REFERENCES
1. Geng ZH, Zhu Y, Li QL, Zhao C, Zhou PH. Enteric nervous system: the bridge between the gut microbiota and neurological disorders. Front Aging Neurosci 2022;14:810483.
2. Tokuhara D, Kurashima Y, Kamioka M, Nakayama T, Ernst P, Kiyono H. A comprehensive understanding of the gut mucosal immune system in allergic inflammation. Allergol Int 2019;68:17-25.
3. Fung TC, Olson CA, Hsiao EY. Interactions between the microbiota, immune and nervous systems in health and disease. Nat Neurosci 2017;20:145-55.
4. Sekirov I, Russell SL, Antunes LCM, Finlay BB. Gut microbiota in health and disease. Physiol Rev 2010;90:859-904.
6. Erny D, Hrabě de Angelis AL, Prinz M. Communicating systems in the body: how microbiota and microglia cooperate. Immunology 2017;150:7-15.
7. Hou K, Wu ZX, Chen XY, et al. Microbiota in health and diseases. Signal Transduct Target Ther 2022;7:135.
8. Gomaa EZ. Human gut microbiota/microbiome in health and diseases: a review. Antonie Van Leeuwenhoek 2020;113:2019-40.
9. Hooper LV, Littman DR, Macpherson AJ. Interactions between the microbiota and the immune system. Science 2012;336:1268-73.
10. Sommer F, Bäckhed F. The gut microbiota - masters of host development and physiology. Nat Rev Microbiol 2013;11:227-38.
11. Clemente JC, Ursell LK, Parfrey LW, Knight R. The impact of the gut microbiota on human health: an integrative view. Cell 2012;148:1258-70.
12. Rinninella E, Raoul P, Cintoni M, et al. What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms 2019;7:14.
14. Blaak EE, Canfora EE, Theis S, et al. Short chain fatty acids in human gut and metabolic health. Benef Microbes 2020;11:411-55.
15. Parada Venegas D, De la Fuente MK, Landskron G, et al. Corrigendum: short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Front Immunol 2019;10:1486.
16. Yu X, Gurry T, Nguyen LTT, Richardson HS, Alm EJ. Prebiotics and community composition influence gas production of the human gut microbiota. mBio 2020;11:e00217-20.
17. Deleu S, Machiels K, Raes J, Verbeke K, Vermeire S. Short chain fatty acids and its producing organisms: an overlooked therapy for IBD? EBioMedicine 2021;66:103293.
18. Chen T, Long W, Zhang C, Liu S, Zhao L, Hamaker BR. Fiber-utilizing capacity varies in Prevotella- versus Bacteroides-dominated gut microbiota. Sci Rep 2017;7:2594.
19. Gibson GR, Hutkins R, Sanders ME, et al. Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol 2017;14:491-502.
20. Fehlbaum S, Prudence K, Kieboom J, et al. In vitro fermentation of selected prebiotics and their effects on the composition and activity of the adult gut microbiota. Int J Mol Sci 2018;19:3097.
21. Vandeputte D, Falony G, Vieira-Silva S, et al. Prebiotic inulin-type fructans induce specific changes in the human gut microbiota. Gut 2017;66:1968-74.
22. Baxter NT, Schmidt AW, Venkataraman A, Kim KS, Waldron C, Schmidt TM. Dynamics of human gut microbiota and short-chain fatty acids in response to dietary interventions with three fermentable fibers. mBio 2019;10:e02566-18.
23. Wang X, Wang T, Zhang Q, Xu L, Xiao X. Dietary supplementation with inulin modulates the gut microbiota and improves insulin sensitivity in prediabetes. Int J Endocrinol 2021;2021:5579369.
24. Le Bastard Q, Chapelet G, Javaudin F, Lepelletier D, Batard E, Montassier E. The effects of inulin on gut microbial composition: a systematic review of evidence from human studies. Eur J Clin Microbiol Infect Dis 2020;39:403-13.
25. Holscher HD. Dietary fiber and prebiotics and the gastrointestinal microbiota. Gut Microbes 2017;8:172-84.
26. McDonald JAK. In vitro models of the human microbiota and microbiome. Emerg Top Life Sci 2017;1:373-84.
27. Rahman S, Ghiboub M, Donkers JM, et al. The progress of intestinal epithelial models from cell lines to gut-on-chip. Int J Mol Sci 2021;22:13472.
