Variability in disease presentation, progression and treatment response has been a central challenge in medicine. Although variability in host factors and genetics are important, it has become evident that the gut microbiome, with its vast genetic and metabolic diversity, must be considered in moving towards individualized treatment. In this Review, we discuss six broad disease groups: infectious disease, cancer, metabolic disease, cardiovascular disease, autoimmune or inflammatory disease, and allergic and atopic diseases. We highlight current knowledge on the gut microbiome in disease pathogenesis and prognosis, efficacy, and treatment-related adverse events and its promise for stratifying existing treatments and as a source of novel therapies. The Review is not meant to be comprehensive for each disease state but rather highlights the potential implications of the microbiome as a tool to individualize treatment strategies in clinical practice. Although early, the outlook is optimistic but challenges need to be overcome before clinical implementation, including improved understanding of underlying mechanisms, longitudinal studies with multiple data layers reflecting gut microbiome and host response, standardized approaches to testing and reporting, and validation in larger cohorts. Given progress in the microbiome field with concurrent basic and clinical studies, the microbiome will likely become an integral part of clinical care within the next decade.

疾病表现、进展和治疗反应的变异性一直是医学面临的主要挑战。尽管宿主因素和遗传学的变异性很重要，但很明显，在走向个体化治疗时必须考虑具有巨大遗传和代谢多样性的肠道微生物组。在这篇综述中，我们讨论了六大类疾病：传染病、癌症、代谢疾病、心血管疾病、自身免疫或炎症性疾病以及过敏和特应性疾病。我们重点介绍肠道微生物组在疾病发病机制和预后、疗效和治疗相关不良事件方面的最新知识，及其对现有治疗方法分层和作为新疗法来源的前景。该综述并不是针对每种疾病状态进行全面的评估，而是强调微生物组作为临床实践中个体化治疗策略工具的潜在影响。虽然前景乐观，但在临床实施之前需要克服挑战，包括提高对潜在机制的理解、反映肠道微生物组和宿主反应的多个数据层的纵向研究、标准化的测试和报告方法以及在更大队列中的验证。鉴于微生物组领域在基础和临床研究方面取得的进展，微生物组很可能在未来十年内成为临床护理不可或缺的一部分。