The gut microbiome has emerged as an important factor affecting human health and disease. The recent development of -omics approaches, including phylogenetic marker-based microbiome profiling, shotgun metagenomics, metatranscriptomics, metaproteomics, and metabolomics, has enabled efficient characterization of microbial communities. These techniques can provide strain-level taxonomic resolution of the taxa present in microbiomes, assess the potential functions encoded by the microbial community and quantify the metabolic activities occurring within a complex microbiome. The application of these meta-omics approaches to clinical samples has identified microbial species, metabolic pathways, and metabolites that are associated with the development and treatment of human diseases. These findings have further facilitated microbiome-targeted drug discovery and efforts to improve human health management. Recent in vitro and in vivo investigations have uncovered the presence of extensive drug-microbiome interactions. These interactions have also been shown to be important contributors to the disparate patient responses to treatment that are often observed during disease therapy. Therefore, developing techniques or frameworks that enable rapid screening, detailed evaluation, and accurate prediction of drug/host-microbiome interactions is critically important in the modern era of microbiome research and precision medicine. Here we review the current status of meta-omics techniques, including integrative multi-omics approaches, for characterizing the microbiome's functionality in the context of health and disease. We also summarize and discuss new frameworks for applying meta-omics approaches and microbiome assays to study drug-microbiome interactions. Lastly, we discuss and exemplify strategies for implementing microbiome-based precision medicines using these meta-omics approaches and high throughput microbiome assays.

中文翻译：

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使用元组学方法推进功能和转化微生物组学研究。

肠道微生物组已成为影响人类健康和疾病的重要因素。-组学方法的最新发展，包括基于系统发育标记的微生物组谱分析，shot弹枪宏基因组学，元转录组学，元蛋白质组学和代谢组学，已使微生物群落的有效表征成为可能。这些技术可以提供微生物组中存在的分类单元的菌株级分类学解析，评估由微生物群落编码的潜在功能，并量化复杂微生物组中发生的代谢活性。这些元组学方法在临床样品中的应用已经确定了与人类疾病的发展和治疗相关的微生物种类，代谢途径和代谢产物。这些发现进一步促进了以微生物组为靶标的药物发现，并为改善人类健康管理做出了努力。最近的体外和体内研究发现存在广泛的药物-微生物组相互作用。这些相互作用也已被证明是疾病治疗期间经常观察到的不同患者对治疗反应的重要促成因素。因此，开发能够快速筛选，详细评估和准确预测药物/宿主-微生物组相互作用的技术或框架在微生物组研究和精密医学的现代时代至关重要。在这里，我们回顾了用于描述健康和疾病背景下微生物组功能的元组学技术（包括集成的多组学方法）的现状。我们还总结并讨论了应用元组学方法和微生物组测定法研究药物-微生物组相互作用的新框架。最后，我们讨论并举例说明了使用这些组学方法和高通量微生物组测定方法实施基于微生物组的精密药物的策略。