Skip to main content
SpringerLink
Log in

Pharmacomicrobiomics

  • Chapter
  • First Online:
Pharmacogenomics in Precision Medicine

Abstract

The safety and efficacy of drugs are the key issues in clinical treatment. Classical pharmacogenomics cannot fully explain the individual differences of drug responses. Pertinent studies indicate that intestinal microorganisms are significantly associated with the efficacy, toxicity, and adverse responses of various drugs. The Human Microbiome Project (HMP) has initiated the research of pharmacomicrobiomics, which mainly studies the interplay between drugs and microorganisms, involving drug absorption and metabolism, transport, microbial metabolites, immune regulation, ectopic and migration, etc. The pharmacomicrobiomics is an important extension and supplement of pharmacogenomics. Due to the infancy of pharmacomicrobiomics, it is urgent to clarify the relationship between human microbiome and rational drug use in clinic, which may be an important supplement to the classical pharmacogenomics. It is of great significance to put the research of pharmacomicrobiomics in the main position to fully explain the individual differences in drug responses.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Doestzada M, Vila AV, Zhernakova A et al (2018) Pharmacomicrobiomics: a novel route towards personalized medicine? Protein Cell 9(5):432–445

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Sun YZ, Zhang DH, Cai SB et al (2018) MDAD: a special resource for microbe-drug associations. Front Cell Infect Mi 8:424. https://doi.org/10.3389/fcimb.2018.00424

    Article  CAS  Google Scholar 

  3. Panebianco C, Andriulli A, Pazienza V (2018) Pharmacomicrobiomics: exploiting the drug-microbiota interactions in anticancer therapies. Microbiome 6:92. https://doi.org/10.1186/s40168-40018-40483-40167

    Article  PubMed  PubMed Central  Google Scholar 

  4. ElRakaiby M, Dutilh BE, Rizkallah MR et al (2014) Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics. OMICS 18(7):402–414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Vazquez-Baeza Y, Callewaert C, Debelius J et al (2018) Impacts of the human gut microbiome on therapeutics. Annu Rev Pharmacol 58:253–270

    Article  CAS  Google Scholar 

  6. Wilkinson EM, Ilhan ZE, Herbst-Kralovetz MM (2018) Microbiota-drug interactions: impact on metabolism and efficacy of therapeutics. Maturitas 112:53–63

    Article  CAS  PubMed  Google Scholar 

  7. Saad R, Rizkallah MR, Aziz RK (2012) Gut pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes. Gut Pathog 4:16. https://doi.org/10.1186/1757-4749-1184-1116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Ejtahed HS, Hasani-Ranjbar S, Larijani B (2017) Human microbiome as an approach to personalized medicine. Altern Ther Health Med 23(6):8–9

    PubMed  Google Scholar 

  9. Aziz RK, Hegazy SM, Yasser R et al (2018) Drug pharmacomicrobiomics and toxicomicrobiomics: from scattered reports to systematic studies of drug-microbiome interactions. Expert Opin Drug Met 14(10):1043–1055

    Article  CAS  Google Scholar 

  10. Rizkallah MR, Saad R, Aziz RK (2010) The human microbiome project, personalized medicine and the birth of pharmacomicrobiomics. Curr Pharmacogenom Personal Med 8:182–193

    Article  CAS  Google Scholar 

  11. Hornung B, dos Santos VAPM, Smidt H et al (2018) Studying microbial functionality within the gut ecosystem by systems biology. Genes Nutr 13:5. https://doi.org/10.1186/s12263-12018-10594-12266

    Article  PubMed  PubMed Central  Google Scholar 

  12. Hadrich D (2018) Microbiome research is becoming the key to better understanding health and nutrition. Front Genet 9:212. https://doi.org/10.3389/fgene.2018.00212

    Article  PubMed  PubMed Central  Google Scholar 

  13. Belizario JE, Napolitano M (2015) Human microbiomes and their roles in dysbiosis, common diseases, and novel therapeutic approaches. Front Microbiol 6:20. https://doi.org/10.1186/1476-1069X-1186-1120

    Article  Google Scholar 

  14. Ewald DR, Sumner SCJ (2018) Human microbiota, blood group antigens, and disease. Wires Syst Biol Med 10(3):e1413. https://doi.org/10.1002/wsbm.1413

    Article  Google Scholar 

  15. Almeida A, Mitchell AL, Boland M et al (2019) A new genomic blueprint of the human gut microbiota. Nature 568(7753):499–504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Choquet H, Meyre D (2010) Genomic insights into early-onset obesity. Genome Med 2:36. https://doi.org/10.1186/gm1157

    Article  PubMed  PubMed Central  Google Scholar 

  17. Goodman AL, Kallstrom G, Faith JJ et al (2011) Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. P Natl Acad Sci USA 108(15):6252–6257

