Our understanding of the human gut microbiome has grown exponentially. Advances in genome sequencing technologies and metagenomics analysis have enabled researchers to study microbial communities and their potential function within the context of a range of human gut related diseases and disorders. However, up until recently, much of this research has focused on characterizing the gut microbiological community structure and understanding its potential through system wide (meta) genomic and transcriptomic-based studies. Thus far, the functional output of these microbiomes, in terms of protein and metabolite expression, and within the broader context of host-gut microbiome interactions, has been limited. Furthermore, these studies highlight our need to address the issues of individual variation, and of samples as proxies. Here we provide a perspective review of the recent literature that focuses on the challenges of exploring the human gut microbiome, with a strong focus on an integrated perspective applied to these themes. In doing so, we contextualize the experimental and technical challenges of undertaking such studies and provide a framework for capitalizing on the breadth of insight such approaches afford. An integrated perspective of the human gut microbiome and the linkages to human health will pave the way forward for delivering against the objectives of precision medicine, which is targeted to specific individuals and addresses the issues and mechanisms in situ.

中文翻译：

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应对人类肠道微生物组挑战的综合多学科视角


我们对人类肠道微生物组的了解呈指数级增长。基因组测序技术和宏基因组学分析的进步使研究人员能够在一系列人类肠道相关疾病和紊乱的背景下研究微生物群落及其潜在功能。然而，直到最近，这项研究的大部分重点是通过全系统（元）基因组和转录组学研究来表征肠道微生物群落结构并了解其潜力。到目前为止，这些微生物组在蛋白质和代谢物表达方面以及在宿主-肠道微生物组相互作用的更广泛背景下的功能输出受到限制。此外，这些研究强调我们需要解决个体差异和样本作为代理的问题。在这里，我们对最近的文献进行了透视回顾，重点关注探索人类肠道微生物组的挑战，并重点关注应用于这些主题的综合视角。在此过程中，我们将进行此类研究的实验和技术挑战置于背景中，并提供一个框架来利用这些方法提供的广泛洞察力。对人类肠道微生物组及其与人类健康的联系的综合视角将为实现精准医疗的目标铺平道路，精准医疗针对特定个体并就地解决问题和机制。