REFERENCES
1. Gill SK, Rossi M, Bajka B, Whelan K. Dietary fibre in gastrointestinal health and disease. Nat Rev Gastroenterol Hepatol 2021;18:101-16.
2. Joint FAO/WHO Food Standards Programme. CODEX Alimentarius (CODEX) Guidelines on Nutrition Labelling CXG 2-1985. 2021. Available from: https://www.fao.org/fao-who-codexalimentarius/sh-proxy/en/?lnk=1&url=https%253A%252F%252Fworkspace.fao.org%252Fsites%252Fcodex%252FStandards%252FCXG%2B2-1985%252FCXG_002e.pdf. [Last accessed on 22 Apr 2024].
3. 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.
4. Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes 2012;3:289-306.
5. Blaak EE, Canfora EE, Theis S, et al. Short chain fatty acids in human gut and metabolic health. Benef Microbes 2020;11:411-55.
6. Hamer HM, Jonkers D, Venema K, Vanhoutvin S, Troost FJ, Brummer RJ. Review article: the role of butyrate on colonic function. Aliment Pharmacol Ther 2008;27:104-19.
7. Cantu-Jungles TM, Bulut N, Chambry E, et al. Dietary fiber hierarchical specificity: the missing link for predictable and strong shifts in gut bacterial communities. mBio 2021;12:e0102821.
8. EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA). Scientific Opinion on the substantiation of a health claim related to “native chicory inulin” and maintenance of normal defecation by increasing stool frequency pursuant to Article 13.5 of Regulation (EC) No 1924/2006. EFSA J 2015;13:3951.
9. EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA). Scientific opinion on the substantiation of health claims related to pectins and reduction of post-prandial glycaemic responses (ID 786), maintenance of normal blood cholesterol concentrations (ID 818) and increase in satiety leading to a reduction in energy intake (ID 4692) pursuant to Article 13(1) of Regulation (EC) No 1924/2006. EFSA J 2010;8:1747. Available from: https://efsa.onlinelibrary.wiley.com/doi/pdf/10.2903/j.efsa.2010.1747. [Last accessed on 22 Apr 2024]
10. Lutter R, Teitsma-Jansen A, Floris E, et al. The dietary intake of carrot-derived rhamnogalacturonan-i accelerates and augments the innate immune and anti-viral interferon response to rhinovirus infection and reduces duration and severity of symptoms in humans in a randomized trial. Nutrients 2021;13:4395.
11. Korpela K. Diet, microbiota, and metabolic health: trade-off between saccharolytic and proteolytic fermentation. Annu Rev Food Sci Technol 2018;9:65-84.
12. So D, Gibson PR, Muir JG, Yao CK. Dietary fibres and IBS: translating functional characteristics to clinical value in the era of personalised medicine. Gut 2021;70:2383-94.
13. Puhlmann ML, de Vos WM. Intrinsic dietary fibers and the gut microbiome: Rediscovering the benefits of the plant cell matrix for human health. Front Immunol 2022;13:954845.
14. Augustin LSA, Aas AM, Astrup A, et al. Dietary fibre consensus from the International Carbohydrate Quality Consortium (ICQC). Nutrients 2020;12:2553.
15. Williams BA, Grant LJ, Gidley MJ, Mikkelsen D. Gut fermentation of dietary fibres: physico-chemistry of plant cell walls and implications for health. Int J Mol Sci 2017;18:2203.
16. Capuano E. The behavior of dietary fiber in the gastrointestinal tract determines its physiological effect. Crit Rev Food Sci Nutr 2017;57:3543-64.
17. Puhlmann ML, de Vos WM. Corrigendum: Back to the roots: revisiting the use of the fiber-rich Cichorium intybus L. Taproots. Adv Nutr 2021;12:1598.
18. Stewart ML, Slavin JL. Particle size and fraction of wheat bran influence short-chain fatty acid production in vitro. Br J Nutr 2009;102:1404-7.
19. Day L, Gomez J, Øiseth SK, Gidley MJ, Williams BA. Faster fermentation of cooked carrot cell clusters compared to cell wall fragments in vitro by porcine feces. J Agric Food Chem 2012;60:3282-90.
