[1]   Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017 May 16;474(11):1823-36. doi: 10.1042/BCJ20160510. PMID: 28512250; PMCID: PMC5433529.

[2]   Gibson GR, Hutkins R, Sanders ME, Prescott SL, Reimer RA, Salminen SJ, Scott K, Stanton C, Swanson KS, Cani PD, 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.

[3]   Fusco W, Lorenzo MB, Cintoni M, Porcari S, Rinninella E, Kaitsas F, Lener E, Mele MC, Gasbarrini A, Collado MC, Cammarota G, Ianiro G. Short-chain fatty-acid-producing bacteria: Key components of the human gut microbiota. Nutrients. 2023 May 6;15(9):2211. doi: 10.3390/nu15092211. PMID: 37432351; PMCID: PMC10180739.

[4]   FAO/WHO. Health and nutritional properties of probiotics in food including powder milk with live lactic acid bacteria. Report of a Joint FAO/WHO Expert Consultation. 2001.

[5]   Abad-Jiménez Z, Vezza T. Obesity: A global health challenge demanding urgent action. Biomedicines. 2025 Feb 18;13(2):502. doi: 10.3390/biomedicines13020502. PMID: 40002915; PMCID: PMC11853126.

[6]   Dempsey E, Corr SC. Lactobacillus spp. for gastrointestinal health: Current and future perspectives. Front Immunol. 2022 Apr 6;13:840245. doi: 10.3389/fimmu.2022.840245. PMID: 35464397; PMCID: PMC9019120.

[7]   Aurora R, Sanford T. Host microbiota contributes to health and response to disease. Mo Med. 2015 Jul-Aug;112(4):317-22. PMID: 26455065; PMCID: PMC6170062.

[8]   Li Z, Zhou J, Liang H, Ye L, Lan L, Lu F, Wang Q, Lei T, Yang X, Cui P, Huang J. Differences in alpha diversity of gut microbiota in neurological diseases. Front Neurosci. 2022 Jun 28;16:879318. doi: 10.3389/fnins.2022.879318. PMID: 35837118; PMCID: PMC9274120.

[9]   Pham VT, Dold S, Rehman A, Bird JK, Steinert RE. Vitamins, the gut microbiome and gastrointestinal health in humans. Nutr Res. 2021;95:35-53. Available from: https://www.sciencedirect.com/science/article/pii/S0271531721000580

[10]          FAO/WHO. Guidelines for the evaluation of probiotics in food. Food and Agriculture Organization of the United Nations and World Health Organization Working Group Report. 2002.

[11]          Fijan S. Microorganisms with claimed probiotic properties: An overview of recent literature. Int J Environ Res Public Health. 2014 May 5;11(5):4745-67. doi: 10.3390/ijerph110504745. PMID: 24859749; PMCID: PMC4053917.

[12]          Huang R, Wu F, Zhou Q, Wei W, Yue J, Xiao B, Luo Z. Lactobacillus and intestinal diseases: Mechanisms of action and clinical applications. Microbiol Res. 2022;260:127019.

[13]          Gavzy SJ, Kensiski A, Lee ZL, Mongodin EF, Ma B, Bromberg JS. Bifidobacterium mechanisms of immune modulation and tolerance. Gut Microbes. 2023 Dec;15(2):2291164. doi: 10.1080/19490976.2023.2291164. PMID: 38055306; PMCID: PMC10730214.

[14]          Norman FF, Pérez-Molina J, Pérez de Ayala A, Jiménez BC, Navarro M, López-Vélez R. Clostridium difficile-associated diarrhea after antibiotic treatment for traveler’s diarrhea. Clin Infect Dis. 2008;46(7):1060-3.

[15]          Teng G, Liu Z, Liu Y, Wu T, Dai Y, Wang H, Wang W. Probiotic Escherichia coli Nissle 1917 expressing elafin protects against inflammation and restores the gut microbiota. Front Microbiol. 2022 May 6;13:819336. doi: 10.3389/fmicb.2022.819336. PMID: 35602072; PMCID: PMC9121173.

[16]          Kriaa A, Bourgin M, Potiron A, Mkaouar H, Jablaoui A, Gérard P, Maguin E, Rhimi M. Microbial impact on cholesterol and bile acid metabolism: current status and future prospects. J Lipid Res. 2019;60(2):323–32.

