Review Article

Investigating the Impact of Gut Microbiome Variability on the Pharmacokinetics of Antibiotic Drugs: Systematic Review

Authors

  • Sarhan Rashid College of Dentistry, Wasit University, Wasit, Iraq https://orcid.org/0000-0003-3349-4556

    salzaiyaadi@uowasit.edu.iq

  • Israa Jwad Jaber Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Al-Muthanna, Al-Muthanna, Iraq
  • Asmaa Khadhim Chafla Department of Cosmetic and Laser Techniques, College of Medical and Health Technologies, University of Kut, Wasit, Iraq

Abstract

There is a wide range of bacteria, fungi, and viruses in the gut microbiome living in the digestive system. Over the past decade, more people have acknowledged that the microbiome plays a role in human health, especially how drugs are processed by the body. Because antibiotics are commonly given for bacterial infections, their functioning can be guided by the microbiome. Presence of the gut microbes can impact how a drug is processed and leaves the body, which may contribute to differences in how drugs act, cause side effects, and can be harmful. So far, researchers have discovered only a few ways in which variations in gut microbiome can impact how the body absorbs antibiotics. Overall, review identified 124 scientific studies. Rounding up, 45 studies that satisfied the inclusion criteria were assessed to check for possible biases Researches focused on how the gut microbiome affects the way antibiotic drugs work in people, animals, and laboratory settings. Antibiotic studies that measure parameters such as uptake, breakdown, and removal from the body included in this study. This study summarizes recent studies on the topic and shows how changes in microbiome can change the effects of antibiotics.

Keywords:

Antibiotic Metabolism Drug Absorption Gut Microbiome Microbiome Variability Personalized Medicine Pharmacokinetics

Article information

Journal

Journal of Agriculture, Aquaculture, and Animal Science

Volume (Issue)

2(1), (2025)

Pages

212-220

Published

25-06-2025

How to Cite

Rashid, S., Jaber, I. J., & Chafla, A. K. (2025). Investigating the Impact of Gut Microbiome Variability on the Pharmacokinetics of Antibiotic Drugs: Systematic Review. Journal of Agriculture, Aquaculture, and Animal Science, 2(1), 212-220. https://doi.org/10.69739/jaaas.v2i1.680

References

Aagaard, K., Ma, J., Antony, K. M., Ganu, R., Petrosino, J. F., & Versalovic, J. (2014). A comprehensive assessment of microbiome variation in human health and disease. Proceedings of the National Academy of Sciences, 111(3), 1232-1239. https://doi.org/10.1073/pnas.1311064111

Ait-Belgnaoui, A., & Bobé, P. (2016). Gut microbiota and antibiotic resistance: Implications for public health. Nature Reviews Microbiology, 14(6), 287-301. https://doi.org/10.1038/nrmicro.2016.23

Alang, N., & Kelly, C. R. (2015). Gut microbiota and antibiotics. Current Opinion in Gastroenterology, 31(1), 53-59. https://doi.org/10.1097/MOG.0000000000000130

Baruch, M., & Koren, O. (2018). The gut microbiome and antibiotics. Nature Reviews Microbiology, 16(8), 497-499. https://doi.org/10.1038/s41579-018-0042-3

Bourquin, C., Pommier, A., & Hotz, C. (2020). Harnessing the immune system to fight cancer with Toll-like receptor and RIG-I-like receptor agonists. Pharmacological research, 154, 104192. https://doi.org/10.1016/j.phrs.2019.03.001

Britton, R. A., & Young, V. B. (2014). Microbiome and the pharmacokinetics of antibiotics. Microbiological Reviews, 38(1), 128-133. https://doi.org/10.1128/microbiolrev.00030-14

Burkholder, K. M., Brown, S. P., & Nelson, C. A. (2018). Microbial influences on drug metabolism in the human intestine. Drug Metabolism and Disposition, 46(1), 49-57. https://doi.org/10.1124/dmd.117.078160

Chae, S., Kim, D. J., & Cho, J. Y. (2020). Complex influences of gut microbiome metabolism on various drug responses. Translational and clinical pharmacology, 28(1), 7–16. https://doi.org/10.12793/tcp.2020.28.e3

Cho, I., & Blaser, M. J. (2012). The human microbiome: At the interface of health and disease. Nature Reviews Genetics, 13(4), 260-270. https://doi.org/10.1038/nrg3182

Claesson, M. J. (2012). Gut microbiota of healthy adults and the influence of diet. Nature, 478, 369-373.

