REFERENCES

1. Teusink B, Smid EJ. Modelling strategies for the industrial exploitation of lactic acid bacteria. Nat Rev Microbiol 2006;4:46-56.

2. Zannini E, Waters DM, Coffey A, Arendt EK. Production, properties, and industrial food application of lactic acid bacteria-derived exopolysaccharides. Appl Microbiol Biotechnol 2016;100:1121-35.

3. Bron PA, Kleerebezem M. Engineering lactic acid bacteria for increased industrial functionality. Bioeng Bugs 2011;2:80-7.

4. Baeshen MN, Al-Hejin AM, Bora RS, et al. Production of biopharmaceuticals in E. coli: current scenario and future perspectives. J Microbiol Biotechnol 2015;25:953-62.

5. Kostic AD, Howitt MR, Garrett WS. Exploring host-microbiota interactions in animal models and humans. Genes Dev 2013;27:701-18.

6. Patterson E, Cryan JF, Fitzgerald GF, Ross RP, Dinan TG, Stanton C. Gut microbiota, the pharmabiotics they produce and host health. Proc Nutr Soc 2014;73:477-89.

7. Marchesi JR, Adams DH, Fava F, et al. The gut microbiota and host health: a new clinical frontier. Gut 2016;65:330-9.

8. 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.

9. Cheng L, Qi C, Zhuang H, Fu T, Zhang X. gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions. Nucleic Acids Res 2020;48:7603.

10. Carding S, Verbeke K, Vipond DT, Corfe BM, Owen LJ. Dysbiosis of the gut microbiota in disease. Microb Ecol Health Dis 2015;26:26191.

11. Wilkins LJ, Monga M, Miller AW. Defining dysbiosis for a cluster of chronic diseases. Sci Rep 2019;9:12918.

12. Green JE, Davis JA, Berk M, et al. Efficacy and safety of fecal microbiota transplantation for the treatment of diseases other than Clostridium difficile infection: a systematic review and meta-analysis. Gut Microbes 2020;12:1-25.

13. Mehta P, Nahass RG, Brunetti L. Acid suppression medications during hospitalization as a risk factor for recurrence of Clostridioides difficile infection: systematic review and meta-analysis. Clin Infect Dis 2021;73:e62-8.

14. Sorbara MT, Pamer EG. Microbiome-based therapeutics. Nat Rev Microbiol 2022;20:365-80.

15. Alam MZ, Maslanka JR, Abt MC. Immunological consequences of microbiome-based therapeutics. Front Immunol 2023;13:1046472.

16. Gulliver EL, Young RB, Chonwerawong M, et al. Review article: the future of microbiome-based therapeutics. Aliment Pharmacol Ther 2022;56:192-208.

17. Manrique P, Dills M, Young MJ. The human gut phage community and its implications for health and disease. Viruses 2017;9:141.

18. Hou K, Wu ZX, Chen XY, et al. Microbiota in health and diseases. Signal Transduct Target Ther 2022;7:135.

19. Miller CP, Bohnhoff M, Rifkind D. The effect of an antibiotic on the susceptibility of the mouse’s intestinal tract to salmonella infection. Trans Am Clin Climatol Assoc 1956;68:51-5; discussion 55-8.

20. Maciel-Fiuza MF, Muller GC, Campos DMS, et al. Role of gut microbiota in infectious and inflammatory diseases. Front Microbiol 2023;14:1098386.

21. Liu P, Lu Y, Li R, Chen X. Use of probiotic lactobacilli in the treatment of vaginal infections: in vitro and in vivo investigations. Front Cell Infect Microbiol 2023;13:1153894.

22. Lev-Sagie A, Goldman-Wohl D, Cohen Y, et al. Vaginal microbiome transplantation in women with intractable bacterial vaginosis. Nat Med 2019;25:1500-4.

23. Lu Y, Yuan X, Wang M, et al. Gut microbiota influence immunotherapy responses: mechanisms and therapeutic strategies. J Hematol Oncol 2022;15:47.

24. Jain T, Sharma P, Are AC, Vickers SM, Dudeja V. New insights into the cancer-microbiome-immune axis: decrypting a decade of discoveries. Front Immunol 2021;12:622064.