[17]          Effendi RMRA, Anshory M, Kalim H, Dwiyana RF, Suwarsa O, Pardo LM, Nijsten TEC, Thio HB. Akkermansia muciniphila  and Faecalibacterium prausnitzii in immune-related diseases. Microorganisms. 2022 Nov 30;10(12):2382. doi: 10.3390/microorganisms10122382. PMID: 36557635; PMCID: PMC9782003.

[18]          Bedu-Ferrari C, Biscarrat P, Langella P, Cherbuy C. Prebiotics and the human gut microbiota: From breakdown mechanisms to the impact on metabolic health. 2022;1–23.

[19]          Davani-Davari D, Negahdaripour M, Karimzadeh I, Seifan M, Mohkam M, Masoumi SJ, Berenjian A, Ghasemi Y. Prebiotics: Definition, types, sources, mechanisms, and clinical applications. Foods. 2019 Mar 9;8(3):92. doi: 10.3390/foods8030092. PMID: 30857316; PMCID: PMC6463098.

[20]          Chen G, Li C, Chen K. Chapter 6 – Fructooligosaccharides: A review on their mechanisms of action and effects. In: Atta-ur-Rahman, editor. Elsevier; 2016. p. 209–29.

[21]          Rosolen MD, Bordini FW, de Oliveira PD, et al. Symbiotic microencapsulation of Lactococcus lactis subsp. lactis R7 using whey and inulin by spray drying. LWT. 2019;115:108411.

[22]          Ali K, Niaz N, Waseem M, Ashraf W, Hussain M, Khalid MU, Tahir AB, Raza A, Khan IM. Xylooligosaccharides: A comprehensive review of production, purification, characterization, and quantification. Food Res Int. 2025;201:115631.

[23]          Pandey KR, Naik SR, Vakil BV. Probiotics, prebiotics and synbiotics: A review. J Food Sci Technol. 2015 Dec;52(12):7577–87. doi: 10.1007/s13197-015-1921-1. PMID: 26604335; PMCID: PMC4648921.

[24]          Rioux KP, Madsen KL, Fedorak RN. The role of enteric microflora in inflammatory bowel disease: human and animal studies with probiotics and prebiotics. Gastroenterol Clin North Am. 2005;34(3):465–82.

[25]          González-Herrera SM, Bermúdez-Quiñones G, Ochoa-Martínez LA, Rutiaga-Quiñones OM, Gallegos-Infante JA. Synbiotics: A technological approach in food applications. J Food Sci Technol. 2021 Mar;58(3):811–24. doi: 10.1007/s13197-020-04532-0. PMID: 33678864; PMCID: PMC7884486.

[26]          Cheng FS, Pan D, Chang B, Jiang M, Sang LX. Probiotic mixture VSL#3: An overview of basic and clinical studies in chronic diseases. World J Clin Cases. 2020 Apr 26;8(8):1361–74. doi: 10.12998/wjcc.v8.i8.1361. Erratum in: World J Clin Cases. 2021 Jul 16;9(20):5752–3. PMID: 32368530; PMCID: PMC7190945.

[27]          Mamaghani ME, Sanaie S, Mahmoudpour A, Hamishehkar H. Effect of probiotic containing Lactobacillus, Bifidobacterium and Streptococcus thermophilus in critically ill patients. Crit Care. 2013;17(Suppl 2):P246. doi: 10.1186/cc12184. PMCID: PMC3642567.

[28]          Collado MC, Moreno Y, Cobo JM, Mateos JA, Hernández M. Molecular detection of Bifidobacterium animalis  DN-173010 in human feces during fermented milk administration. Food Res Int. 2006;39(5):530–5.

[29]          Janssen Duijghuijsen L, van den Belt M, Rijnaarts I, Vos P, Guillemet D, Witteman B, de Wit N. Acacia fiber or probiotic supplements to relieve gastrointestinal complaints in patients with constipation-predominant IBS: A 4-week randomized double-blinded placebo-controlled intervention trial. Eur J Nutr. 2024;63(5):1983–94.

[30]          Perraudeau F, McMurdie P, Bullard J, Cheng A, Cutcliffe C, Deo A, Eid J, Gines J, Iyer M, Justice N, Loo WT, Nemchek M, Schicklberger M, Souza M, Stoneburner B, Tyagi S, Kolterman O. Improvements to postprandial glucose control in subjects with type 2 diabetes: A multicenter, double-blind, randomized placebo-controlled trial of a novel probiotic formulation. BMJ Open Diabetes Res Care. 2020 Jul;8(1):e001319. doi: 10.1136/bmjdrc-2020-001319. PMID: 32675291; PMCID: PMC7368581.