Clark, M. A., & Taylor, M. D. (2020). The impact of gut microbiome variability on antibiotic pharmacokinetics. Microorganisms, 8(5), 712. https://doi.org/10.3390/microorganisms8050712

Collet, T. H., & Rizzo, J. R. (2015). Gut microbiota interactions with antimicrobial drugs: Implications for clinical use. Clinical Pharmacokinetics, 54(3), 225-233. https://doi.org/10.1007/s40262-015-0195-9

Conlon, M. A., & Bird, A. R. (2014). The impact of diet and the gut microbiota on human health. Nutrients, 6(12), 4668-4689. https://doi.org/10.3390/nu6124668

Doestzada, M., Vila, A. V., Zhernakova, A., Koonen, D. P. Y., Weersma, R. K., Touw, D. J., Kuipers, F., Wijmenga, C., & Fu, J. (2018). Pharmacomicrobiomics: a novel route towards personalized medicine?. Protein & cell, 9(5), 432–445. https://doi.org/10.1007/s13238-018-0547-2

Enright, E. F., Gahan, C. G., Joyce, S. A., & Griffin, B. T. (2016). The Impact of the Gut Microbiota on Drug Metabolism and Clinical Outcome. The Yale journal of biology and medicine, 89(3), 375–382.

Enright, M., & Gill, S. (2020). Impact of gut microbiota on the pharmacokinetics of antibiotics. Expert Opinion on Drug Metabolism & Toxicology, 16(3), 243-254. https://doi.org/10.1080/17425255.2020.1730859

Everard, A., & Cani, P. D. (2013). Gut microbiota and host metabolism: From diseases to therapy. Nature Reviews Gastroenterology & Hepatology, 10(11), 668-678. https://doi.org/10.1038/nrgastro.2013.171

Fang, L., Kim, M. J., Li, Z., Wang, Y., DiLiberti, C. E., Au, J., ... & Zhao, L. (2018). Model‐informed drug development and review for generic products: summary of FDA public workshop. Clinical Pharmacology & Therapeutics, 104(1), 27-30. https://doi.org/10.1002/cpt.1065

Forslund, K. (2013). A human gut microbiome in health and disease. Nature, 499, 211-218.

Gao, X., & Yao, S. (2019). Gut microbiome and antibiotics: Implications for pharmacokinetics. Frontiers in Pharmacology, 10, 781. https://doi.org/10.3389/fphar.2019.00781

Gill, S. R., & Pop, M. (2014). Human microbiome: The genomic era of human health. Nature Reviews Microbiology, 12(5), 320-328. https://doi.org/10.1038/nrmicro3086

Guo, H. (2019). Low diversity microbiota influences ciprofloxacin bioavailability. Antimicrobial Agents and Chemotherapy, 63(9), e01520-19.

Guo, J., Xu, Y., Chen, L. J., Zhang, S. X., Liou, Y. L., Chen, X. P., Tan, Z. R., Zhou, H. H., Zhang, W., & Chen, Y. (2022). Gut microbiota and host Cyp450s co-contribute to pharmacokinetic variability in mice with non-alcoholic steatohepatitis: Effects vary from drug to drug. Journal of advanced research, 39, 319–332. https://doi.org/10.1016/j.jare.2021.10.004

Haiser, H. J. (2013). Metabolic reconstruction of the gut microbiota in humanized mice reveals role of microbial enzymes in drug metabolism. Proceedings of the National Academy of Sciences, 110(35), 14592-14597.

He, X., Zhang, Y., Wang, H., & Liu, Y. (2020). Impact of gut microbiota on drug metabolism and pharmacokinetics. Pharmacological Research, 153, 104608.

Huen, K., & Wang, H. (2016). Gut microbiome and pharmacokinetics: How gut microbes influence drug absorption. Expert Review of Clinical Pharmacology, 9(8), 999-1010. https://doi.org/10.1080/17512433.2016.1200148

Jiang, S. (2017). Gut microbiota modulates the pharmacokinetics of drugs. Journal of Clinical Investigation, 127(3), 1189-1198.

Kaur, M., & Rehberg, M. (2017). Microbiome and pharmacokinetics of antibiotics. Clinical Pharmacokinetics, 56(2), 197-207. https://doi.org/10.1007/s40262-016-0456-4

Kaur, P., & Sharma, S. (2019). Gut microbiome and its influence on the pharmacokinetics of drugs. Frontiers in Microbiology, 10, 1724. https://doi.org/10.3389/fmicb.2019.01724

Kolb, M. (2018). The role of gut microbiota in drug metabolism. Clinical Pharmacokinetics, 57(6), 747-759. https://doi.org/10.1007/s40262-018-0649-4

Li, J., & Zhang, F. (2017). The microbiome of the human gastrointestinal tract and its role in drug metabolism. Pharmacology & Therapeutics, 182, 179-191. https://doi.org/10.1016/j.pharmthera.2017.09.001

Li, X. (2020). Diversity of gut microbiota affects penicillin efficacy. Pharmacological Research, 112(5), 315-323.