20. Yao H, Flanagan BM, Williams BA, Mikkelsen D, Gidley MJ. Particle size of dietary fibre has diverse effects on in vitro gut fermentation rate and end-products depending on food source. Food Hydrocolloid 2023;134:108096.
21. Tuncil YE, Thakkar RD, Marcia ADR, Hamaker BR, Lindemann SR. Divergent short-chain fatty acid production and succession of colonic microbiota arise in fermentation of variously-sized wheat bran fractions. Sci Rep 2018;8:16655.
22. De Paepe K, Verspreet J, Rezaei MN, et al. Modification of wheat bran particle size and tissue composition affects colonisation and metabolism by human faecal microbiota. Food Funct 2019;10:379-96.
23. Rovalino-Córdova AM, Fogliano V, Capuano E. Effect of bean structure on microbiota utilization of plant nutrients: an in-vitro study using the simulator of the human intestinal microbial ecosystem (SHIME®). J Funct Foods 2020;73:104087.
24. Low DY, Williams BA, D’Arcy BR, Flanagan BM, Gidley MJ. In vitro fermentation of chewed mango and banana: particle size, starch and vascular fibre effects. Food Funct 2015;6:2464-74.
25. Widaningrum, Flanagan BM, Williams BA, Sonni F, Mikkelsen D, Gidley MJ. Fruit and vegetable insoluble dietary fibre in vitro fermentation characteristics depend on cell wall type. Bioact Carbohydr Diet Fibre 2020;23:100223.
26. Solvang M, Farquharson FM, Sanhueza D, Horgan G, Russell WR, Louis P. Beyond purified dietary fibre supplements: compositional variation between cell wall fibre from different plants influences human faecal microbiota activity and growth in vitro. Environ Microbiol 2023;25:1484-504.
27. Puhlmann ML, Jokela R, van Dongen KCW, et al. Dried chicory root improves bowel function, benefits intestinal microbial trophic chains and increases faecal and circulating short chain fatty acids in subjects at risk for type 2 diabetes. Gut Microb 2022;3:e4.
28. Neis EP, van Eijk HM, Lenaerts K, et al. Distal versus proximal intestinal short-chain fatty acid release in man. Gut 2019;68:764-5.
29. Canfora EE, van der Beek CM, Jocken JWE, et al. Colonic infusions of short-chain fatty acid mixtures promote energy metabolism in overweight/obese men: a randomized crossover trial. Sci Rep 2017;7:2360.
30. Brodkorb A, Egger L, Alminger M, et al. INFOGEST static in vitro simulation of gastrointestinal food digestion. Nat Protoc 2019;14:991-1014.
31. Minekus M, Alminger M, Alvito P, et al. A standardised static in vitro digestion method suitable for food - an international consensus. Food Funct 2014;5:1113-24.
32. Thibault JF. Automated-method for the determination of pectic substances. Leb und Technol 1979;12:247-51.
33. Ramasamy US, Gruppen H, Schols HA. Structural and water-holding characteristics of untreated and ensiled chicory root pulp. J Agric Food Chem 2013;61:6077-85.
34. Logtenberg MJ, Akkerman R, An R, et al. Fermentation of chicory fructo-oligosaccharides and native inulin by infant fecal microbiota attenuates pro-inflammatory responses in immature dendritic cells in an infant-age-dependent and fructan-specific way. Mol Nutr Food Res 2020;64:e2000068.
35. de Preter V, Vanhoutte T, Huys G, Swings J, Rutgeerts P, Verbeke K. Baseline microbiota activity and initial bifidobacteria counts influence responses to prebiotic dosing in healthy subjects. Aliment Pharmacol Ther 2008;27:504-13.
36. Kolida S, Meyer D, Gibson GR. A double-blind placebo-controlled study to establish the bifidogenic dose of inulin in healthy humans. Eur J Clin Nutr 2007;61:1189-95.
37. Healey G, Murphy R, Butts C, Brough L, Whelan K, Coad J. Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study. Br J Nutr 2018;119:176-89.
38. Korpela K, Flint HJ, Johnstone AM, et al. Gut microbiota signatures predict host and microbiota responses to dietary interventions in obese individuals. PLoS One 2014;9:e90702.
