病患對同種藥物反應異質性是個人化醫學所重視的問題，不但會影響病患的健康也可能造成臨床財務負擔，而腸道宏觀菌相 (gut microbiome) 檢測可以探討因人而異的用藥後差異（如：呈現不同的藥效、藥物毒性及特異性）與腸道微菌叢 (gut microbiota) 變化之關聯性。尤其，抗癌藥的雙向藥物—微生物組交互作用 (bi-directional drug–microbiome interactions) 可能成為重要研究與開發創新的治療策略。近年來，隨著次世代定序技術 (next generation sequencing, NGS) 的進步，使得總體基因組學的發展愈趨成熟，從而能夠識別和量化所有人體中存在的微生物，而有人類第二基因體之稱的腸道微菌叢，則被認為是影響藥物反應的其中因素，因此，寄望藉由調整腸道微菌叢的組成來改善藥物反應與安全性，儼然成為主要的研究目標。藥物腸道微菌組學 (pharmacogenomics) 是一個研究微菌叢變異和藥理學關聯性的新興領域，大致上，藥物（包含西藥與傳統中藥）經口服後與腸道菌叢的相互作用可分成 (1) 藥物調節腸道微菌叢的組成；(2) 藥物調節腸道微菌叢的代謝；(3) 腸道微菌叢轉化藥物代謝物。在這篇綜述中，我們回顧了藥物與腸道微菌叢之間的相互作用，以及所產生的藥物代謝產物與藥理作用的關聯性，期許未來藥物腸道微菌組學，能為量身訂做的個人化精準醫療提供重要的基礎。

Inter-individual heterogeneity in drug response is an important issue that affects patient wellbeing. It can also lead to financial burdens in clinical use. The gut microbiome can explore the relationship of intestinal microbiota variation, person-specific difference, and idiosyncrasy about drug reactions, efficacy, or toxicity. Especially, bi-directional drug–microbiome interactions of anticancer drugs may become an important research and development for innovative treatment strategies. In addition, next-generation sequencing (NGS) has been used to advance metagenomics. NGS is an excellent tool for identifying and quantifying all microorganisms present in humans. One of these microorganisms, the gut microbiomes, has also been called the second genome. This is due to the discovery that gut microbiomes have a significant influence on drug response. Therefore, the gut microbiome is an essential target for improving drug efficacy and safety. Pharmacomicrobiomics is a rising field investigating the correlation between gut microbiomes variation and pharmacology. In this review, we provide a historical overview of pharmacomicrobiomics along with an examination of current state-of-the-art knowledge on the complex interactions between gut microbiomes, hosts, and drugs. The review shows that after oral administration, medications, including traditional Chinese medicines, can interact with gut microbiome in three ways: (1) modulating the composition of gut microbiomes; (2) modifying the metabolism of gut microbiomes; (3) the biotransformation of gut microbiomes. The review shows that pharmacomicrobiomics approach will provide an important foundation in personalized and precision medicine in the future.