25. Ağagündüz D, Cocozza E, Cemali Ö, et al. Understanding the role of the gut microbiome in gastrointestinal cancer: a review. Front Pharmacol 2023;14:1130562.

26. Vétizou M, Pitt JM, Daillère R, et al. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science 2015;350:1079-84.

27. Hamada K, Yoshimura K, Hirasawa Y, et al. Antibiotic usage reduced overall survival by over 70% in non-small cell lung cancer patients on anti-PD-1 immunotherapy. Anticancer Res 2021;41:4985-93.

28. Davar D, Dzutsev AK, McCulloch JA, et al. Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients. Science 2021;371:595-602.

29. Baruch EN, Youngster I, Ben-Betzalel G, et al. Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients. Science 2021;371:602-9.

30. Sivan A, Corrales L, Hubert N, et al. Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science 2015;350:1084-9.

31. Routy B, Lenehan JG, Miller WH Jr, et al. Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial. Nat Med 2023;29:2121-32.

32. Tanoue T, Morita S, Plichta DR, et al. A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature 2019;565:600-5.

33. Scheline RR. Drug metabolism by intestinal microorganisms. J Pharm Sci 1968;57:2021-37.

34. Weersma RK, Zhernakova A, Fu J. Interaction between drugs and the gut microbiome. Gut 2020;69:1510-9.

35. Doestzada M, Vila AV, Zhernakova A, et al. Pharmacomicrobiomics: a novel route towards personalized medicine? Protein Cell 2018;9:432-45.

36. Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Mapping human microbiome drug metabolism by gut bacteria and their genes. Nature 2019;570:462-7.

37. Lima S, Rupert A, Jin W, et al. The gut microbiome regulates efficacy of sulfasalazine therapy for spondyloarthritis in inflammatory bowel disease. Inflamm Bowel Dis 2023;29:S72-3.

38. Wu H, Esteve E, Tremaroli V, et al. Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug. Nat Med 2017;23:850-8.

39. Ahmadi S, Razazan A, Nagpal R, et al. Metformin reduces aging-related leaky gut and improves cognitive function by beneficially modulating gut microbiome/goblet cell/mucin axis. J Gerontol A Biol Sci Med Sci 2020;75:e9-21.

40. Zhu X, Shen J, Feng S, et al. Akkermansia muciniphila, which is enriched in the gut microbiota by metformin, improves cognitive function in aged mice by reducing the proinflammatory cytokine interleukin-6. Microbiome 2023;11:120.

41. Ting NLN, Lau HCH, Yu J. Cancer pharmacomicrobiomics: targeting microbiota to optimise cancer therapy outcomes. Gut 2022;71:1412-25.

42. Haiser HJ, Seim KL, Balskus EP, Turnbaugh PJ. Mechanistic insight into digoxin inactivation by Eggerthella lenta augments our understanding of its pharmacokinetics. Gut Microbes 2014;5:233-8.

43. Dobkin JF, Saha JR, Butler VPB Jr, Neu HC, Lindenbaum J. Digoxin-inactivating bacteria: identification in human gut flora. Science 1983;220:325-7.

44. Rekdal VM, Bess EN, Bisanz JE, Turnbaugh PJ, Balskus EP. Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism. Science 2019;364:eaau6323.

45. Zhang Y, He X, Mo C, et al. Association between microbial tyrosine decarboxylase gene and levodopa responsiveness in patients with Parkinson disease. Neurology 2022;99:e2443-53.

46. Geller LT, Barzily-Rokni M, Danino T, et al. Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine. Science 2017;357:1156-60.

47. Luo Y, Zhou T. Connecting the dots: targeting the microbiome in drug toxicity. Med Res Rev 2022;42:83-111.

48. Mahdy MS, Azmy AF, Dishisha T, et al. Irinotecan-gut microbiota interactions and the capability of probiotics to mitigate Irinotecan-associated toxicity. BMC Microbiol 2023;23:53.