28. Eslami Amirabadi H, Donkers JM, Wierenga E, et al. Intestinal explant barrier chip: long-term intestinal absorption screening in a novel microphysiological system using tissue explants. Lab Chip 2022;22:326-42.
29. Schuren F, Agamennone V, Keijser B, Abeln E, van der Vossen J, Montijn R. The i-screen: a versatile preclinical platform for gut microbiota studies. J Prob Health 2019;7:212.
30. Ladirat SE, Schols HA, Nauta A, et al. High-throughput analysis of the impact of antibiotics on the human intestinal microbiota composition. J Microbiol Methods 2013;92:387-97.
31. Wiese M, Schuren FHJ, Smits WK, et al. 2’-Fucosyllactose inhibits proliferation of Clostridioides difficile ATCC 43599 in the CDi-screen, an in vitro model simulating Clostridioides difficile infection. Front Cell Infect Microbiol 2022;12:991150.
32. Agamennone V, van den Broek TJ, de Kat Angelino-Bart A, Hoevenaars FPM, van der Kamp JW, Schuren FHJ. Individual and group-based effects of in vitro fiber interventions on the fecal microbiota. Microorganisms 2023;11:2001.
33. R Core Team. R: A Language and Environment for Statistical Computing. 2016. Available from: https://www.R-project.org/. [Last accessed on 22 Feb 2024]
35. McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 2013;8:e61217.
36. Stacklies W, Redestig H, Scholz M, Walther D, Selbig J. pcaMethods - a bioconductor package providing PCA methods for incomplete data. Bioinformatics 2007;23:1164-7.
37. Oksanen J, Simpson GL, Blanchet FG, et al. Package ‘vegan’: Community ecology package. 2022. Available from: https://cran.r-project.org/web/packages/vegan/vegan.pdf. [Last accessed on 22 Feb 2024].
38. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010;26:139-40.
39. Hoffman GE, Roussos P. Dream: powerful differential expression analysis for repeated measures designs. Bioinformatics 2021;37:192-201.
40. Stevens LJ, van Lipzig MMH, Erpelinck SLA, et al. A higher throughput and physiologically relevant two-compartmental human ex vivo intestinal tissue system for studying gastrointestinal processes. Eur J Pharm Sci 2019;137:104989.
41. Hatton GB, Yadav V, Basit AW, Merchant HA. Animal farm: considerations in animal gastrointestinal physiology and relevance to drug delivery in humans. J Pharm Sci 2015;104:2747-76.
42. Donkers JM, Höppener EM, Grigoriev I, et al. Advanced epithelial lung and gut barrier models demonstrate passage of microplastic particles. Micropl Nanopl 2022;2:6.
43. Westerhout J, van de Steeg E, Grossouw D, et al. A new approach to predict human intestinal absorption using porcine intestinal tissue and biorelevant matrices. Eur J Pharm Sci 2014;63:167-77.
44. Hoffman GE, Schadt EE. variancePartition: interpreting drivers of variation in complex gene expression studies. BMC Bioinformatics 2016;17:483.
45. Vinolo MAR, Rodrigues HG, Nachbar RT, Curi R. Regulation of inflammation by short chain fatty acids. Nutrients 2011;3:858-76.
46. Yao Y, Cai X, Fei W, Ye Y, Zhao M, Zheng C. The role of short-chain fatty acids in immunity, inflammation and metabolism. Crit Rev Food Sci Nutr 2022;62:1-12.
47. Chelakkot C, Ghim J, Ryu SH. Mechanisms regulating intestinal barrier integrity and its pathological implications. Exp Mol Med 2018;50:1-9.
49. Fasano A, Not T, Wang W, et al. Zonulin, a newly discovered modulator of intestinal permeability, and its expression in coeliac disease. Lancet 2000;355:1518-9.
50. Wood Heickman LK, DeBoer MD, Fasano A. Zonulin as a potential putative biomarker of risk for shared type 1 diabetes and celiac disease autoimmunity. Diabetes Metab Res Rev 2020;36:e3309.
