Endocrinol Metab 2022;33:247-65.
36. Akdis CA. Does the epithelial barrier hypothesis explain the increase in allergy, autoimmunity and other chronic conditions? Nat Rev Immunol 2021;21:739-51.
37. Derrien M, Vaughan EE, Plugge CM, de Vos WM.
38. Ottman N, Davids M, Suarez-Diez M, et al. Genome-scale model and omics analysis of metabolic capacities of
39. van Passel MW, Kant R, Zoetendal EG, et al. The genome of
40. Li Z, Ke H, Wang Y, et al. Global trends in
41. Depommier C, Everard A, Druart C, et al. Supplementation with
42. Turck D, Bohn T, Castenmiller J, et al. EFSA Panel on Nutrition. Safety of pasteurised
43. Raftar S, Ashrafian F, Yadegar A, et al. The protective effects of live and pasteurized
44. Chelakkot C, Choi Y, Kim DK, et al.
45. Ashrafian F, Shahriary A, Behrouzi A, et al.
46. Ashrafian F, Keshavarz Azizi Raftar S, Lari A, et al. Extracellular vesicles and pasteurized cells derived from
47. Kang CS, Ban M, Choi EJ, et al. Extracellular vesicles derived from gut microbiota, especially
48. Ottman N, Reunanen J, Meijerink M, et al. Pili-like proteins of
49. Ligthart K, Belzer C, de Vos WM, Tytgat HLP. Bridging bacteria and the gut: functional aspects of type IV pili. Trends Microbiol 2020;28:340-8.
50. Rooijers K, Kolmeder C, Juste C, et al. An iterative workflow for mining the human intestinal metaproteome. BMC Genomics 2011;12:6.
51. Wang J, Xiang R, Wang R, et al. The variable oligomeric state of Amuc_1100 from
52. Mou L, Peng X, Chen Y, et al. Crystal structure of monomeric Amuc_1100 from
53. de Vos WM, Tytgat HLP, Swarts DC. AMUC-1100 polypeptide variants for effecting immune signalling and/or affecting intestinal barrier function and/or modulating metabolic status. Available from: https://research.wur.nl/en/publications/amuc-1100-polypeptide-variants-for-effecting-immune-signalling-an [Last accessed on 7 Mar 2023].
54. Liu Y, Yang M, Tang L, et al. TLR4 regulates RORγt+ regulatory T-cell responses and susceptibility to colon inflammation through interaction with
55. Dong X, Liu M, Liu X, Liu M, Zhang X, Wang G. [Prokaryotic expression of Amuc_1100 protein and its effects on high-fat diet rats combined streptozotocin injection]. Wei Sheng Yan Jiu 2020;49:785-822.
56. Deng SS, Chen J, Liu X, Dong XY, Zhang XL, Wang GQ. [Protective Effects of
57. Zhang FL, Yang YL, Zhang Z, et al. Surface-Displayed Amuc_1100 From
58. Naiel MAE, Negm SS, Ghazanfar S, Shukry M, Abdelnour SA. The risk assessment of high-fat diet in farmed fish and its mitigation approaches: A review. J Anim Physiol Anim Nutr (Berl) 2022; doi: 10.1111/jpn.13759.
59. Wang L, Tang L, Feng Y, et al. A purified membrane protein from
60. Lavelle A, Sokol H. Gut microbiota-derived metabolites as key actors in inflammatory bowel disease. Nat Rev Gastroenterol Hepatol 2020;17:223-37.
61. Agus A, Planchais J, Sokol H. Gut microbiota regulation of tryptophan metabolism in health and disease. Cell Host Microbe 2018;23:716-24.
62. Gu Z, Pei W, Shen Y, et al.
63. Laursen MF, Sakanaka M, von Burg N, et al.
64. Cervantes-Barragan L, Chai JN, Tianero MD, et al.
65. Zelante T, Iannitti RG, Cunha C, et al. Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity 2013;39:372-85.
66. Stasi C, Sadalla S, Milani S. The relationship between the serotonin metabolism, gut-microbiota and the gut-brain axis. Curr Drug Metab 2019;20:646-55.
67. Latorre E, Layunta E, Grasa L, et al. Intestinal serotonin transporter inhibition by toll-like receptor 2 activation. A feedback modulation. PLoS One 2016;11:e0169303.
68. Wang J, Xu W, Wang R, Cheng R, Tang Z, Zhang M. The outer membrane protein Amuc_1100 of
69. Cheng R, Xu W, Wang J, Tang Z, Zhang M. The outer membrane protein Amuc_1100 of
70. Sun Y, Zhu H, Cheng R, Tang Z, Zhang M. Outer membrane protein Amuc_1100 of
71. Cheng R, Zhu H, Sun Y, Hang T, Zhang M. The modified outer membrane protein Amuc_1100 of
72. Chen S, Qian K, Zhang G, Zhang M.
73. Lam RS, O'Brien-Simpson NM, Lenzo JC, et al. Macrophage depletion abates Porphyromonas gingivalis-induced alveolar bone resorption in mice. J Immunol 2014;193:2349-62.