39. Van den Abbeele P, Belzer C, Goossens M, et al. Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model. ISME J 2013;7:949-61.
40. 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.
41. Thomson A, Smart K, Somerville MS, et al. The Ussing chamber system for measuring intestinal permeability in health and disease. BMC Gastroenterol 2019;19:98.
42. R Core Team. R: A language and environment for statistical computing. The R Project for Statistical Computing. Vienna, Austria. 2023. Available from: https://www.r-project.org/. [Last accessed 22 Apr 2024].
43. Kassambara A. rstatix: Pipe-friendly framework for basic statistical tests. R package version 0.7.2. 2023. Available from: https://cran.r-project.org/package=rstatix. [Last accessed 22 Apr 2024].
44. Mair P, Wilcox R. Robust statistical methods in R using the WRS2 package. Behav Res Methods 2020;52:464-88.
46. Wickham H, Chang W, Henry L, et al. ggplot2: Elegant graphics for data analysis. Springer-Verlag New York; 2016. Available from: https://ggplot2.tidyverse.org. [Last accessed 22 Apr 2024].
47. Korpela K. mare: Microbiota Analysis in R Easily. R package version 1.0. 2016. Available from: https://github.com/katrikorpela/mare. [Last accessed 22 Apr 2024].
48. Oksanen J, Simpson GL, Blanchet FG, et al. vegan: Community Ecology Package. R package version 2.6-4. 2022. Available from: https://cran.r-project.org/package=vegan. [Last accessed 22 Apr 2024].
49. Shetty SA, Zuffa S, Bui TPN, Aalvink S, Smidt H, De Vos WM. Reclassification of Eubacterium hallii as Anaerobutyricum hallii gen. nov., comb. nov., and description of Anaerobutyricum soehngenii sp. nov., a butyrate and propionate-producing bacterium from infant faeces. Int J Syst Evol Microbiol 2018;68:3741-6.
50. Münch A, Ström M, Söderholm JD. Dihydroxy bile acids increase mucosal permeability and bacterial uptake in human colon biopsies. Scand J Gastroenterol 2007;42:1167-74.
51. Raimondi F, Santoro P, Barone MV, et al. Bile acids modulate tight junction structure and barrier function of Caco-2 monolayers via EGFR activation. Am J Physiol Gastrointest Liver Physiol 2008;294:G906-13.
52. Stenman LK, Holma R, Eggert A, Korpela R. A novel mechanism for gut barrier dysfunction by dietary fat: epithelial disruption by hydrophobic bile acids. Am J Physiol Gastrointest Liver Physiol 2013;304:G227-34.
53. Zeng H, Safratowich BD, Cheng WH, Larson KJ, Briske-Anderson M. Deoxycholic acid modulates cell-junction gene expression and increases intestinal barrier dysfunction. Molecules 2022;27:723.
54. Patova OA, Feltsinger LS, Kosolapova NV, Khlopin VA, Golovchenko VV. Properties of cell wall polysaccharides of raw nectarine fruits after treatment under conditions that modulate gastric digestion. Int J Biol Macromol 2023;245:125460.
55. Patova OA, Feltsinger LS, Khramova DS, Chelpanova TI, Golovchenko VV. Effect of in vitro gastric digestion conditions on physicochemical properties of raw apple fruit cell wall polysaccharides. Food Hydrocolloid 2022;129:107661.
56. Capuano E, Pellegrini N. An integrated look at the effect of structure on nutrient bioavailability in plant foods. J Sci Food Agric 2019;99:493-8.
57. Tuncil YE, Nakatsu CH, Kazem AE, et al. Delayed utilization of some fast-fermenting soluble dietary fibers by human gut microbiota when presented in a mixture. J Funct Foods 2017;32:347-57.
58. Lu S, Flanagan BM, Williams BA, Mikkelsen D, Gidley MJ. Cell wall architecture as well as chemical composition determines fermentation of wheat cell walls by a faecal inoculum. Food Hydrocolloid 2020;107:105858.
59. Lu S, Mikkelsen D, Flanagan BM, Williams BA, Gidley MJ. Interaction of cellulose and xyloglucan influences in vitro fermentation outcomes. Carbohydr Polym 2021;258:117698.
