INTRODUCTION: It is well known that the response to and metabolism of the drugs entering the human body varies widely across individuals. One of the reasons is that such interpersonal differences may be related to gut microbes. On one hand, drugs or xenobiotics entering the human body may affect the composition of the gut microbiome; on the other hand, the gut microbiota may alter the absorption, distribution, metabolism and excretion (abbreviated as ADME) process of drugs or xenobiotics vice versa. However, the majority of studies focused on the interaction of general population cohorts with the gut microbiota, which is incompatible with the real clinic. For example, the gut microbiota is closely associated with the progression and treatment of irritable bowel syndrome, a common functional disorder of the gastrointestinal tract. Under the disease status, the composition of the gut microbiota is altered affecting the pharmacokinetics, efficacy and toxicity of xenobiotics. Concerning irritable bowel syndrome, a few studies reported that the xenobiotics administration process was gut microbial-mediated, while it also affected drug efficacy and toxicity. Thus, the correlation between gut microbiota and xenobiotics administration, especially the drugs administered, should be elucidated. METHOD: This review paper links differences between the gut microbiome and drug metabolism, which play a significant role in the implications for medical therapy and drug development in irritable bowel syndrome indications. RESULT: The human intestinal microbiota permeates the ADME process of orally administered drugs and has the potential to further modify the efficacy and toxicity of agents through the mediation of various enzymes, while at the same time, medications could also alter the composition and function of the human intestinal microbiota.