51. Schierack P, Nordhoff M, Pollmann M, et al. Characterization of a porcine intestinal epithelial cell line for in vitro studies of microbial pathogenesis in swine. Histochem Cell Biol 2006;125:293-305.
52. Walsh MD, Clendenning M, Williamson E, et al. Expression of MUC2, MUC5AC, MUC5B, and MUC6 mucins in colorectal cancers and their association with the CpG island methylator phenotype. Mod Pathol 2013;26:1642-56.
53. Moncada DM, Kammanadiminti SJ, Chadee K. Mucin and Toll-like receptors in host defense against intestinal parasites. Trends Parasitol 2003;19:305-11.
54. Sag D, Ayyildiz ZO, Gunalp S, Wingender G. The role of TRAIL/DRs in the modulation of immune cells and responses. Cancers 2019;11:1469.
55. Falschlehner C, Schaefer U, Walczak H. Following TRAIL’s path in the immune system. Immunology 2009;127:145-54.
56. Bernhard S, Hug S, Stratmann AEP, et al. Interleukin 8 elicits rapid physiological changes in neutrophils that are altered by inflammatory conditions. J Innate Immun 2021;13:225-41.
57. Meng L, Song Z, Liu A, Dahmen U, Yang X, Fang H. Effects of lipopolysaccharide-binding protein (LBP) single nucleotide polymorphism (SNP) in infections, inflammatory diseases, metabolic disorders and cancers. Front Immunol 2021;12:681810.
58. Weckmann M, Collison A, Simpson JL, et al. Critical link between TRAIL and CCL20 for the activation of TH2 cells and the expression of allergic airway disease. Nat Med 2007;13:1308-15.
59. Sierro F, Dubois B, Coste A, Kaiserlian D, Kraehenbuhl JP, Sirard JC. Flagellin stimulation of intestinal epithelial cells triggers CCL20-mediated migration of dendritic cells. Proc Natl Acad Sci U S A 2001;98:13722-7.
60. Schilderink R, Verseijden C, Seppen J, et al. The SCFA butyrate stimulates the epithelial production of retinoic acid via inhibition of epithelial HDAC. Am J Physiol Gastrointest Liver Physiol 2016;310:G1138-46.
61. Chriett S, Dąbek A, Wojtala M, Vidal H, Balcerczyk A, Pirola L. Prominent action of butyrate over β-hydroxybutyrate as histone deacetylase inhibitor, transcriptional modulator and anti-inflammatory molecule. Sci Rep 2019;9:742.
62. Hecker J, Freijer K, Hiligsmann M, Evers SMAA. Burden of disease study of overweight and obesity; the societal impact in terms of cost-of-illness and health-related quality of life. BMC Public Health 2022;22:46.
63. van den Broek-Altenburg E, Atherly A, Holladay E. Changes in healthcare spending attributable to obesity and overweight: payer- and service-specific estimates. BMC Public Health 2022;22:962.
64. Singh S, Qian AS, Nguyen NH, et al. Trends in U.S. health care spending on inflammatory bowel diseases, 1996-2016. Inflamm Bowel Dis 2022;28:364-72.
65. CDC. Health and economic costs of chronic diseases. 2023. Available from: https://www.cdc.gov/chronicdisease/about/costs/index.htm. [Last accessed on 22 Feb 2024].
66. Quaranta G, Guarnaccia A, Fancello G, et al. Fecal microbiota transplantation and other gut microbiota manipulation strategies. Microorganisms 2022;10:2424.
67. Donkers JM, van der Vaart JI, van de Steeg E. Gut-on-a-chip research for drug development: implications of chip design on preclinical oral bioavailability or intestinal disease studies. Biomimetics 2023;8:226.
68. Wang H, Bastian SEP, Cheah KY, Lawrence A, Howarth GS. Escherichia coli Nissle 1917-derived factors reduce cell death and late apoptosis and increase transepithelial electrical resistance in a model of 5-fluorouracil-induced intestinal epithelial cell damage. Cancer Biol Ther 2014;15:560-9.