60. Rose DJ, Keshavarzian A, Patterson JA, Venkatachalam M, Gillevet P, Hamaker BR. Starch-entrapped microspheres extend in vitro fecal fermentation, increase butyrate production, and influence microbiota pattern. Mol Nutr Food Res 2009;53 Suppl 1:S121-30.
61. Wang SP, Rubio LA, Duncan SH, et al. Pivotal roles for pH, lactate, and lactate-utilizing bacteria in the stability of a human colonic microbial ecosystem. mSystems 2020;5:e00645-20.
62. Ganda Mall JP, Casado-Bedmar M, Winberg ME, Brummer RJ, Schoultz I, Keita ÅV. A β-glucan-based dietary fiber reduces mast cell-induced hyperpermeability in ileum from patients with Crohn’s disease and control subjects. Inflamm Bowel Dis 2017;24:166-78.
63. Ganda Mall JP, Löfvendahl L, Lindqvist CM, Brummer RJ, Keita ÅV, Schoultz I. Differential effects of dietary fibres on colonic barrier function in elderly individuals with gastrointestinal symptoms. Sci Rep 2018;8:13404.
64. Hamer HM, Jonkers DMAE, Bast A, et al. Butyrate modulates oxidative stress in the colonic mucosa of healthy humans. Clin Nutr 2009;28:88-93.
65. O’Connell Motherway M, Houston A, O’Callaghan G, et al. A Bifidobacterial pilus-associated protein promotes colonic epithelial proliferation. Mol Microbiol 2019;111:287-301.
66. Gutierrez A, Pucket B, Engevik MA. Bifidobacterium and the intestinal mucus layer. Microbiome Res Rep 2023;2:36.
67. Isenring J, Bircher L, Geirnaert A, Lacroix C. In vitro human gut microbiota fermentation models: opportunities, challenges, and pitfalls. Microbiome Res Rep 2023;2:2.
68. Shkoporov AN, O’Regan O, Smith L, et al. Dynamic nature of viral and bacterial communities in human faeces. iScience 2024;27:108778.
69. Poppe J, Vieira-Silva S, Raes J, Verbeke K, Falony G. Systematic optimization of fermentation conditions for in vitro fermentations with fecal inocula. Front Microbiol 2023;14:1198903.
70. Gao Q, Li K, Zhong R, et al. Supplementing glycerol to inoculum induces changes in pH, SCFA profiles, and microbiota composition in in-vitro batch fermentation. Fermentation 2022;8:18.
71. Ács N, Holohan R, Dunne LJ, et al. Comparing in vitro faecal fermentation methods as surrogates for phage therapy application. Viruses 2022;14:2632.
72. Gnanasekaran T, Assis Geraldo J, Ahrenkiel DW, et al. Ecological adaptation and succession of human fecal microbial communities in an automated in vitro fermentation system. mSystems 2021;6:e0023221.
73. Long W, Xue Z, Zhang Q, et al. Differential responses of gut microbiota to the same prebiotic formula in oligotrophic and eutrophic batch fermentation systems. Sci Rep 2015;5:13469.
74. Pirkola L, Dicksved J, Loponen J, Marklinder I, Andersson R. Fecal microbiota composition affects in vitro fermentation of rye, oat, and wheat bread. Sci Rep 2023;13:99.
75. Louis P, Duncan SH, Sheridan PO, Walker AW, Flint HJ. Microbial lactate utilisation and the stability of the gut microbiome. Gut Microb 2022;3:e3.
76. Louis P, Flint HJ. Formation of propionate and butyrate by the human colonic microbiota. Environ Microbiol 2017;19:29-41.
77. Engels C, Ruscheweyh HJ, Beerenwinkel N, Lacroix C, Schwab C. The common gut microbe Eubacterium hallii also contributes to intestinal propionate formation. Front Microbiol 2016;7:713.
78. Shetty SA, Kuipers B, Atashgahi S, Aalvink S, Smidt H, de Vos WM. Inter-species metabolic interactions in an in-vitro minimal human gut microbiome of core bacteria. NPJ Biofilms Microbiomes 2022;8:21.
