Effects of Antibiotics on Intestinal Microbiota and Potential Treatment Options

Öz

The gut microbiota is a complex ecosystem that significantly impacts digestion, immunity, and overall health. Although antibiotics are valuable in treating infections, they can cause long-term harmful effects on the host by altering the composition and functions of the microbiota. These effects include reduced microbial diversity, changes in the functional attributes of the microbiota, and the formation of antibiotic-resistant strains. This situation can lead to other complications such as digestive issues, weakened immune system, obesity, diabetes, allergic and autoimmune diseases, neurodevelopmental disorders, and certain cancers. In recent years, the increase in antibiotic use has heightened the likelihood of these problems becoming more acute or prevalent in the future. Antibiotic resistance is a global crisis, and the rising use of antibiotics over time necessitates research into their effects on microbiota and health. This review highlights the adverse effects of antibiotics on gut health and emphasizes various strategies to mitigate these effects, such as probiotics, prebiotics, fecal microbiota transplantation, and phage therapy.

Anahtar Kelimeler

• Antibiotic
• FMT
• Gut Microbiota
• Precision medicine
• Probiotic

Antibiyotiklerin Barsak Mikrobiyotası Üzerindeki Etkileri ve Potansiyel Tedavi Seçenekleri

Öz

Barsak mikrobiyotası; sindirim, immünite ve genel sağlık üzerinde önemli bir etkiye sahip karmaşık bir ekosistemdir. Antibiyotikler, enfeksiyonları tedavi etmede önemli olmasına rağmen, mikrobiyota bileşimini ve işlevlerini değiştirerek konakçı için uzun vadeli zararlı etkilere neden olabilmektedir. Bu etkiler arasında mikrobiyal çeşitliliğin azalması, mikrobiyotanın işlevsel özelliklerinde değişiklikler ve antibiyotiğe dirençli suşların oluşması yer almaktadır. Bu durum, sindirim sorunları, immün sistemin zayıflaması, obezite, diyabet, alerjik ve otoimmün hastalıklar, nörogelişimsel bozukluklar ve bazı kanserler gibi diğer komplikasyonlara yol açabilir. Son yıllarda antibiyotik kullanımındaki artış, bu sorunların gelecekte daha akut veya yaygın hale gelme olasılığını artırmaktadır. Antibiyotik direnci küresel bir kriz olup, zamanla artan antibiyotik kullanımının mikrobiyota ve sağlık üzerindeki etkilerinin araştırılmasını gerektirmektedir. Bu derleme, antibiyotiklerin barsak sağlığı üzerindeki olumsuz etkilerini ve bu etkileri azaltmak için probiyotikler, prebiyotikler, fekal mikrobiyota transplantasyonu ve faj tedavisi gibi çeşitli stratejileri vurgulamaktadır.

Anahtar Kelimeler

• Antibiyotik
• Barsak Mikrobiyotası
• Bireyselleştirilmiş Tıp
• FMT
• Probiyotik

Kaynakça

1. 1. Kumari R, Yadav Y, Misra R, et al. Emerging frontiers of antibiotics use and their impacts on the human gut microbiome. Microbiol Res. 2022;263:127127.
2. 2. Becattini S, Taur Y, Pamer EG. Antibiotic-induced changes in the intestinal microbiota and disease. Trends Mol Med. 2016;22(6):458-478.
3. 3. Ramirez J, Guarner F, Bustos Fernandez L, Maruy A, Sdepanian VL, Cohen H. Antibiotics as major disruptors of gut microbiota. Front Cell Infect Microbiol. 2020;10:572912.
4. 4. Adedeji WA. The treasure called antibiotics. Annals of Ibadan Postgraduate Medicine. 2016;14(2):56–57.
5. 5. 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(1):e1260.
6. 6. Safarchi A, Al-Qadami G, Tran CD, Conlon M. Understanding dysbiosis and resilience in the human gut microbiome: Biomarkers, interventions, and challenges. Front Microbiol. 2025;16:1559521.
7. 7. Madhogaria B, Bhowmik P, Kundu A. Correlation between human gut microbiome and diseases. Infectious Medicine. 2022;1(3):180-191.
8. 8. Hou K, Wu ZX, Chen XY, et al. Microbiota in health and diseases. Sig Transduct Target Ther 2022;7:135.