[31]          Patel RM, Underwood MA. Probiotics and necrotizing enterocolitis. Semin Pediatr Surg. 2018;27:39–46.

[32]          Aguilera XEL, Manzano A, Pirela D, Bermúdez V. Probiotics and gut microbiota in obesity: Myths and realities of a new health revolution. J Pers Med. 2022;12:1282.

[33]          Martins E, da Silva LN, Carmo M. Probiotics, prebiotics, and synbiotics in childhood diarrhea. Braz J Med Biol Res. 2024;57:e13205.

[34]          Hempel S, Newberry SJ, Maher AR, Wang Z, Miles JN, Shanman R, Johnsen B, Shekelle PG. Probiotics for the prevention and treatment of antibiotic-associated diarrhea: A systematic review and meta-analysis. JAMA. 2012;307:1959–69.

[35]          López-Gómez L, Alcorta A, Abalo R. Probiotics and probiotic-like agents against chemotherapy-induced intestinal mucositis: A narrative review. J Pers Med. 2023;13:1487.

[36]          Du Z, Li J, Li W, Fu H, Ding J, Ren G, Zhou L, Pi X, Ye X. Effects of prebiotics on the gut microbiota in vitro associated with functional diarrhea in children. Front Microbiol. 2023;14:1233840.

[37]          Odriozola A, González A, Odriozola I, Álvarez-Herms J, Corbi F. Microbiome-based precision nutrition: Prebiotics, probiotics and postbiotics. Adv Genet. 2024;111:237–310.

[38]          Kaźmierczak-Siedlecka K, Skonieczna-Żydecka K, Biliński J, Roviello G, Iannone LF, Atzeni A, Sobocki BK, Połom K. Gut microbiome modulation and fecal microbiota transplantation following allogenic hematopoietic stem cell transplantation. Cancers. 2021;13:4665.

[39]          Millman JF, Kondrashina A, Walsh C, Busca K, Karawugodage A, Park J, Sirisena S, Martin F-P, Felice VD, Lane JA. Biotics as novel therapeutics in targeting signs of skin ageing via the gut–skin axis. Ageing Res Rev. 2024;102:102518.

[40]          Balendra V, Rosenfeld R, Amoroso C, Castagnone C, Rossino MG, Garrone O, Ghidini M. Postbiotics as adjuvant therapy in cancer care. Nutrients. 2024;16:2400.

[41]          Kumar D, Bishnoi M, Kondepudi KK, Sharma SS. Gut microbiota-based interventions for Parkinson’s disease: Neuroprotective mechanisms and current perspective. Probiotics Antimicrob Proteins. 2025;1–23.

[42]          Murtaza G, Abbas Z, Gul S, Karam A, Cheema N, Zahra M, et al. Review on synergistic effects of probiotics, prebiotics, and synbiotics on gut microbiota homeostasis. Indus J Biosci Res. 2024;2(2):50–7.

[43]          Carlson JL, Erickson JM, Lloyd BB, Slavin JL. Health effects and sources of prebiotic dietary fiber. Curr Dev Nutr. 2018;2(3):nzy005.

[44]          Martin CR, Osadchiy V, Kalani A, Mayer EA. The brain–gut–microbiome axis. Cell Mol Gastroenterol Hepatol. 2018 Apr 12;6(2):133–48. doi: 10.1016/j.jcmgh.2018.04.003. PMID: 30023410; PMCID: PMC6047317.

[45]          Wang X, Yuan W, Yang C, Wang Z, Zhang J, Xu D, Sun X, Sun W. Emerging role of gut microbiota in autoimmune diseases. Front Immunol. 2024 May 3;15:1365554. doi: 10.3389/fimmu.2024.1365554. PMID: 38765017; PMCID: PMC11099291.

[46]          Mohammad S, Thiemermann C. Role of metabolic endotoxemia in systemic inflammation and potential interventions. Front Immunol. 2021 Jan 11;11:594150. doi: 10.3389/fimmu.2020.594150. PMID: 33505393; PMCID: PMC7829348.

[47]          Abdalqadir N, Adeli K. GLP-1 and GLP-2 orchestrate intestine integrity, gut microbiota, and immune system crosstalk. 2022.

[48]          Nathani RR, Sodhani S, Vadakekut ES. Irritable bowel syndrome. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2025 Jan. Updated 2025 Sep 15.

[49]          Markowiak P, Śliżewska K. Effects of probiotics, prebiotics, and synbiotics on human health. Nutrients. 2017 Sep 15;9(9):1021. doi: 10.3390/nu9091021. PMID: 28914794; PMCID: PMC5622781.