69. Khodaii Z, Ghaderian SMH, Natanzi MM. Probiotic bacteria and their supernatants protect enterocyte cell lines from enteroinvasive Escherichia coli (EIEC) invasion. Int J Mol Cell Med 2017;6:183-9.
70. Rocha-Ramírez LM, Hernández-Chiñas U, Moreno-Guerrero SS, Ramírez-Pacheco A, Eslava CA. In vitro effect of the cell-free supernatant of the Lactobacillus casei strain IMAU60214 against the different pathogenic properties of Diarrheagenic Escherichia coli. Microorganisms 2023;11:1324.
71. Bermudez-Brito M, Muñoz-Quezada S, Gómez-Llorente C, Matencio E, Romero F, Gil A. Lactobacillus paracasei CNCM I-4034 and its culture supernatant modulate Salmonella-induced inflammation in a novel transwell co-culture of human intestinal-like dendritic and Caco-2 cells. BMC Microbiol 2015;15:79.
72. Gonzales J, Marchix J, Aymeric L, et al. Fecal supernatant from adult with autism spectrum disorder alters digestive functions, intestinal epithelial barrier, and enteric nervous system. Microorganisms 2021;9:1723.
73. Nguyen TLA, Vieira-Silva S, Liston A, Raes J. How informative is the mouse for human gut microbiota research? Dis Model Mech 2015;8:1-16.
74. Marzorati M, Vanhoecke B, De Ryck T, et al. The HMI™ module: a new tool to study the Host-Microbiota Interaction in the human gastrointestinal tract in vitro. BMC Microbiol 2014;14:133.
75. Shah P, Fritz JV, Glaab E, et al. A microfluidics-based in vitro model of the gastrointestinal human-microbe interface. Nat Commun 2016;7:11535.
76. Morelli M, Kurek D, Ng CP, Queiroz K. Gut-on-a-chip models: current and future perspectives for host - microbial interactions research. Biomedicines 2023;11:619.
77. Scott KP, Martin JC, Duncan SH, Flint HJ. Prebiotic stimulation of human colonic butyrate-producing bacteria and bifidobacteria, in vitro. FEMS Microbiol Ecol 2014;87:30-40.
78. Sawicki CM, Livingston KA, Obin M, Roberts SB, Chung M, McKeown NM. Dietary fiber and the human gut microbiota: application of evidence mapping methodology. Nutrients 2017;9:125.
79. Scotti E, Boué S, Sasso GL, et al. Exploring the microbiome in health and disease: implications for toxicology. Toxicol Res Appl 2017;1:239784731774188.
80. Singh V, Lee G, Son H, et al. Butyrate producers, “The Sentinel of Gut”: their intestinal significance with and beyond butyrate, and prospective use as microbial therapeutics. Front Microbiol 2022;13:1103836.
81. Belotserkovsky I, Sansonetti PJ, Jenkins C, et al. Escherichia coli, a versatile pathogen. Springer Cham; 2018.
82. dos Reis RS, Horn F. Enteropathogenic Escherichia coli, Samonella, Shigella and Yersinia: cellular aspects of host-bacteria interactions in enteric diseases. Gut Pathog 2010;2:8.
83. Chen J, Chen X, Ho CL. Recent development of probiotic Bifidobacteria for treating human diseases. Front Bioeng Biotechnol 2021;9:770248.
84. O’Callaghan A, van Sinderen D. Bifidobacteria and their role as members of the human gut microbiota. Front Microbiol 2016;7:925.
85. Belenguer A, Duncan SH, Calder AG, et al. Two routes of metabolic cross-feeding between Bifidobacterium adolescentis and butyrate-producing anaerobes from the human gut. Appl Environ Microbiol 2006;72:3593-9.
86. Guilloteau P, Zabielski R, Hammon HM, Metges CC. Nutritional programming of gastrointestinal tract development. Is the pig a good model for man? Nutr Res Rev 2010;23:4-22.
87. Hodgkinson K, El Abbar F, Dobranowski P, et al. Butyrate’s role in human health and the current progress towards its clinical application to treat gastrointestinal disease. Clin Nutr 2023;42:61-75.
88. Anshory M, Effendi RMRA, Kalim H, et al. Butyrate properties in immune-related diseases: friend or foe? Fermentation 2023;9:205.