9. 9. Klein-Petersen AW, Köhler-Forsberg O, Benros ME. Infections, antibiotic treatment and the Microbiome in relation to schizophrenia. Schizophr Res. 2021;234:71-77.
10. 10. Miller WD, Keskey R, Alverdy JC. Sepsis and the microbiome: A vicious cycle. J Infect Dis. 2021;223(12 Suppl 2):S264-S269.
11. 11. Dörner PJ, Anandakumar H, Röwekamp I, et al. Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung. Nat Commun. 2024;15:2788.
12. 12. Konstantinidis T, Tsigalou C, Karvelas A, Stavropoulou E, Voidarou C, Bezirtzoglou E. Effects of antibiotics upon the gut microbiome: A review of the literature. Biomedicines. 2020;8(11):502.
13. 13. Blaser MJ. Antibiotic use and its consequences for the normal microbiome. Science. 2016;352(6285):544-545.
14. 14. Dieterich W, Schink M, Zopf Y. Microbiota in the gastrointestinal tract. Med Sci (Basel). 2018;6(4):116.
15. 15. Martinez-Guryn K, Leone V, Chang EB. Regional diversity of the gastrointestinal microbiome. Cell Host Microbe. 2019;26(3):314-324.
16. 16. Eckburg PB, Bik EM, Bernstein CN, et al. Diversity of the human intestinal microbial flora. Science. 2005;308:1635–1638.
17. 17. The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–214.
18. 18. Krajmalnik-Brown R, Ilhan ZE, Kang DW, DiBaise JK. Effects of gut microbes on nutrient absorption and energy regulation. Nutr Clin Pract. 2012;27(2):201-14.
19. 19. Wiertsema SP, van Bergenhenegouwen J, Garssen J, Knippels LMJ. The interplay between the gut microbiome and the immune system in the context of infectious diseases throughout life and the role of nutrition in optimizing treatment strategies. Nutrients. 2021;13(3):886.
20. 20. Scheithauer TPM, Rampanelli E, Nieuwdorp M, et al. Gut Microbiota as a trigger for metabolic inflammation in obesity and type 2 diabetes. Front Immunol. 2020;11:571731.
21. 21. Kumar A, Pramanik J, Goyal N, et al. Gut Microbiota in Anxiety and Depression: Unveiling the Relationships and Management Options. J Pharm. 2023;16(4):565.
22. 22. Nakhal MM, Yassin LK, Alyaqoubi R, et al. The microbiota–gut–brain axis and neurological disorders: A comprehensive review. Life. 2024;14(10):1234.
23. 23. Pickard JM, Zeng MY, Caruso R, Núñez G. Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease. Immunol Rev 2017;279(1):70-89.
24. 24. Horrocks V, King OG, Yip AYG, Marques IM, McDonald JAK. Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization. Microbiology 2023;169(8):001377.
25. 25. Wilson ID, Nicholson JK. Gut microbiome interactions with drug metabolism, efficacy, and toxicity. Transl Res. 2017;179:204-222.
26. 26. Rowland I, Gibson G, Heinken A, et al. Gut microbiota functions: metabolism of nutrients and other food components. Eur J Nutr. 2018;57(1):1-24.
27. 27. Afzaal M, Saeed F, Shah YA, et al. Human gut microbiota in health and disease: Unveiling the relationship. Front microbiol. 2022;13.
28. 28. Aziz T, Hussain N, Hameed Z, Lin L. Elucidating the role of diet in maintaining gut health to reduce the risk of obesity, cardiovascular and other age-related inflammatory diseases: recent challenges and future recommendations. Gut Microbes. 2024;16(1):2297864.
29. 29. Francino MP. Antibiotics and the human gut microbiome: Dysbioses and accumulation of resistances. Front Microbiol. 2016;6:1543.
30. 30. Ohland CL, Jobin C. Microbial activities and intestinal homeostasis: A delicate balance between health and disease. Cell Mol Gastroenterol Hepatol. 2015;1(1):28-40.
31. 31. Isibor PO, Akinduti PA, Aworunse OS, et al. Significance of African diets in biotherapeutic modulation of the gut microbiome. Bioinform Biol Insights. 2021;15:11779322211012697.
32. 32. Vincent JL, Bassetti M, François B, et al. Antonelli Advances in antibiotic therapy in the critically ill Crit. Care. 2016;20(1):1-13.