[50]          Bedani R, Rossi EA, Saad SMI. Impact of inulin and okara on Lactobacillus acidophilus  La-5 and Bifidobacterium animalis  Bb-12 viability in a fermented soy product and probiotic survival under in vitro simulated gastrointestinal conditions. Food Microbiol. 2013;34(2):382–9.

[51]          Vancamelbeke M, Vermeire S. The intestinal barrier: a fundamental role in health and disease. Expert Rev Gastroenterol Hepatol. 2017 Sep;11(9):821–834. doi:10.1080/17474124.2017.1343143.

[52]          Rogers GB, Keating DJ, Young RL, Wong ML, Licinio J, Wesselingh S. From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways. Mol Psychiatry. 2016;21:738–748.

[53]          Di Vincenzo F, Del Gaudio A, Petito V, Lopetuso LR, Scaldaferri F. Gut microbiota, intestinal permeability, and systemic inflammation: a narrative review. Intern Emerg Med. 2024 Mar;19(2):275–293. doi:10.1007/s11739-023-03374-w.

[54]          Flannigan KL, Geem D, Harusato A, Denning TL. Intestinal antigen-presenting cells: key regulators of immune homeostasis and inflammation. Am J Pathol. 2015 Jul;185(7):1809–1819. doi:10.1016/j.ajpath.2015.02.024.

[55]          Parada Venegas D, De la Fuente MK, Landskron G, González MJ, Quera R, Dijkstra G, et al. Short-chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Front Immunol. 2019;10:277. doi:10.3389/fimmu.2019.00277.

[56]          Campbell C, Rudensky A. Roles of regulatory T cells in tissue pathophysiology and metabolism. Cell Metab. 2020;31(1):18–25.

[57]          Oh B, Kim BS, Kim JW, Kim JS, Koh SJ, Kim BG, et al. The effect of probiotics on gut microbiota during Helicobacter pylori eradication: randomized controlled trial. Helicobacter. 2016;21:165–174.

[58]          Adolfsson O, Meydani SN, Russell RM. Yogurt and gut function. Am J Clin Nutr. 2004;80(2):245–256.

[59]          O’Callaghan AA, Corr SC. Establishing boundaries: the relationship that exists between intestinal epithelial cells and gut-dwelling bacteria. Microorganisms. 2019;7(12):663. doi:10.3390/microorganisms7120663.

[60]          La Fata G, Weber P, Mohajeri MH. Probiotics and the gut immune system: indirect regulation. Probiotics Antimicrob Proteins. 2018;10:11–21.

[61]          Luettig J, Rosenthal R, Barmeyer C, Schulzke JD. Claudin-2 as a mediator of leaky gut barrier during intestinal inflammation. Tissue Barriers. 2015;3(1–2):e977176. doi:10.4161/21688370.2014.977176.

[62]          Hodgkinson K, El Abbar F, Dobranowski P, Manoogian J, Butcher J, Figeys D, et al. Butyrate’s role in human health and current progress toward its clinical application to treat gastrointestinal disease. Clin Nutr. 2023;42(2):61–75.

[63]          Liu Z, Jiang Y, Fan Q, Li S, Wang Y. The role of butyric acid and microorganisms in chronic inflammatory diseases and microbiome-based therapeutics. J Inflamm Res. 2025;18:13465–13487. doi:10.2147/JIR.S540163.

[64]          Xiao J, Guo X, Wang Z. Crosstalk between hypoxia-inducible factor-1α and short-chain fatty acids in inflammatory bowel disease: key clues toward unraveling the mystery. Front Immunol. 2024;15:1385907. doi:10.3389/fimmu.2024.1385907.

[65]          Monteagudo-Mera A, Rastall RA, Gibson GR, Charalampopoulos D, Chatzifragkou A. Adhesion mechanisms mediated by probiotics and prebiotics and their potential impact on human health. Appl Microbiol Biotechnol. 2019;103:6463–6472.

[66]          Tan JK, Macia L, Mackay CR. Dietary fiber and SCFAs in the regulation of mucosal immunity. J Allergy Clin Immunol. 2023;151(2):361–370. doi:10.1016/j.jaci.2022.11.007.

[67]          Fang K, Jin X, Hong SH. Probiotic Escherichia coli inhibits biofilm formation of pathogenic E. coli   via extracellular activity of DegP. Sci Rep. 2018;8:4939.