49. Chamseddine AN, Ducreux M, Armand JP, et al. Intestinal bacterial β-glucuronidase as a possible predictive biomarker of irinotecan-induced diarrhea severity. Pharmacol Ther 2019;199:1-15.

50. Parvez MM, Basit A, Jariwala PB, et al. Quantitative investigation of Irinotecan metabolism, transport, and gut microbiome activation. Drug Metab Dispos 2021;49:683-93.

51. Takeno S, Sakai T. Involvement of the intestinal microflora in nitrazepam-induced teratogenicity in rats and its relationship to nitroreduction. Teratology 1991;44:209-14.

52. Konishi K, Fukami T, Gotoh S, Nakajima M. Identification of enzymes responsible for nitrazepam metabolism and toxicity in human. Biochem Pharmacol 2017;140:150-60.

53. Alexander JL, Wilson ID, Teare J, Marchesi JR, Nicholson JK, Kinross JM. Gut microbiota modulation of chemotherapy efficacy and toxicity. Nat Rev Gastroenterol Hepatol 2017;14:356-65.

54. Pinto-Cardoso S, Klatt NR, Reyes-Terán G. Impact of antiretroviral drugs on the microbiome: unknown answers to important questions. Curr Opin HIV AIDS 2018;13:53-60.

55. Rueda-Ruzafa L, Cruz F, Cardona D, et al. Opioid system influences gut-brain axis: dysbiosis and related alterations. Pharmacol Res 2020;159:104928.

56. Meng J, Yu H, Ma J, et al. Morphine induces bacterial translocation in mice by compromising intestinal barrier function in a TLR-dependent manner. PLoS One 2013;8:e54040.

57. Iida N, Dzutsev A, Stewart CA, et al. Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment. Science 2013;342:967-70.

58. Derosa L, Routy B, Fidelle M, et al. Gut bacteria composition drives primary resistance to cancer immunotherapy in renal cell carcinoma patients. Eur Urol 2020;78:195-206.

59. Kennedy K, Khaddour K, Ramnath N, Weinberg F. The lung microbiome in carcinogenesis and immunotherapy treatment. Cancer J 2023;29:61-9.

60. Wei L, Wen XS, Xian CJ. Chemotherapy-induced intestinal microbiota dysbiosis impairs mucosal homeostasis by modulating toll-like receptor signaling pathways. Int J Mol Sci 2021;22:9474.

61. Le Bastard Q, Ward T, Sidiropoulos D, et al. Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice. Sci Rep 2018;8:6219.

62. Dubin K, Callahan MK, Ren B, et al. Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis. Nat Commun 2016;7:10391.

63. van der Hee B, Wells JM. Microbial regulation of host physiology by short-chain fatty acids. Trends Microbiol 2021;29:700-12.

64. Rios-Covián D, Ruas-Madiedo P, Margolles A, Gueimonde M, de los Reyes-Gavilán CG, Salazar N. Intestinal short chain fatty acids and their link with diet and human health. Front Microbiol 2016;7:185.

65. Corrêa-Oliveira R, Fachi JL, Vieira A, Sato FT, Vinolo MAR. Regulation of immune cell function by short-chain fatty acids. Clin Transl Immunology 2016;5:e73.

66. Petrosino JF. The microbiome in precision medicine: the way forward. Genome Med 2018;10:12.

67. Ke W, Saba JA, Yao CH, et al. Dietary serine-microbiota interaction enhances chemotherapeutic toxicity without altering drug conversion. Nat Commun 2020;11:2587.

68. Patangia DV, Anthony Ryan C, Dempsey E, Paul Ross R, Stanton C. Impact of antibiotics on the human microbiome and consequences for host health. Microbiologyopen 2022;11:e1260.

69. Becattini S, Taur Y, Pamer EG. Antibiotic-induced changes in the intestinal microbiota and disease. Trends Mol Med 2016;22:458-78.

70. Nagata N, Nishijima S, Miyoshi-Akiyama T, et al. Population-level metagenomics uncovers distinct effects of multiple medications on the human gut microbiome. Gastroenterology 2022;163:1038-52.