33. 33. Vonaesch P, Morien E, Andrianonimiadana L, et al. Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(36):E8489–E8498.
34. 34. Łukasik J, Dierikx T, Johnston BC, de Meij T, Szajewska H. Systematic review: effect of probiotics on antibiotic-induced microbiome disruption. Benef Microbes. 2024;15(5):431-447.
35. 35. Huang C, Feng S, Huo F, Liu H. Effects of four antibiotics on the diversity of the intestinal microbiota. Microbiol Spectr. 2022;10(2):e0190421.
36. 36. Bien J, Palagani V, Bozko P. The intestinal microbiota dysbiosis and Clostridium difficile infection: is there a relationship with inflammatory bowel disease? Therap Adv Gastroenterol. 2013;6(1):53-68.
37. 37. Hoskinson C, Maria V, Medeleanu W, et al. Antibiotics taken within the first year of life are linked to infant gut microbiome disruption and elevated atopic dermatitis risk. J Allergy Clin Immunol. 2024;154(1):131-142.
38. 38. Li P, Chang X, Chen X, et al. Early-life antibiotic exposure increases the risk of childhood overweight and obesity in relation to dysbiosis of gut microbiota: a birth cohort study. Ann Clin Microbiol Antimicrob. 2022;21:46.
39. 39. Kesavelu D, Jog P. Current understanding of antibiotic-associated dysbiosis and approaches for its management. Ther Adv Infect Dis. 2023;10:20499361231154443.
40. 40. Guarner F, Bustos Fernandez L, Cruchet S,et al. Gut dysbiosis mediates the association between antibiotic exposure and chronic disease. Front Med (Lausanne). 2024;11:1477882.
41. 41. Cho I, Yamanishi S, Cox L, et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature. 2012;488:621–626.
42. 42. Choo JM, Kanno T, Zain NM, et al. Divergent relationships between fecal microbiota and metabolome following distinct antibiotic-induced disruptions. mSphere 2. 2017;e00005–17.
43. 43. Salam MA, Al-Amin MY, Salam MT, et al. Antimicrobial resistance: A growing serious threat for global public health. Healthcare (Basel). 2023;11(13):1946.
44. 44. Dadgostar P. Antimicrobial Resistance: Implications and Costs. Infect Drug Resist. 2019;12:3903-3910.
45. 45. World Health Organization (2018). WHO report on surveillance of antibiotic consumption: 2016-2018 early implementation. Available at: http://apps.who.int/iris/bitstream/handle/10665/277359/9789241514880-eng.pdf?ua=1 (Accessed 20 April, 2025).
46. 46. Pancu DF, Scurtu A, Macasoi IG, et al. Antibiotics: Conventional therapy and natural compounds with antibacterial activity-A pharmaco-toxicological screening. Antibiotics. 2021;10(4):401.
47. 47. Ghuneim LJ, Raghuvanshi R, Neugebauer KA, et al. Complex and unexpected outcomes of antibiotic therapy against a polymicrobial infection. ISME J. 2022;16(9):2065-2075.
48. 48. Ramakrishna BS, Patankar R. Antibiotic-associated Gut Dysbiosis. J Assoc Physicians India 2023;71(11):62-68.
49. 49. Alm RA, Lahiri SD. Narrow-spectrum antibacterial agents-benefits and challenges. Antibiotics (Basel). 2020;9(7):418.
50. 50. Grada A, Bunick CG. Spectrum of antibiotic activity and its relevance to the microbiome. JAMA Netw Open. 2021;4(4):e215357.
51. 51. Spigaglia P. Clostridioides difficile and Gut Microbiota: From colonization to infection and treatment. Pathogens. 2024;13(8):646.
52. 52. Cook MA, Wright GD. The past, present, and future of antibiotics. Sci Transl Med. 2022;14(657):eabo7793.
53. 53. Muteeb G, Rehman MT, Shahwan M, Aatif M. Origin of Antibiotics and Antibiotic Resistance, and Their Impacts on Drug Development: A Narrative Review. Pharmaceuticals 2023;16(11):1615.
54. 54. Sirwan KA, Safin H, Karzan Q, et al. Antimicrobial resistance: Impacts, challenges, and future prospects. Journal of Medicine, Surgery, and Public Health. 2024;2:100081.
55. 55. Lathakumari RH, Vajravelu LK, Satheesan A, Ravi S, Thulukanam J. Antibiotics and the gut microbiome: Understanding the impact on human health. Medicine in Microecology. 2024;20:100106.