74. Coretti L, Cuomo M, Florio E, et al. Subgingival dysbiosis in smoker and non-smoker patients with chronic periodontitis. Mol Med Rep 2017;15:2007-14.
75. Huck O, Mulhall H, Rubin G, et al.
76. Mulhall H, DiChiara JM, Deragon M, Iyer R, Huck O, Amar S.
77. Krzyszczyk P, Schloss R, Palmer A, Berthiaume F. The role of macrophages in acute and chronic wound healing and interventions to promote pro-wound healing phenotypes. Front Physiol 2018;9:419.
78. Yoon HS, Cho CH, Yun MS, et al.
79. Krieger JP, Santos da Conceição EP, Sanchez-Watts G, et al. Glucagon-like peptide-1 regulates brown adipose tissue thermogenesis via the gut-brain axis in rats. Am J Physiol Regul Integr Comp Physiol 2018;315:R708-20.
80. Ellingsgaard H, Hauselmann I, Schuler B, et al. Interleukin-6 enhances insulin secretion by increasing glucagon-like peptide-1 secretion from L cells and alpha cells. Nat Med 2011;17:1481-9.
81. Yoon HS, Cho CH, Yun MS, et al.
82. Gwang-pyo G, Hyo-shin Y, Jung-hwan J, Hyeon-joo Y, Tae-wook N. Patent WO2020076136A2: Akkermansia muciniphila strain and use thereof. 2020. Available from: https://patents.google.com/patent/WO2020076136A2/en?oq=WO2020076136A2 [Last accessed on 13 Mar 2023].
83. Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011;8:785-6.
84. Cani PD, Knauf C. A newly identified protein from
85. Kim BC, Lee CH, Kim JH, et al. Patent 10-2020-0129059: Peptides for the prevention or treatment of inflammatory bowel disease [Korean]In: Haneul Patent & Law Firm, editor. South Korea: Korean Intellectual Property Office; 2020.
86. Qian K, Chen S, Wang J, Sheng K, Wang Y, Zhang M. A β-
87. Meng X, Zhang J, Wu H, Yu D, Fang X.
88. Jiang Y, Xu Y, Zheng C, et al. Acetyltransferase from
89. Koh A, De Vadder F, Kovatcheva-Datchary P, Bäckhed F. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell 2016;165:1332-45.
90. Blaak EE, Canfora EE, Theis S, et al. Short chain fatty acids in human gut and metabolic health. Benef Microbes 2020;11:411-55.
91. Zarrinpar A, Chaix A, Yooseph S, Panda S. Diet and feeding pattern affect the diurnal dynamics of the gut microbiome. Cell Metab 2014;20:1006-17.
92. Xie J, Li H, Zhang X, et al. The Akkermansia muciniphila metabolite harmaline protects the host from systemic viral infection through the bile acid-TGR5-NF-κB axis. In. Cell Metabolism; Preprint. Review Complete.
93. Xie J, Li H, Zhang X, et al. Microbial metabolite harmaline protects against virus-induced systemic inflammation. Nat Microbiol 2023;8:10-1.
94. Khan FA, Maalik A, Iqbal Z, Malik I. Recent pharmacological developments in β-carboline alkaloid “harmaline”. Eur J Pharmacol 2013;721:391-4.
95. Brito-da-Costa AM, Dias-da-Silva D, Gomes NGM, Dinis-Oliveira RJ, Madureira-Carvalho Á. Toxicokinetics and toxicodynamics of ayahuasca alkaloids
96. Bag P, Ojha D, Mukherjee H, et al. A dihydro-pyrido-indole potently inhibits HSV-1 infection by interfering the viral immediate early transcriptional events. Antiviral Res 2014;105:126-34.
97. Martin-Gallausiaux C, Garcia-Weber D, Lashermes A, et al.
98. Garcia-Vello P, Tytgat HLP, Gray J, et al. Peptidoglycan from
99. Bae M, Cassilly CD, Liu X, et al.
100. Vollmer W, Blanot D, de Pedro MA. Peptidoglycan structure and architecture. FEMS Microbiol Rev 2008;32:149-67.
101. Boneca IG, Dussurget O, Cabanes D, et al. A critical role for peptidoglycan
102. Griffin ME, Espinosa J, Becker JL, et al.
103. Zhang Q, Linke V, Overmyer KA, et al. Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by
104. López-Lara IM, Sohlenkamp C, Geiger O. Membrane lipids in plant-associated bacteria: their biosyntheses and possible functions. Mol Plant Microbe Interact 2003;16:567-79.
105. Lee JS, Song WS, Lim JW, et al. An integrative multiomics approach to characterize anti-adipogenic and anti-lipogenic effects of
106. Roshanravan N, Bastani S, Tutunchi H, et al. A comprehensive systematic review of the effectiveness of
107. Abuqwider JN, Mauriello G, Altamimi M.