[68]          Piewngam P, Zheng Y, Nguyen TH, Dickey SW, Joo HS, Villaruz AE, et al. Pathogen elimination by probiotic Bacillus via signalling interference. Nature. 2018;562:532–537.

[69]          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;165:1332–1345.

[70]          Nogal A, Valdes AM, Menni C. The role of short-chain fatty acids in the interplay between gut microbiota and diet in cardio-metabolic health. Gut Microbes. 2021;13(1):1–24. doi:10.1080/19490976.2021.1897212.

[71]          Rowland I, Gibson G, Heinken A, Scott K, Swann J, Thiele I, Tuohy K. Gut microbiota functions: metabolism of nutrients and other food components. Eur J Nutr. 2018;57:1–24.

[72]          Roediger WE. Role of anaerobic bacteria in the metabolic welfare of the colonic mucosa in man. Gut. 1980;21:793–798.

[73]          Saban Güler M, Arslan S, Ağagündüz D, Cerqua I, Pagano E, Berni Canani R, Capasso R. Butyrate: a potential mediator of obesity and microbiome via different mechanisms of actions. Food Res Int. 2025;199:115420.

[74]          Rui L. Energy metabolism in the liver. Compr Physiol. 2014;4(1):177–197. doi:10.1002/cphy.c130024.

[75]          Han X, Ma Y, Ding S, Fang J, Liu G. Regulation of dietary fiber on intestinal microorganisms and its effects on animal health. Anim Nutr. 2023;14:356–369.

[76]          Duscha A, Gisevius B, Hirschberg S, Yissachar N, Stangl GI, Eilers E, et al. Propionic acid shapes the multiple sclerosis disease course by an immunomodulatory mechanism. Cell. 2020;180:1067–1080.e16.

[77]          Cunningham M, Azcarate-Peril MA, Barnard A, Benoit V, Grimaldi R, Guyonnet D, et al. Shaping the future of probiotics and prebiotics. Trends Microbiol. 2021;29:667–685.

[78]          Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42:D490–D495.

[79]          Cantarel BL, Lombard V, Henrissat B. Complex carbohydrate utilization by the healthy human microbiome. PLoS One. 2012;7(6):e28742. doi:10.1371/journal.pone.0028742.

[80]          Amin K, Tranchimand S, Benvegnu T, Abdel-Razzak Z, Chamieh H. Glycoside hydrolases and glycosyltransferases from hyperthermophilic archaea: insights on their characteristics and applications in biotechnology. Biomolecules. 2021;11(11):1557. doi:10.3390/biom11111557.

[81]          Armendáriz-Ruiz M, Rodríguez-González JA, Camacho-Ruíz RM, Mateos-Díaz JC. Carbohydrate esterases: an overview. Methods Mol Biol. 2018;1835:39–68.

[82]          Kaoutari AE, Armougom F, Gordon JI, Raoult D, Henrissat B. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol. 2013;11:497–504.

[83]          Lapébie P, Lombard V, Drula E, Terrapon N, Henrissat B. Bacteroidetes use thousands of enzyme combinations to break down glycans. Nat Commun. 2019;10:2043. doi:10.1038/s41467-019-10068-5.

[84]          Magne F, Gotteland M, Gauthier L, Zazueta A, Pesoa S, Navarrete P, Balamurugan R. The Firmicutes/Bacteroidetes ratio: a relevant marker of gut dysbiosis in obese patients? Nutrients. 2020;12(5):1474. doi:10.3390/nu12051474.

[85]          Sheridan PO, Martin JC, Lawley TD, Browne HP, Harris HMB, Bernalier-Donadille A, et al. Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes. Microb Genom. 2016;2:e000043.

[86]          Schwalm ND, Groisman EA. Navigating the gut buffet: control of polysaccharide utilization in Bacteroides spp. Trends Microbiol. 2017;25:1005–1015.

[87]          Abolhasani FS, Vaghefinanekaran N, Yarahmadi A, Akrami S, Mirmahdavi S, Yousefi MH, et al. Outer membrane vesicles in gram-negative bacteria and its correlation with pathogenesis. Front Immunol. 2025;16:1541636. doi:10.3389/fimmu.2025.1541636.

[88]          Thomas F, Hehemann JH, Rebuffet E, Czjzek M, Michel G. Environmental and gut Bacteroidetes: the food connection. Front Microbiol. 2011;2:93. doi:10.3389/fmicb.2011.00093.