56. 56. Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Nageshwar Reddy D. Role of the normal gut microbiota. World J Gastroenterol 2015;21(29):8787-803.
57. 57. Cantarutti A, Rescigno P, Da Borso C, et al. Association Between Early-Life Exposure to Antibiotics and Development of Child Obesity: Population-Based Study in Italy. JMIR Public Health Surveill. 2024;10:e51734.
58. 58. Lu Y, Wang Y, Wang J, Lowe AJ, Grzeskowiak LE, Hu YJ. Early-life antibiotic exposure and childhood asthma trajectories: a national population-based birth cohort. Antibiotics. 2023;12(2):314.
59. 59. Kamel M, Aleya S, Alsubih M, Aleya L. Microbiome Dynamics: A Paradigm Shift in Combatting Infectious Diseases. J Pers Med. 2024;14(2):217.
60. 60. Sadeghpour HF. Gut microbiota and autoimmune diseases: Mechanisms, treatment, challenges, and future recommendations. Curr Clin Micro Rpt. 2024;11:18–33.
61. 61. Suliman BA. Potential clinical implications of molecular mimicry-induced autoimmunity. Immun Inflamm Dis. 2024;12(2):e1178.
62. 62. Sun L, Zhang X, Zhang Y, et al. Antibiotic-Induced Disruption of Gut Microbiota Alters Local Metabolomes and Immune Responses. Front cell infect microbiol. 2019;9:99.
63. 63. Ma T, Shen X, Shi X, et al. Targeting gut microbiota and metabolism as the major probiotic mechanism - An evidence-based review. Trends Food Sci Technol. 2023;138:178-198.
64. 64. Kashyap PC, Chia N, Nelson H, Segal E, Elinav E. Microbiome at the frontier of personalized medicine. Mayo Clin Proc. 2017;92(12):1855-1864.
65. 65. Ha DR, Haste NM, Gluckstein DP. The role of antibiotic stewardship in promoting appropriate antibiotic use. Am J Lifestyle Med. 2017;13(4):376-383.
66. 66. Majumder MAA, Rahman S, Cohall D, et al. Antimicrobial Stewardship: Fighting Antimicrobial Resistance and Protecting Global Public Health. Infect Drug Resist. 2020;13:4713-4738.
67. 67. Laxminarayan R. Antibiotic effectiveness: balancing conservation against innovation. Science. 2014;345:1299–1301.
68. 68. Petrosino JF. The microbiome in precision medicine: the way forward. Genome Med 2018;10:12.
69. 69. Shuklaa V, Singha S, Vermab S, Vermab S, Rizvib AA, Abbasb M. Targeting the microbiome to improve human health with the approach of personalized medicine: Latest aspects and current updates. Clinical Nutrition ESPEN. 2024;63:813–820.
70. 70. Cheng YW, Fischer M. Fecal Microbiota Transplantation. Clin Colon Rectal Surg. 2023;36(2):151-156.
71. 71. Bober JR, Beisel CL, Nair NU. Synthetic biology approaches to engineer probiotics and members of the human microbiota for biomedical applications. Annu Rev Biomed Eng. 2018;20:277-300.
72. 72. Ji J, Jin W, Liu SJ, Jiao Z, Li X. Probiotics, prebiotics, and postbiotics in health and disease. MedComm. 2023;4(6):e420.
73. 73. Ma Z, Zuo T, Frey N. et al. A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation. Sig Transduct Target Ther. 2024;9:237.
74. 74. Rafique N, Jan SY, Dar AH, et al. Promising bioactivities of postbiotics: A comprehensive review. J Agric Food Res. 2023;14:100708.
75. 75. Gulliver EL, Young RB, Chonwerawong M, et al. Review article: the future of microbiome-based therapeutics. Aliment Pharmacol Ther. 2022;56(2):192-208.
76. 76. Al-Habsi N, Al-Khalili M, Haque SA, Elias M, Olqi NA, Al Uraimi T. Health benefits of prebiotics, probiotics, synbiotics, and postbiotics. Nutrients. 2024;16(22):3955.
77. 77. Baldi S, Mundula T, Nannini G, Amedei A. Microbiota shaping - the effects of probiotics, prebiotics, and fecal microbiota transplant on cognitive functions: A systematic review. World J Gastroenterol. 2021;27(39):6715-6732.
78. 78. Mazziotta C, Tognon M, Martini F, Torreggiani E, Rotondo JC. Probiotics mechanism of action on immune cells and beneficial effects on human health. Cells. 2023;12(1):184.
