STAMP:基于 raw counts 、简单易用的 metagenomic communities 生物学差异鉴定工具


Identifying biologically relevant differences between metagenomic communities


Motivation: Metagenomics is the study of genetic material recovered directly from environmental samples. Taxonomic and functional differences between metagenomic samples can highlight the influence of ecological factors on patterns of microbial life in a wide range of habitats. Statistical hypothesis tests can help us distinguish ecological influences from sampling artifacts, but knowledge of only the P-value from a statistical hypothesis test is insufficient to make inferences about biological relevance. Current reporting practices for pairwise comparative metagenomics are inadequate, and better tools are needed for comparative metagenomic analysis.

Results: We have developed a new software package, STAMP, for comparative metagenomics that supports best practices in analysis and reporting. Examination of a pair of iron mine metagenomes demonstrates that deeper biological insights can be gained using statistical techniques available in our software. An analysis of the functional potential of ‘Candidatus Accumulibacter phosphatis’ in two enhanced biological phosphorus removal metagenomes identified several subsystems that differ between the A.phosphatis stains in these related communities, including phosphate metabolism, secretion and metal transport.

Availability: Python source code and binaries are freely available from our website at






对 metagenome 数据进行Profiling(物种系统分类谱,taxonomy profile 以及功能谱 functional profile )是解析metagenome 数据的第一步,但是深入了解环境样本的功能以及机理的一个重要手段就是比较,并通过控制变量因素(或者自然差异条件)预测哪些因素驱动 metagenomic communities 上的变化。

现在metagenome 测序数据很容易给出物种分类和功能分类的信息并使用counts (reads数目)来进行表征, STAMP 提供比较友好的用户界面(官方提供 Windows 和 Linux 两个版本)、以及多种可选的统计策略(分为两个样本、两个分组以及多组统计等),数据可视化形式也多种多样(barplot、headtmap、PCA Plot等),Odd Ratio、 relative risk、以及差异丰度等对差异分类进行过滤, 没有生物信息学经验也可以很容易使用。



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