[89]          Hayase E, Hayase T, Mukherjee A, Stinson SC, Jamal MA, Ortega MR, Sanchez CA, et al. Bacteroides ovatus alleviates dysbiotic microbiota-induced intestinal graft-versus-host disease. Res Sq [Preprint]. 2023;rs.3.rs-2460097. Updated in: Cell Host Microbe. 2024;32(9):1621–1636.e6.

[90]          Munoz J, James K, Bottacini F, Van Sinderen D. Biochemical analysis of cross-feeding behaviour between two common gut commensals when cultivated on plant-derived arabinogalactan. Microb Biotechnol. 2020;13:1733–1747.

[91]          Cuskin F, Lowe EC, Temple MJ, Zhu Y, Cameron EA, Pudlo NA, Porter NT, Urs K, Thompson AJ, Cartmell A, et al. Human Gut Bacteroidetes can utilize yeast mannan through a selfish mechanism. Nature. 2015;517:165–169.

[92]          Sichert A, Cordero OX. Polysaccharide-bacteria interactions from the lens of evolutionary ecology. Front Microbiol. 2021 Oct 8;12:705082. doi: 10.3389/fmicb.2021.705082. PMID: 34690949; PMCID: PMC8531407.

[93]          Klassen L, Reintjes G, Tingley JP, Jones DR, Hehemann JH, Smith AD, Schwinghamer TD, Arnosti C, Jin L, Alexander TW, et al. Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria. Microbiome. 2021;9:23.

[94]          McCartney AL. Application of molecular biological methods for studying probiotics and the gut flora. Br J Nutr. 2002;88 Suppl 1:S29–S37.

[95]          Piewngam P, Chiou J, Ling J, Liu R, Pupa P, Zheng Y, Otto M. Enterococcal bacteremia in mice is prevented by oral administration of probiotic Bacillus spores. Sci Transl Med. 2021;13:eabf4692.

[96]          Huang W, Ma T, Liu Y, Kwok LY, Li Y, Jin H, Zhao F, Shen X, Shi X, Sun Z, et al. Spraying compound probiotics improves growth performance and immunity and modulates gut microbiota and blood metabolites of suckling piglets. Sci China Life Sci. 2023;66:1092–1107.

[97]          Ismail NI, Nawawi KNM, Hsin DCC, Hao KW, Mahmood NRKN, Chearn GLC, Wong Z, Tamil AM, Joseph H, Raja Ali RA. Probiotic containing Lactobacillus reuteri DSM 17648 as an adjunct treatment for Helicobacter pylori infection: A randomized, double-blind, placebo-controlled trial. Helicobacter. 2023;28(6):e13017.

[98]          Shadnoush M, Hosseini RS, Khalilnezhad A, Navai L, Goudarzi H, Vaezjalali M. Effects of probiotics on gut microbiota in patients with inflammatory bowel disease: A double-blind, placebo-controlled clinical trial. Korean J Gastroenterol. 2015;65:215–221.

[99]          Mills S, Yang B, Smith GJ, Stanton C, Ross RP. Efficacy of Bifidobacterium longum alone or in multi-strain probiotic formulations during early life and beyond. Gut Microbes. 2023;15(1):2186098.

[100]       Zhu H, Cao C, Wu Z, Zhang H, Sun Z, Wang M, Xu H, Zhao Z, Wang Y, Pei G, et al. The probiotic L. casei Zhang slows the progression of acute and chronic kidney disease. Cell Metab. 2021;33:1926–1942.e8.

[101]       Klein A, Friedrich U, Vogelsang H, Jahreis G. Lactobacillus acidophilus  74-2 and Bifidobacterium animalis  subsp. lactis DGCC 420 modulate unspecific cellular immune response in healthy adults. Eur J Clin Nutr. 2008;62(5):584–593.

[102]       Ouwehand AC. A review of dose-responses of probiotics in human studies. Benef Microbes. 2017;8(2):143–151.

[103]       Khalesi S, Bellissimo N, Vandelanotte C, et al. A review of probiotic supplementation in healthy adults: Helpful or hype? Eur J Clin Nutr. 2019;73(1):24–37.

[104]       Rampelli S, Candela M, Severgnini M, et al. A probiotics-containing biscuit modulates the intestinal microbiota in the elderly. J Nutr Health Aging. 2013;17(2):166–172.

[105]       De Vries J, Le Bourgot C, Calame W, Respondek F. Effects of β-fructans fiber on bowel function: A systematic review and meta-analysis. Nutrients. 2019;11(1):91.

[106]       Turnbaugh PJ, Bäckhed F, Fulton L, Gordon JI. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe. 2008;3(4):213–223.