79. 79. Ma J, Lyu Y, Liu X, et al. Engineered probiotics. Microb Cell Fact 2022;21:72.
80. 80. Li DY, Li LQ, Jie J, Liu G. Nucleases in gene-editing technologies: past and prologue Natl Sci Open. 2023;25:20220067.
81. 81. Nazir A, Hussain FHN, Raza A. Advancing microbiota therapeutics: the role of synthetic biology in engineering microbial communities for precision medicine. Front Bioeng Biotechnol. 2024;12:1511149.
82. 82. Chandrasekaran P, Weiskirchen S, Weiskirchen R. Effects of Probiotics on Gut Microbiota: An Overview. Int J Mol Sci. 2024;25(11):6022.
83. 83. Gibson GR, Roberfroid MB. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr. 1995;125(6):1401-1412.
84. 84. 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(8):491-502.
85. 85. Slavin J. Fiber and prebiotics: mechanisms and health benefits. Nutrients. 2013;5(4):1417‐1435.
86. 86. Bindels LB, Delzenne NM, Cani PD, Walter J. Towards a more comprehensive concept for prebiotics. Nat Rev Gastroenterol Hepatol. 2015;12(5):303‐310.
87. 87. 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(6):1332‐1345.
88. 88. Barratt MJ, Nuzhat S, Ahsan K, et al. Bifidobacterium infantis treatment promotes weight gain in Bangladeshi infants with severe acute malnutrition. Sci Transl Med. 2022;14(640):eabk1107.
89. 89. Jagtiani E, Adsare S. Microencapulsation: Probiotics, Prebiotics, and Nutraceuticals. J Nanotechnol Nanomaterials. 2022;3(1):34-60.
90. 90. Simon E, Călinoiu LF, Mitrea L, Vodnar DC. Probiotics, prebiotics, and synbiotics: Implications and beneficial effects against irritable bowel syndrome. Nutrients. 2021;13(6):2112.
91. 91. Sergeev IN, Aljutaily T, Walton G, Huarte E. Effects of synbiotic supplement on human gut microbiota, body composition and weight loss in obesity. Nutrients. 2020;12(1):222.
92. 92. Soveral LF, Korczaguin GG, Schmidt PS, Nunes IS, Fernandes C, Zárate-Bladés CR. Immunological mechanisms of fecal microbiota transplantation in recurrent Clostridioides difficile infection. World J Gastroenterol. 2022;28(33):4762-4772.
93. 93. Mullish BH, Allegretti JR. The contribution of bile acid metabolism to the pathogenesis of Clostridioides difficile infection. Therap Adv Gastroenterol. 2021;14:17562848211017725.
94. 94. Wang Y, Zhang S, Borody TJ, Zhang F. Encyclopedia of fecal microbiota transplantation: a review of effectiveness in the treatment of 85 diseases. Chin Med J (Engl). 2022;135(16):1927-1939.
95. 95. Quraishi MN, Widlak M, Bhala N, et al. Systematic review with meta-analysis: the efficacy of faecal microbiota transplantation for the treatment of recurrent and refractory Clostridium difficile infection. Aliment Pharmacol Ther. 2017;46(5):479-493.
96. 96. Imdad A, Nicholson MR, Tanner-Smith EE, et al. Fecal transplantation for treatment of inflammatory bowel disease. Cochrane Database Syst. Rev. 2018;11:CD012774.
97. 97. Khanna S, Assi M, Lee C, et al. Efficacy and safety of RBX2660 in PUNCH CD3, a phase III, Randomized, double-blind, placebo-controlled trial with a bayesian primary analysis for the prevention of recurrent Clostridioides difficile infection. Drugs. 2022;82(15):1527-1538.
98. 98. Yu Y, Wang W, Zhang F. The next generation fecal microbiota transplantation: To transplant bacteria or virome. Adv Sci (Weinh). 2023;10(35):e2301097.
99. 99. Hamamah S, Gheorghita R, Lobiuc A, Sirbu IO, Covasa M. Fecal microbiota transplantation in non-communicable diseases: Recent advances and protocols. Front Med. 2022;9:1060581.
100. 100. Karimi M, Shirsalimi N, Hashempour Z, et al. Safety and efficacy of fecal microbiota transplantation (FMT) as a modern adjuvant therapy in various diseases and disorders: a comprehensive literature review. Front Immunol. 2024;15:1439176.
101. 101. Cui L, Watanabe S, Miyanaga K, et al. A Comprehensive Review on Phage Therapy and Phage-Based Drug Development. Antibiotics. 2024;13(9):870.