71. Zmora N, Zeevi D, Korem T, Segal E, Elinav E. Taking it personally: personalized utilization of the human microbiome in health and disease. Cell Host Microbe 2016;19:12-20.

72. Wagenaar CA, van de Put M, Bisschops M, et al. The effect of dietary interventions on chronic inflammatory diseases in relation to the microbiome: a systematic review. Nutrients 2021;13:3208.

73. De Filippis F, Vitaglione P, Cuomo R, Berni Canani R, Ercolini D. Dietary interventions to modulate the gut microbiome - how far away are we from precision medicine. Inflamm Bowel Dis 2018;24:2142-54.

74. Houghton D, Hardy T, Stewart C, et al. Systematic review assessing the effectiveness of dietary intervention on gut microbiota in adults with type 2 diabetes. Diabetologia 2018;61:1700-11.

75. Wang LS, Mo YY, Huang YW, et al. Effects of dietary interventions on gut microbiota in humans and the possible impacts of foods on patients’ responses to cancer immunotherapy. eFood 2020;1:279-87.

76. Chrysostomou D, Roberts LA, Marchesi JR, Kinross JM. Gut microbiota modulation of efficacy and toxicity of cancer chemotherapy and immunotherapy. Gastroenterology 2023;164:198-213.

77. Davis C, Bryan J, Hodgson J, Murphy K. Definition of the mediterranean diet; a literature review. Nutrients 2015;7:9139-53.

78. Compher CW. Fruits, vegetables, and whole grains win again. Am J Clin Nutr 2021;114:420-1.

79. Galgano F, Mele MC, Tolve R, et al. Strategies for producing low FODMAPs foodstuffs: challenges and perspectives. Foods 2023;12:856.

80. Paoli A, Mancin L, Bianco A, Thomas E, Mota JF, Piccini F. Ketogenic diet and microbiota: friends or enemies? Genes 2019;10:534.

81. Ghosh TS, Rampelli S, Jeffery IB, et al. Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries. Gut 2020;69:1218-28.

82. Horn J, Mayer DE, Chen S, Mayer EA. Role of diet and its effects on the gut microbiome in the pathophysiology of mental disorders. Transl Psychiatry 2022;12:164.

83. Klimenko NS, Odintsova VE, Revel-Muroz A, Tyakht AV. The hallmarks of dietary intervention-resilient gut microbiome. NPJ Biofilms Microbiomes 2022;8:77.

84. Leeming ER, Johnson AJ, Spector TD, Le Roy CI. Effect of diet on the gut microbiota: rethinking intervention duration. Nutrients 2019;11:2862.

85. Bourdeau-Julien I, Castonguay-Paradis S, Rochefort G, et al. The diet rapidly and differentially affects the gut microbiota and host lipid mediators in a healthy population. Microbiome 2023;11:26.

86. 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.

87. Bindels LB, Delzenne NM, Cani PD, Walter J. Towards a more comprehensive concept for prebiotics. Nat Rev Gastroenterol Hepatol 2015;12:303-10.

88. Davani-Davari D, Negahdaripour M, Karimzadeh I, et al. Prebiotics: definition, types, sources, mechanisms, and clinical applications. Foods 2019;8:92.

89. Rios-Covian D, Gueimonde M, Duncan SH, Flint HJ, de los Reyes-Gavilan CG. Enhanced butyrate formation by cross-feeding between Faecalibacterium prausnitzii and Bifidobacterium adolescentis. FEMS Microbiol Lett 2015;362:fnv176.

90. Roy S, Dhaneshwar S. Correction to “Role of prebiotics, probiotics, and synbiotics in management of inflammatory bowel disease: current perspectives”. World J Gastroenterol 2023;29:5178-9.

91. Hall DA, Voigt RM, Cantu-Jungles TM, et al. An open label, non-randomized study assessing a prebiotic fiber intervention in a small cohort of Parkinson’s disease participants. Nat Commun 2023;14:926.

92. Megur A, Daliri EBM, Baltriukienė D, Burokas A. Prebiotics as a tool for the prevention and treatment of obesity and diabetes: classification and ability to modulate the gut microbiota. Int J Mol Sci 2022;23:6097.