89. Recharla N, Geesala R, Shi XZ. Gut microbial metabolite butyrate and its therapeutic role in inflammatory bowel disease: a literature review. Nutrients 2023;15:2275.
90. Peng L, He Z, Chen W, Holzman IR, Lin J. Effects of butyrate on intestinal barrier function in a Caco-2 cell monolayer model of intestinal barrier. Pediatr Res 2007;61:37-41.
91. Peng L, Li ZR, Green RS, Holzman IR, Lin J. Butyrate enhances the intestinal barrier by facilitating tight junction assembly via activation of AMP-activated protein kinase in Caco-2 cell monolayers. J Nutr 2009;139:1619-25.
92. Kinoshita M, Suzuki Y, Saito Y. Butyrate reduces colonic paracellular permeability by enhancing PPARγ activation. Biochem Biophys Res Commun 2002;293:827-31.
93. Tabat MW, Marques TM, Markgren M, Löfvendahl L, Brummer RJ, Wall R. Acute effects of butyrate on induced hyperpermeability and tight junction protein expression in human colonic tissues. Biomolecules 2020;10:766.
94. Donkers JM, Eslami Amirabadi H, van de Steeg E. Intestine-on-a-chip: next level in vitro research model of the human intestine. Curr Opin Toxicol 2021;25:6-14.
95. Siddiqui MT, Cresci GAM. The immunomodulatory functions of butyrate. J Inflamm Res 2021;14:6025-41.
96. Zheng L, Kelly CJ, Battista KD, et al. Microbial-derived butyrate promotes epithelial barrier function through IL-10 receptor-dependent repression of claudin-2. J Immunol 2017;199:2976-84.
97. Ratajczak W, Rył A, Mizerski A, Walczakiewicz K, Sipak O, Laszczyńska M. Immunomodulatory potential of gut microbiome-derived short-chain fatty acids (SCFAs). Acta Biochim Pol 2019;66:1-12.
98. Vinolo MAR, Rodrigues HG, Hatanaka E, Sato FT, Sampaio SC, Curi R. Suppressive effect of short-chain fatty acids on production of proinflammatory mediators by neutrophils. J Nutr Biochem 2011;22:849-55.
99. Park J, Kim M, Kang SG, et al. Short-chain fatty acids induce both effector and regulatory T cells by suppression of histone deacetylases and regulation of the mTOR-S6K pathway. Mucosal Immunol 2015;8:80-93.
100. Liu L, Li L, Min J, et al. Butyrate interferes with the differentiation and function of human monocyte-derived dendritic cells. Cell Immunol 2012;277:66-73.
101. Arpaia N, Campbelle C, Fan X, et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 2013;504:451-5.
102. van Nuenen MHMC, Venema K, van Der Woude JCJ, Kuipers EJ. The metabolic activity of fecal microbiota from healthy individuals and patients with inflammatory bowel disease. Dig Dis Sci 2004;49:485-91.
103. van Nuenen MHMC, de Ligt RAF, Doornbos RP, van der Woude JCJ, Kuipers EJ, Venema K. The influence of microbial metabolites on human intestinal epithelial cells and macrophages in vitro. FEMS Immunol Med Microbiol 2005;45:183-9.
104. Dengler F, Kraetzig A, Gäbel G. Butyrate protects porcine colon epithelium from hypoxia-induced damage on a functional level. Nutrients 2021;13:305.
105. van Deuren T, Blaak EE, Canfora EE. Butyrate to combat obesity and obesity-associated metabolic disorders: current status and future implications for therapeutic use. Obes Rev 2022;23:e13498.
106. Vernocchi P, Del Chierico F, Putignani L. Gut microbiota profiling: metabolomics based approach to unravel compounds affecting human health. Front Microbiol 2016;7:1144.
107. Bauermeister A, Mannochio-Russo H, Costa-Lotufo LV, Jarmusch AK, Dorrestein PC. Mass spectrometry-based metabolomics in microbiome investigations. Nat Rev Microbiol 2022;20:143-60.
108. Segers K, Declerck S, Mangelings D, Vander Heyden Y, Van Eeckhaut A. Analytical techniques for metabolomic studies: a review. Bioanalysis 2019;11:2297-318.