[107]       Sonnenburg JL, Bäckhed F. Diet–microbiota interactions as moderators of human metabolism. Nature. 2016;535(7610):56–64.

[108]       Xu Y, Wang N, Tan HY, Li S, Zhang C, Feng Y. Function of Akkermansia muciniphila  in obesity: Interactions with lipid metabolism, immune response and gut systems. Front Microbiol. 2020;11:219.

[109]       Berthoud HR. The vagus nerve, food intake and obesity. Regul Pept. 2008;149(1–3):15–25.

[110]       Frost G, Sleeth ML, Sahuri-Arisoylu M, et al. The short-chain fatty acid acetate reduces appetite via a central homeostatic mechanism. Nat Commun. 2014;5:1–11.

[111]       Cameron D, Hock QS, Kadim M, et al. Probiotics for gastrointestinal disorders: proposed recommendations for children of the Asia-Pacific region. World J Gastroenterol. 2017;23(45):7952–7964.

[112]       Sitkin S, Pokrotnieks J. Clinical potential of anti-inflammatory effects of Faecalibacterium prausnitzii and butyrate in inflammatory bowel disease. Inflamm Bowel Dis. 2019;25(4):e40–e41.

[113]       Astó E, Méndez I, Audivert S, et al. The efficacy of probiotics, prebiotic inulin-type fructans, and synbiotics in human ulcerative colitis: a systematic review and meta-analysis. Nutrients. 2019;11(2):293.

[114]       Torres J, Ellul P, Langhorst J, et al. European Crohn’s and Colitis Organisation topical review on complementary medicine and psychotherapy in inflammatory bowel disease. J Crohns Colitis. 2019;13(6):673–685D.

[115]       Guarino A, Ashkenazi S, Gendrel D, et al. ESPGHAN/ESPID evidence-based guidelines for the management of acute gastroenteritis in children in Europe. J Pediatr Gastroenterol Nutr. 2014;59(1):132–152.

[116]       Arslanoglu S, Moro GE, Boehm G, et al. Early neutral prebiotic oligosaccharide supplementation reduces the incidence of some allergic manifestations in the first 5 years of life. J Biol Regul Homeost Agents. 2012;26(3 Suppl):49–59.

[117]       Szajewska H, Canani RB, Guarino A, et al. Probiotics for the prevention of antibiotic-associated diarrhea in children. J Pediatr Gastroenterol Nutr. 2016;62(3):495–506.

[118]       Carabotti M, Scirocco A, Maselli MA, Severi C. The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems. Ann Gastroenterol. 2015;28(2):203–209.

[119]       Gabella G. Autonomic Nervous System. In: Paxinos G, editor. The Rat Nervous System. 3rd ed. Academic Press; 2004. p. 77–109.

[120]       Wang HX, Wang YP. Gut microbiota–brain axis. Chin Med J (Engl). 2016;129(19):2373–2380.

[121]       Bellono NW, Bayrer JR, Leitch DB, et al. Enterochromaffin cells are gut chemosensors that couple to sensory neural pathways. Cell. 2017;170(1):185–198.e16.

[122]       Hillman ET, Lu H, Yao T, Nakatsu CH. Microbial ecology along the gastrointestinal tract. Microbes Environ. 2017;32(4):300–313.

[123]       Bravo JA, Forsythe P, Chew MV, et al. Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proc Natl Acad Sci U S A. 2011;108(38):16050–16055.

[124]       Sgritta M, Dooling SW, Buffington SA, Momin EN, Francis MB, Britton RA, Costa-Mattioli M. Mechanisms underlying microbial-mediated changes in social behavior in mouse models of autism spectrum disorder. Neuron. 2019;101(2):246–259.e6.

[125]       Fenster K, Freeburg B, Hollard C, Wong C, Rønhave Laursen R, Ouwehand AC. The production and delivery of probiotics: A review of a practical approach. Microorganisms. 2019;7(3):83.

[126]       Ghaffarian R, Herrero E, Oh H, Raghavan S, Muro S. Chitosan–alginate microcapsules provide gastric protection and intestinal release of ICAM-1-targeting nanocarriers, enabling GI targeting in vivo. Adv Funct Mater. 2016;26.

[127]       Leschonski KP, Mortensen MS, Hansen LBS, Krogh KBRM, Kabel MA, Laursen MF. Structure-dependent stimulation of gut bacteria by arabinoxylo-oligosaccharides (AXOS): A review. Gut Microbes. 2024;16(1):2430419.