93. Salminen S, Collado MC, Endo A, et al. The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics. Nat Rev Gastroenterol Hepatol 2021;18:649-67.

94. EFSA Panel on Biological Hazards (BIOHAZ); Koutsoumanis K, Allende A, Alvarez-Ordóñez A, et al. Update of the list of qualified presumption of safety (QPS) recommended microbiological agents intentionally added to food or feed as notified to EFSA 18: suitability of taxonomic units notified to EFSA until March 2023. EFSA J 2023;21:e08092.

95. Piqué N, Berlanga M, Miñana-Galbis D. Health benefits of heat-killed (Tyndallized) probiotics: an overview. Int J Mol Sci 2019;20:2534.

96. Dronkers TMG, Ouwehand AC, Rijkers GT. Global analysis of clinical trials with probiotics. Heliyon 2020;6:e04467.

97. Swanson KS, Gibson GR, Hutkins R, et al. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of synbiotics. Nat Rev Gastroenterol Hepatol 2020;17:687-701.

98. Gomez Quintero DF, Kok CR, Hutkins R. The future of synbiotics: rational formulation and design. Front Microbiol 2022;13:919725.

99. Taverniti V, Guglielmetti S. The immunomodulatory properties of probiotic microorganisms beyond their viability (ghost probiotics: proposal of paraprobiotic concept). Genes Nutr 2011;6:261-74.

100. Duarte M, Oliveira AL, Oliveira C, Pintado M, Amaro A, Madureira AR. Current postbiotics in the cosmetic market - an update and development opportunities. Appl Microbiol Biotechnol 2022;106:5879-91.

101. Cicenia A, Scirocco A, Carabotti M, Pallotta L, Marignani M, Severi C. Postbiotic activities of lactobacilli-derived factors. J Clin Gastroenterol 2014;48 Suppl 1:S18-22.

102. Liang B, Xing D. The current and future perspectives of postbiotics. Probiotics Antimicrob Proteins 2023;15:1626-43.

103. Li M, Mao J, Diaz I, et al. Multi-omic approach to decipher the impact of skincare products with pre/postbiotics on skin microbiome and metabolome. Front Med 2023;10:1165980.

104. Rafique N, Jan SY, Dar AH, et al. Promising bioactivities of postbiotics: a comprehensive review. J Agric Food Res 2023;14:100708.

105. Thorakkattu P, Khanashyam AC, Shah K, et al. Postbiotics: current trends in food and pharmaceutical industry. Foods 2022;11:3094.

106. Satokari R. Modulation of gut microbiota for health by current and next-generation probiotics. Nutrients 2019;11:1921.

107. López-Moreno A, Acuña I, Torres-Sánchez A, et al. Next generation probiotics for neutralizing obesogenic effects: taxa culturing searching strategies. Nutrients 2021;13:1617.

108. Cani PD, de Vos WM. Next-generation beneficial microbes: the case of Akkermansia muciniphila. Front Microbiol 2017;8:1765.

109. Depommier C, Van Hul M, Everard A, Delzenne NM, De Vos WM, Cani PD. Pasteurized Akkermansia muciniphila increases whole-body energy expenditure and fecal energy excretion in diet-induced obese mice. Gut Microbes 2020;11:1231-45.

110. Abot A, Brochot A, Pomié N, et al. Pasteurized Akkermansia muciniphila improves glucose metabolism is linked with increased hypothalamic nitric oxide release. Heliyon 2023;9:e18196.

111. Stavropoulou E, Bezirtzoglou E. Probiotics in medicine: a long debate. Front Immunol 2020;11:2192.

112. da Silva JTS, Nagata CLP. Efficacy of prebiotics in promoting a healthy gut microbiota in adults and elderly persons in the community. Nutrire 2021;46:18.

113. Wang S, Xiao Y, Tian F, et al. Rational use of prebiotics for gut microbiota alterations: specific bacterial phylotypes and related mechanisms. J Funct Foods 2020;66:103838.

114. Martinson JNV, Walk ST. Escherichia coli residency in the gut of healthy human adults. EcoSal Plus 2020;9:10.1128/ecosalplus.esp-0003.

