测序技术的发展使的肠道菌群的组成和功能分析在近年来取得了长足的进步，揭示了菌群在很多人体生理活动及疾病中的重要作用。一系列的分析方法也主要针对二代测序平台发展起来，包括16S rRNA基础上的组成分析和基于鸟枪法的功能宏基因组分析等。但现在已有的测序方法和分析技术仍然有一定的进步空间，尤其是在对单核苷酸多态性，结构和拷贝数变异的分析上；一部分原因是二代测序本身读长的限制，另一部分则是分析软件的精度。我们计划利用最先进的三代测序技术弥补二代测序现有的问题，并进行方法学上的改进，使我们能够准确的挖掘在菌群内的这些深层次变异。在建立一系列高精度的参考集之后，我们将对现有的公开数据进行进一步的挖掘，分析这些深度变异的出现频率和影响它们丰度的诸多因素；以及这些深度变异在疾病中可能的作用等。我们的工作将在更精细的水平上进行菌群的组成和功能分析，以及这些变异的生物学作用及意义。

The field of gut microbiome research has benefited greatly from the recent developments of next-generation sequencing techniques, and it has become clear that gut microbiome plays a critical role in human physiology as well as diseases. A collection of methods have been developed for second generation sequencing platforms (Illumina), including 16S rRNA and functional metagenomic-based analysis. However, limited by the read length of Illumina platforms, as well as analytical methods, detailed genetic mutations including SNP, SV and CNVs have not been thoroughly investigated. Here, we propose the application of third-generation sequencing (Sequel) and complement Illumina platforms, and develop new methods to effectively identify such mutations. After building a reliable reference, we will further carry out data-mining in public data and examine the prevalence and underlying forces of those mutations; while in the disease context we'll analyse their roles in host health and disease development. Our work aims at providing in-depth information of microbiome composition and functionality, plus the biological significance of above-mentioned genetic mutations.