    Article  CAS  Google Scholar 

  18. Serino M, Blasco-Baque V, Burcelin R (2012) Microbes on-air gut and tissue microbiota as targets in type 2 diabetes. J Clin Gastroenterol 46(9):S27–S28

    Article  PubMed  Google Scholar 

  19. Nicholson JK, Everett JR, Lindon JC (2012) Longitudinal pharmacometabonomics for predicting patient responses to therapy: drug metabolism, toxicity and efficacy. Expert Opin Drug Metab Toxicol 8(2):135–139

    Article  CAS  PubMed  Google Scholar 

  20. Balasopoulou A, Patrinos GP, Katsila T (2016) Pharmacometabolomics informs viromics toward precision medicine. Front Pharmacol 7:411. https://doi.org/10.3389/fphar.2016.00411

    Article  PubMed  PubMed Central  Google Scholar 

  21. Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R et al (2019) Mapping human microbiome drug metabolism by gut bacteria and their genes. Nature 570(7762):462–467

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Ma C, Han M, Heinrich B et al (2018) Gut microbiome-mediated bile acid metabolism regulates liver cancer via NKT cells. Science 360(6391):eaan5931. https://doi.org/10.1126/science.aan5931

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Dietert RR, Dietert JM (2015) The microbiome and sustainable healthcare. Healthcare (Basel) 3(1):100–129

    Article  Google Scholar 

  24. Snijders AM, Langley SA, Kim YM et al (2016) Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome. Nat Microbiol 2:16221

    Article  CAS  PubMed  Google Scholar 

  25. Zhernakova DV, Le TH, Kurilshikov A et al (2018) Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome. Nat Genet 50(11):1524–1532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Bouter KE, van Raalte DH, Groen AK et al (2017) Role of the gut microbiome in the pathogenesis of obesity and obesity-related metabolic dysfunction. Gastroenterology 152(7):1671–1678

    Article  CAS  PubMed  Google Scholar 

  27. Lloyd-Price J, Mahurkar A, Rahnavard G et al (2017) Strains, functions and dynamics in the expanded human microbiome project. Nature 550(7674):61–66

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Cussotto S, Clarke G, Dinan TG (2019) Psychotropics and the microbiome: a chamber of secrets… . Psychopharmacology 236(5):1411–1432

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Aagaard K, Ma J, Antony KM et al (2014) The placenta harbors a unique microbiome. Sci Transl Med 6(237):237–265

    Article  CAS  Google Scholar 

  30. Claesson MJ, Cusack S, O’Sullivan O et al (2011) Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci U S A 108:4586–4591

    Article  CAS  PubMed  Google Scholar 

  31. Liu L, Tabung FK, Zhang XH et al (2018) Diets that promote colon inflammation associate with risk of colorectal carcinomas that contain fusobacterium nucleatum. Clin Gastroenterol Hepatol 16(10):1622–1631. https://doi.org/10.1016/j.cgh.2018.1604.1030

    Article  PubMed  PubMed Central  Google Scholar 

  32. David LA, Maurice CF, Carmody RN et al (2014) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505(7484):559–563

    Article  CAS  PubMed  Google Scholar 

  33. Nogueira T, David PHC, Pothier J (2019) Antibiotics as both friends and foes of the human gut microbiome: the microbial community approach. Drug Develop Res 80(1):86–97

    Article  CAS  Google Scholar 

  34. Chen MY, Shao L, Zhang W et al (2018) Metabolic analysis of Panax notoginseng saponins with gut microbiota-mediated biotransformation by HPLC-DAD-Q-TOF-MS/MS. J Pharm Biomed Anal 150:199–207

    Article  CAS  PubMed  Google Scholar 

  35. Giuliano V, Bassotti G, Mourvaki E et al (2010) Small intestinal bacterial overgrowth and warfarin dose requirement variability. Thromb Res 126(1):12–17

    Article  CAS  PubMed  Google Scholar 

  36. Aziz RK (2018) Interview with Prof. Ramy K. Aziz, Cairo University. The dawn of pharmacomicrobiomics. OMICS 22(4):295–297

    Article  CAS  PubMed  Google Scholar 

  37. Peppercorn MA, Goldman P (1972) The role of intestinal bacteria in the metabolism of salicylazosulfapyridine. J Pharmacol Exp Ther 181(3):555–562

    CAS  PubMed  Google Scholar 

  38. Yoo DH, Kim IS, Van Le TK et al (2014) Gut microbiota-mediated drug interactions between lovastatin and antibiotics. Drug Metab Dispos 42(9):1508–1513

    Article  PubMed  CAS  Google Scholar 

  39. Matuskova Z, Anzenbacher P, Vecera R et al (2017) Effect of lactobacillus casei on the pharmacokinetics of amiodarone in male Wistar rats. Eur J Drug Metab Pharmacokinet 42(1):29–36