115. Paquet JC, Claus SP, Cordaillat-Simmons M, et al. Entering first-in-human clinical study with a single-strain live biotherapeutic product: input and feedback gained from the EMA and the FDA. Front Med 2021;8:716266.

116. Early clinical trials with live biotherapeutic products: chemistry, manufacturing, and control information. 2016. Available from: https://www.fda.gov/files/vaccines,%20blood%20&%20biologics/published/Early-Clinical-Trials-With-Live-Biotherapeutic-Products--Chemistry--Manufacturing--and-Control-Information--Guidance-for-Industry.pdf. [Last accessed on 15 Mar 2024]

117. Cordaillat-Simmons M, Rouanet A, Pot B. Live biotherapeutic products: the importance of a defined regulatory framework. Exp Mol Med 2020;52:1397-406.

118. Rouanet A, Bolca S, Bru A, et al. Live biotherapeutic products, a road map for safety assessment. Front Med 2020;7:237.

119. European Directorate for the Quality of Medicines & HealthCare (EDQM). Live Biotherapeutic Products (LBPs): European Pharmacopoeia Commission sets unprecedented quality requirements. Available from: https://www.edqm.eu/en/w/live-biotherapeutic-products-lbps-european-pharmacopoeia-commission-sets-unprecedented-quality-requirements. [Last accessed on 15 Mar 2024].

120. de Vos WM, Tilg H, Van Hul M, Cani PD. Gut microbiome and health: mechanistic insights. Gut 2022;71:1020-32.

121. 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.

122. Yip AYG, King OG, Omelchenko O, et al. Antibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites. Nat Commun 2023;14:5094.

123. Kim S, Covington A, Pamer EG. The intestinal microbiota: antibiotics, colonization resistance, and enteric pathogens. Immunol Rev 2017;279:90-105.

124. Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A 2011;108 Suppl 1:4554-61.

125. Relman DA. The human microbiome: ecosystem resilience and health. Nutr Rev 2012;70 Suppl 1:S2-9.

126. Saha S, Tariq R, Tosh PK, Pardi DS, Khanna S. Faecal microbiota transplantation for eradicating carriage of multidrug-resistant organisms: a systematic review. Clin Microbiol Infect 2019;25:958-63.

127. Hanssen NMJ, de Vos WM, Nieuwdorp M. Fecal microbiota transplantation in human metabolic diseases: from a murky past to a bright future? Cell Metab 2021;33:1098-110.

128. Groen AK, Nieuwdorp M. An evaluation of the therapeutic potential of fecal microbiota transplantation to treat infectious and metabolic diseases. EMBO Mol Med 2017;9:1-3.

129. Khoruts A, Weingarden AR. Emergence of fecal microbiota transplantation as an approach to repair disrupted microbial gut ecology. Immunol Lett 2014;162:77-81.

130. Friedman ND, Pollard J, Stupart D, et al. Prevalence of Clostridium difficile colonization among healthcare workers. BMC Infect Dis 2013;13:459.

131. Cold F, Baunwall SMD, Dahlerup JF, Petersen AM, Hvas CL, Hansen LH. Systematic review with meta-analysis: encapsulated faecal microbiota transplantation - evidence for clinical efficacy. Therap Adv Gastroenterol 2021;14:17562848211041004.

132. Baunwall SMD, Lee MM, Eriksen MK, et al. Faecal microbiota transplantation for recurrent Clostridioides difficile infection: an updated systematic review and meta-analysis. EClinicalMedicine 2020;29-30:100642.

133. Seekatz AM, Theriot CM, Rao K, et al. Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection. Anaerobe 2018;53:64-73.

134. Shetty SA, Hugenholtz F, Lahti L, Smidt H, de Vos WM. Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies. FEMS Microbiol Rev 2017;41:182-99.

135. Costello SP, Conlon MA, Vuaran MS, Roberts-Thomson IC, Andrews JM. Faecal microbiota transplant for recurrent Clostridium difficile infection using long-term frozen stool is effective: clinical efficacy and bacterial viability data. Aliment Pharmacol Ther 2015;42:1011-8.