102. 102. Sheraz M, Shi H, Banerjee S. Human microbiome and bacteriophages: Impacts on health and disease. Curr Clin Micro Rpt. 2025;12:7.
103. 103. Cao F, Wang X, Wang L, et al. Evaluation of the efficacy of a bacteriophage in the treatment of pneumonia induced by multidrug resistance Klebsiella pneumoniae in mice. Biomed Res Int. 2015;2015:752930.
104. 104. Fong SA, Drilling A, Morales S, et al. Activity of bacteriophages in removing biofilms of Pseudomonas aeruginosa isolates from chronic rhinosinusitis patients. Front Cell Infect Microbiol. 2017;7:1–11.
105. 105. Schooley RT, Biswas B, Gill JJ, et al. Development and use of personalized bacteriophage‐based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection. Antimicrob Agents Chemother. 2017;61(10):1–15.
106. 106. Jennes S, Merabishvili M, Soentjens P, et al. Use of bacteriophages in the treatment of colistin‐only‐sensitive Pseudomonas aeruginosa septicaemia in a patient with acute kidney injury‐a case report. Critical Care. 2017;21(1),2016–2018.
107. 107. Letkiewicz S, Miedzybrodzki R, Fortuna W, Weber‐Dabrowska B, Górski A. Eradication of Enterococcus faecalis by phage therapy in chronic bacterial prostatitis—case report. Folia Microbiologica. 2009;54(5):457–461.
108. 108. Markoishvili K, Tsitlanadze G, Katsarava R, Glenn J, Sulakvelidze A. A novel sustained‐release matrix based on biodegradable poly(ester amide)s and impregnated with bacteriophages and an antibiotic shows promise in management of infected venous stasis ulcers and other poorly healing wounds. International Journal of Dermatology. 2002;41:453–458.
109. 109. Dedrick RM, Guerrero‐Bustamante CA, Garlena RA, et al. Engineered bacteriophages for treatment of a patient with a disseminated drug resistant Mycobacterium abscessus. Nature Medicine. 2019;25(5):730–733.
110. 110. Allaband C, McDonald D, Vazquez-Baeza, et al. Microbiome 101: Studying, analyzing, and interpreting gut microbiome data for clinicians. Clin. Gastroenterol. Hepatol. 2019;17:218–230.
111. 111. Gaulke CA, Sharpton TJ. The influence of ethnicity and geography on human gut microbiome composition. Nat Med. 2018;24:1495–1496.
112. 112. Clemente JC, Pehrsson, EC, Blaser MJ, et al. The microbiome of uncontacted Amerindians. Sci Adv. 2015;1:e1500183.
113. 113. Sonnenburg JL, Sonnenburg ED. Vulnerability of the industrialized microbiota. Science. 2019;366:eaaw9255.
114. 114. Principi N, Petropulacos K, Esposito S. Genetic variations and antibiotic-related adverse events. Pharmaceuticals (Basel). 2024;17(3):331.
115. 115. Gong L, Zhang CM, Lv JF, Zhou HH, Fan L. Polymorphisms in cytochrome P450 oxidoreductase and its effect on drug metabolism and efficacy. Pharmacogenet Genomics. 2017;27(9):337-346.
116. 116. Stoeltje L, Luc JK, Haddad T, Schrankel CS. The roles of ABCB1/P-glycoprotein drug transporters in regulating gut microbes and inflammation: insights from animal models, old and new. Philos Trans R Soc Lond B Biol Sci. 2024;379(1901):20230074.
117. 117. Sunuwar J, Azad RK. A machine learning framework to predict antibiotic resistance traits and yet unknown genes underlying resistance to specific antibiotics in bacterial strains. Brief Bioinform. 2021;22(6):bbab179.
118. 118. Mohseni P, Abozar Ghorbani. Exploring the synergy of artificial intelligence in microbiology: Advancements, challenges, and future prospects. CSBJ. 2024;1:100005.
119. 119. Mohr AE, Ortega-Santos CP, Whisner CM, Klein-Seetharaman J, Jasbi P. Navigating challenges and opportunities in multi-omics integration for personalized healthcare. Biomedicines. 2024;12(7):1496.
120. 120. Lange L, Berg G, Cernava T,et al. Microbiome ethics, guiding principles for microbiome research, use and knowledge management. Environ Microbiome. 2022;17(1):50.