Microbiome analysis involves determining the composition and function of a community of microorganisms in a particular location. For the gastroenterologist, this technology opens up a rapidly evolving set of challenges and opportunities for generating novel insights into the health of patients on the basis of microbiota characterizations from intestinal, hepatic or extraintestinal samples. Alterations in gut microbiota composition correlate with intestinal and extraintestinal disease and, although only a few mechanisms are known, the microbiota are still an attractive target for developing biomarkers for disease detection and management as well as potential therapeutic applications. In this Review, we summarize the major decision points confronting new entrants to the field or for those designing new projects in microbiome research. We provide recommendations based on current technology options and our experience of sequencing platform choices. We also offer perspectives on future applications of microbiome research, which we hope convey the promise of this technology for clinical applications.

微生物组分析涉及确定特定位置的微生物群落的组成和功能。对于肠胃病专家而言，这项技术带来了迅速发展的挑战和机遇，这些挑战和机遇基于对肠道，肝脏或肠外样本中微生物群的表征，对患者的健康产生了新颖的见解。肠道微生物群组成的改变与肠道和肠道外疾病相关，尽管只有少数机制已知，但是微生物群仍然是开发用于疾病检测和治疗以及潜在治疗应用的生物标志物的有吸引力的靶标。在本综述中，我们总结了该领域新进入者或微生物组研究新项目设计者面临的主要决策点。我们根据当前的技术选择以及我们在测序平台选择方面的经验提供建议。我们还提供了有关微生物组研究未来应用的观点，我们希望这些观点传达了该技术在临床应用中的希望。