136. Youngster I, Russell GH, Pindar C, Ziv-Baran T, Sauk J, Hohmann EL. Oral, capsulized, frozen fecal microbiota transplantation for relapsing Clostridium difficile infection. JAMA 2014;312:1772-8.

137. Kao D, Roach B, Silva M, et al. Effect of oral capsule- vs colonoscopy-delivered fecal microbiota transplantation on recurrent Clostridium difficile infection: a randomized clinical trial. JAMA 2017;318:1985-93.

138. Mehta SR, Yen EF. Microbiota-based therapies Clostridioides difficile infection that is refractory to antibiotic therapy. Transl Res 2021;230:197-207.

139. de Groot P, Nikolic T, Pellegrini S, et al. Faecal microbiota transplantation halts progression of human new-onset type 1 diabetes in a randomised controlled trial. Gut 2021;70:92-105.

140. Gangwani MK, Aziz M, Aziz A, et al. Fresh versus frozen versus lyophilized fecal microbiota transplant for recurrent Clostridium difficile infection: a systematic review and network meta-analysis. J Clin Gastroenterol 2023;57:239-45.

141. Saha S, Khanna S. Stool banking for fecal microbiota transplantation: ready for prime time? Hepatobiliary Surg Nutr 2021;10:110-2.

142. Pérez-Nadales E, Cano Á, Recio M, et al. Randomised, double-blind, placebo-controlled, phase 2, superiority trial to demonstrate the effectiveness of faecal microbiota transplantation for selective intestinal decolonisation of patients colonised by carbapenemase-producing Klebsiella pneumoniae (KAPEDIS). BMJ Open 2022;12:e058124.

143. Peterson DA, Frank DN, Pace NR, Gordon JI. Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe 2008;3:417-27.

144. Manrique P, Bolduc B, Walk ST, van der Oost J, de Vos WM, Young MJ. Healthy human gut phageome. Proc Natl Acad Sci U S A 2016;113:10400-5.

145. Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ. Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nat Commun 2017;8:1784.

146. Schmidt TSB, Li SS, Maistrenko OM, et al. Drivers and determinants of strain dynamics following fecal microbiota transplantation. Nat Med 2022;28:1902-12.

147. Conceição-Neto N, Deboutte W, Dierckx T, et al. Low eukaryotic viral richness is associated with faecal microbiota transplantation success in patients with UC. Gut 2018;67:1558-9.

148. Routy B, Le Chatelier E, Derosa L, et al. Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science 2018;359:91-7.

149. Park SY, Seo GS. Fecal microbiota transplantation: is it safe? Clin Endosc 2021;54:157-60.

150. Jiang ZD, Jenq RR, Ajami NJ, et al. Safety and preliminary efficacy of orally administered lyophilized fecal microbiota product compared with frozen product given by enema for recurrent Clostridium difficile infection: a randomized clinical trial. PLoS One 2018;13:e0205064.

151. Wang S, Xu M, Wang W, et al. Systematic review: adverse events of fecal microbiota transplantation. PLoS One 2016;11:e0161174.

152. Gosálbez L. Fecal microbiota transplantation (FMT): global industry and regulatory overview. Available from: https://www.microbiometimes.com/fecal-microbiota-transplantation-fmt-global-industry-and-regulatory-overview/. [Last accessed on 15 Mar 2024].

153. Faecal microbiota transplantation. EU-IN Horizon Scanning Report. 2022. Available from: https://www.ema.europa.eu/en/documents/report/faecal-microbiota-transplantation-eu-horizon-scanning-report_en.pdf. [Last accessed on 15 Mar 2024].

154. Regulation (EU) No 536/2014 of the European Parliament and of the Council of 16 April 2014 on clinical trials on medicinal products for human use, and repealing Directive 2001/20/EC Relevant text for EEA purposes. Available from: http://data.europa.eu/eli/reg/2014/536/oj/spa. [Last accessed on 15 Mar 2024].