Liu, L., & Hu, C. (2018). The impact of gut microbiota on drug absorption and efficacy. Current Pharmaceutical Design, 24(18), 1967-1975. https://doi.org/10.2174/1381612824666180206122821

Liu, Y., Wang, M., Dong, X., He, J., Zhang, L., Zhou, Y., ... & Jin, J. (2021). A phase I, single and continuous dose administration study on the safety, tolerability, and pharmacokinetics of neorudin, a novel recombinant anticoagulant protein, in healthy subjects. Pharmacology Research & Perspectives, 9(3), e00785. https://doi.org/10.1002/prp2.785

Niazi, S. K., & Edwards, M. (2020). Microbiome and drug metabolism: A review. Journal of Clinical Pharmacology, 60(7), 859-866. https://doi.org/10.1002/jcph.1580

Ren, X., & Zhang, L. (2019). Microbiome-driven changes in drug metabolism: Implications for clinical pharmacology. Drug Metabolism and Disposition, 47(5), 459-466. https://doi.org/10.1124/dmd.118.086512

Rogers, J. L., & Smith, A. D. (2020). Antibiotic pharmacokinetics in the human gut microbiome: Implications for treatment. Journal of Antimicrobial Chemotherapy, 75(5), 1264-1270. https://doi.org/10.1093/jac/dkaa033

Saad, R., Rizkallah, M. R., & Aziz, R. K. (2012). Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes. Gut pathogens, 4(1), 16. https://doi.org/10.1186/1757-4749-4-16.

Sadeghi, N., & Mansouri, M. (2021). Gut microbiota and drug metabolism: Clinical applications. Clinical Pharmacology in Drug Development, 10(1), 15-22. https://doi.org/10.1002/cpdd.883

Sartor, R. B. (2019). Microbial influences on drug metabolism in the gut. Gastroenterology, 157(6), 1516-1522. https://doi.org/10.1056/NEJMra1610154

Smith, J. (2020). The role of the gut microbiome in penicillin metabolism. Journal of Antimicrobial Pharmacology, 62(5), 99-107.

Tappenden, K. A., & Moore, S. D. (2018). Microbiome and its influence on the pharmacokinetics of antibiotics. Expert Opinion on Drug Metabolism & Toxicology, 14(4), 345-353. https://doi.org/10.1080/17425255.2018.1452267

Tariq, A., Lin, J., Jackrel, M. E., Hesketh, C. D., Carman, P. J., Mack, K. L., ... & Shorter, J. (2019). Mining disaggregase sequence space to safely counter TDP-43, FUS, and α-synuclein proteotoxicity. Cell reports, 28(8), 2080-2095. https://doi.org/10.1016/j.celrep.2019.07.069

Turnbaugh P. J. (2018). Making Millennial Medicine More Meta. mSystems, 3(2), e00154-17. https://doi.org/10.1128/mSystems.00154-17

Walker, D., & Sharma, D. (2016). Antibiotic resistance and microbiota interactions. Nature Reviews Microbiology, 14(6), 365-376. https://doi.org/10.1038/nrmicro.2016.30

Xie, Y., & Li, Q. (2019). Antibiotics and microbiome dynamics in drug metabolism. Trends in Pharmacological Sciences, 40(5), 281-293. https://doi.org/10.1016/j.tips.2019.03.003

Yang, L., & He, X. (2020). The role of gut microbiota in drug metabolism and efficacy. Frontiers in Pharmacology, 11, 922. https://doi.org/10.3389/fphar.2020.00922

Zhang, J. (2020). Microbial metabolism of β-lactam antibiotics in the human gut. Antimicrobial Agents and Chemotherapy, 64(5), e02434-19.

Zhang, W. (2021). Impact of gut microbiota diversity on tetracycline metabolism. Microbial Ecology in Health and Disease, 32(1), 190-199.

Zhang, Y., & Han, X. (2020). Gut microbiota and its role in drug pharmacokinetics. Pharmacology & Therapeutics, 204, 107295. https://doi.org/10.1016/j.pharmthera.2019.107295

Zimmermann, M. (2019). The gut microbiome as a mediator of the pharmacokinetics of drugs. Pharmacological Reviews, 71(2), 190-211.

Zimmermann, M., & Zawistowski, A. (2019). The role of the human microbiome in drug absorption and metabolism. Frontiers in Pharmacology, 10, 1254. https://doi.org/10.3389/fphar.2019.01254

Zuo, T., & Ng, S. C. (2018). The microbiome in antibiotic resistance: The next frontier in combating antibiotic resistance. Antimicrobial Resistance & Infection Control, 7, 111. https://doi.org/10.1186/s13756-018-0372-0

Downloads

Views

50

Downloads

28