[128]       Buccheri S, James S, Mafham M, et al. Large simple randomized controlled trials—from drugs to medical devices: lessons from recent experience. Trials. 2025;26(1):24. Erratum in: Trials. 2025;26(1):80.

[129]       Gupta A, Sanwal N, Bareen MA, Barua S, Sharma N, Joshua Olatunji O, Prakash Nirmal N, Sahu JK. Trends in functional beverages: functional ingredients, processing technologies, stability, health benefits, and consumer perspective. Food Res Int. 2023;170:113046.

[130]       Vernocchi P, Del Chierico F, Putignani L. Gut microbiota profiling: metabolomics-based approach to unravel compounds affecting human health. Front Microbiol. 2016;7:1144.

[131]       Zhang L, Chen F, Zeng Z, et al. Advances in metagenomics and its application in environmental microorganisms. Front Microbiol. 2021;12:766364.

[132]       Shaheen N, Khursheed W, Gurung B, Wang S. Akkermansia muciniphila : A key player in gut microbiota-based disease modulation. Microbiol Res. 2025;301:128317.

[133]       Holscher HD. Dietary fiber and prebiotics and the gastrointestinal microbiota. Gut Microbes. 2017;8(2):172–184.

[134]       Gwak MG, Chang SY. Gut-brain connection: microbiome, gut barrier, and environmental sensors. Immune Netw. 2021;21(3):e20.

[135]       Lyu L, Li X, Feng R, et al. Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing. Genome Res. 2023;33(3):401–411.

[136]       Suez J, Zmora N, Elinav E. Probiotics in the next-generation sequencing era. Gut Microbes. 2020;11(1):77–93.

[137]       Ferguson LR, Barnett MP. Why are omics technologies important to understanding the role of nutrition in inflammatory bowel diseases? Int J Mol Sci. 2016;17(10):1763.

[138]       Hajjo R, Sabbah DA, Al Bawab AQ. Unlocking the potential of the human microbiome for identifying disease diagnostic biomarkers. Diagnostics (Basel). 2022;12(7):1742.

[139]       Bah YR, Baba K, Mustafa DNAB, et al. Bacteroides- and Prevotella-enriched gut microbial clusters associate with metabolic risks. Gut Pathog. 2025;17(1):55.

[140]       Shanmugham M, Bellanger S, Leo CH. Gut-derived metabolite trimethylamine-N-oxide (TMAO) in cardio-metabolic diseases: detection, mechanism, and potential therapeutics. 2023.

[141]       Wensel CR, Pluznick JL, Salzberg SL, Sears CL. Next-generation sequencing: insights to advance clinical investigations of the microbiome. J Clin Invest. 2022;132(7):e154944.

[142]       Wachholz Junior D, Kubota LT. CRISPR-based electrochemical biosensors: an alternative for point-of-care diagnostics? Talanta. 2024;278:126467.

[143]       Herman C, Barker BM, Bartelli TF, et al. A review of engraftment assessments following fecal microbiota transplant. Gut Microbes. 2025;17(1):2525478.

[144]       McFarland LV, Evans CT, Goldstein EJC. Strain-specificity and disease-specificity of probiotic efficacy: a systematic review and meta-analysis. Front Med (Lausanne). 2018;5:124.

[145]       Raturi A, Chandran S. Neonatal sepsis: aetiology, pathophysiology, diagnostic advances and management strategies. Clin Med Insights Pediatr. 2024;18:11795565241281337.

[146]       Hrncir T. Gut microbiota dysbiosis: triggers, consequences, diagnostic and therapeutic options. Microorganisms. 2022;10(3):578.

[147]       Saedi S, Derakhshan S, Hasani A, et al. Recent advances in gut microbiome modulation: effect of probiotics, prebiotics, synbiotics, and postbiotics in inflammatory bowel disease prevention and treatment. Curr Microbiol. 2024;82(1):12.

[148]       Vallejo-Cordoba B, Castro-López C, García HS, González-Córdova AF, Hernández-Mendoza A. Postbiotics and paraprobiotics: a review of current evidence and emerging trends. In: da Cruz AG, Prudencio ES, Esmerino EA, da Silva MCB, editors. Probiotic and Prebiotics in Foods: Challenges, Innovations and Advances. Academic Press; 2020. p. 1–34.

[149]       Cai Z, Wang S, Li J. Treatment of inflammatory bowel disease: a comprehensive review. Front Med (Lausanne). 2021; 8:765474.