155. Integrated addendum to ICH E6(R1): guideline for good clinical practice E6(R2). Available from: https://database.ich.org/sites/default/files/E6_R2_Addendum.pdf. [Last accessed on 15 Mar 2024]

156. Guideline on the requirements for quality documentation concerning biological investigational medicinal products in clinical trials. Available from: https://www.ema.europa.eu/en/documents/scientific-guideline/guideline-requirements-quality-documentation-concerning-biological-investigational-medicinal-products-clinical-trials-revision-2_en.pdf. [Last accessed on 15 Mar 2024].

157. FDA. FDA approves first orally administered fecal microbiota product for the prevention of recurrence of Clostridioides difficile infection. Available from: https://www.fda.gov/news-events/press-announcements/fda-approves-first-orally-administered-fecal-microbiota-product-prevention-recurrence-clostridioides. [Last accessed on 15 Mar 2024].

158. BiomeBank. BiomeBank announces world first regulatory approval for donor derived microbiome drug. 2022. Available from: https://www.biomebank.com/news/biomebank-announces-world-first-regulatory-approval-for-donor-derived-microbiome-drug/. [Last accessed on 15 Mar 2024].

159. FDA. VOWST. Available from: https://www.fda.gov/vaccines-blood-biologics/vowst. [Last accessed on 15 Mar 2024]

160. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature 2007;449:804-10.

161. Oliveira FS, Brestelli J, Cade S, et al. MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. Nucleic Acids Res 2018;46:D684-91.

162. Wu S, Sun C, Li Y, et al. GMrepo: a database of curated and consistently annotated human gut metagenomes. Nucleic Acids Res 2020;48:D545-53.

163. Katz K, Shutov O, Lapoint R, Kimelman M, Brister JR, O’Sullivan C. The sequence read archive: a decade more of explosive growth. Nucleic Acids Res 2022;50:D387-90.

164. MIT Professional Education. Artificial intelligence vs machine learning: what’s the difference? Available from: https://professionalprograms.mit.edu/blog/technology/machine-learning-vs-artificial-intelligence/. [Last accessed on 15 Mar 2024].

165. Russell SJ, Norvig P. Artificial intelligence : a modern approach. Third edition. Available from: https://people.engr.tamu.edu/guni/csce421/files/AI_Russell_Norvig.pdf. [Last accessed 15 Mar 2024].

166. LeCun Y, Bengio Y, Hinton G. Deep learning. Nature 2015;521:436-44.

167. Ghannam RB, Techtmann SM. Machine learning applications in microbial ecology, human microbiome studies, and environmental monitoring. Comput Struct Biotechnol J 2021;19:1092-107.

168. Acharjee A, Singh U, Choudhury SP, Gkoutos GV. The diagnostic potential and barriers of microbiome based therapeutics. Diagnosis 2022;9:411-20.

169. Ratiner K, Abdeen SK, Goldenberg K, Elinav E. Utilization of host and microbiome features in determination of biological aging. Microorganisms 2022;10:668.

170. Su Q, Liu Q, Lau RI, et al. Faecal microbiome-based machine learning for multi-class disease diagnosis. Nat Commun 2022;13:6818.

171. Wani AK, Roy P, Kumar V, Mir TUG. Metagenomics and artificial intelligence in the context of human health. Infect Genet Evol 2022;100:105267.

172. Marcos-Zambrano LJ, Karaduzovic-Hadziabdic K, Loncar Turukalo T, et al. Applications of machine learning in human microbiome studies: a review on feature selection, biomarker identification, disease prediction and treatment. Front Microbiol 2021;12:634511.

173. Radjabzadeh D, Bosch JA, Uitterlinden AG, et al. Gut microbiome-wide association study of depressive symptoms. Nat Commun 2022;13:7128.

174. Sudhakar P, Machiels K, Verstockt B, Korcsmaros T, Vermeire S. Computational biology and machine learning approaches to understand mechanistic microbiome-host interactions. Front Microbiol 2021;12:618856.

175. Belcour A, Frioux C, Aite M, Bretaudeau A, Hildebrand F, Siegel A. Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. Elife 2020;9:e61968.

Microbiome Research Reports
ISSN 2771-5965 (Online)

Portico

All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/

Portico

All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/