    Article  CAS  PubMed  Google Scholar 

  40. Maurice CF, Haiser HJ, Turnbaugh PJ (2013) Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152(1–2):39–50

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Yan AW, Fouts DE, Brandl J et al (2011) Enteric dysbiosis associated with a mouse model of alcoholic liver disease. Hepatology 53(1):96–105

    Article  CAS  PubMed  Google Scholar 

  42. Clark NP, Delate T, Riggs CS et al (2014) Warfarin interactions with antibiotics in the ambulatory care setting. JAMA Intern Med 174(3):409–416

    Article  CAS  PubMed  Google Scholar 

  43. Haiser JH, Gootenberg BG, Chatman K (2013) Predicting and manipulating cardiac drug inactivation by the human gut bacterium eggerthella lenta. Science:295–298

    Google Scholar 

  44. Wu B, Chen M, Gao Y et al (2019) In vivo pharmacodynamic and pharmacokinetic effects of metformin mediated by the gut microbiota in rats. Life Sci 226:185–192

    Article  CAS  PubMed  Google Scholar 

  45. Vétizou M, Pitt JM, Daillère R et al (2015) Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science 350(6264):1079–1084

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  46. Routy B, Chatelier EL, Derosa L et al (2018) Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors. Science 359:91–97

    Article  CAS  PubMed  Google Scholar 

  47. Stein A, Voigt W, Jordan K (2010) Chemotherapy-induced diarrhea: pathophysiology, frequency and guideline-based management. Ther Adv Med Oncol 2(1):51–63

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Higuchi K, Umegaki E, Watanabe T et al (2009) Present status and strategy of NSAIDs-induced small bowel injury. J Gastroenterol 44(9):879–888

    Article  PubMed  Google Scholar 

  49. Yip LY, Aw CC, Lee SH et al (2018) The liver-gut microbiota axis modulates hepatotoxicity of tacrine in the rat. Hepatology 67(1):282–295

    Article  CAS  PubMed  Google Scholar 

  50. Bubnov RV, Babenko LP, Lazarenko LM et al (2018) Specific properties of probiotic strains: relevance and benefits for the host. EPMA J 9(2):205–223

    Article  PubMed  PubMed Central  Google Scholar 

  51. Coskunpinar E, Islamzade F, Yilmaz EP et al (2018) The importance of fecal transplantation in personalized medicine. Bezmialem Sci 6(4):305–311

    Article  Google Scholar 

  52. Abdollahi-Roodsaz S, Abramson SB, Scher JU (2016) The metabolic role of the gut microbiota in health and rheumatic disease: mechanisms and interventions. Nat Rev Rheumatol 12(8):446–455

    Article  CAS  PubMed  Google Scholar 

  53. Tsigalou C, Stavropoulou E, Bezirtzoglou E (2018) Current insights in microbiome shifts in Sjogren’s syndrome and possible therapeutic interventions. Front Immunol 9:1106. https://doi.org/10.3389/fimmu.2018.01106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Suwal S, Wu Q, Liu WL et al (2018) The probiotic effectiveness in preventing experimental colitis is correlated with host gut microbiota. Front Microbiol 9:2675. https://doi.org/10.3389/fmicb.2018.02675

    Article  PubMed  PubMed Central  Google Scholar 

  55. Rinninella E, Raoul P, Cintoni M et al (2019) What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms 7:14. https://doi.org/10.3390/microorganisms7010014

    Article  CAS  PubMed Central  Google Scholar 

  56. Rinninella E, Mele MC, Merendino N et al (2018) The role of diet, micronutrients and the gut microbiota in age-related macular degeneration: new perspectives from the gut-retina axis. Nutrients 10(11):1677. https://doi.org/10.3390/nu10111677

    Article  CAS  PubMed Central  Google Scholar 

  57. Ju TT, Shoblak Y, Gao YH et al (2017) Initial gut microbial composition as a key factor driving host response to antibiotic treatment, as exemplified by the presence or absence of commensal Escherichia coli. Appl Environ Microb 83(17):e01107–e01117

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China

    Weihua Huang & Wei Zhang

  2. Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China

    Weihua Huang & Wei Zhang

Authors
  1. Weihua Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wei Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. School of Pharmacy, Fudan University, Shanghai, Shanghai, China

    Weimin Cai

  2. Xiangya Hospital, Central South University, Changsha, Hunan, China

    Zhaoqian Liu

  3. School of Pharmacy, Suzhou University, Suzhou, Jiangsu, China

    Liyan Miao

  4. School of Pharmacy, Fudan University, Shanghai, Shanghai, China

    Xiaoqiang Xiang

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Huang, W., Zhang, W. (2020). Pharmacomicrobiomics. In: Cai, W., Liu, Z., Miao, L., Xiang, X. (eds) Pharmacogenomics in Precision Medicine. Springer, Singapore. https://doi.org/10.1007/978-981-15-3895-7_10

Download citation

Publish with us

Policies and ethics

Search

Navigation