Plot samples rarefaction curves(稀释性曲线)

稀释性曲线[1]是从样本中随机抽取一定数量的个体,统计这些个体所代表的物种数目,并以个体数与物种数来构建曲线。它可以用来比较测序数据量不同的样本中物种的丰富度,也可以用来说明样本的测序数据量是否合理。采用对序列进行随机抽样的方法,以抽到的序列数与它们所能代表OTU的数目构建rarefaction curve,当曲线趋向平坦时,说明测序数据量合理,更多的数据量只会产生少量新的OTU,反之则表明继续测序还可能产生较多新的OTU。因此,通过作稀释性曲线,可得出样本的测序深度情况。

输入:

OTU Table文件:

OTU ID    Bio1 Bio2 Bio3 Bio4 Bio5 Bio6 Bio7 Bio8 Bio9 Bio10

OTU1        0       0       0       0       0       6       34     104  367  254

OTU2        52     335  18     49     0       0       0       0       0       0

OTU3        0       0       0       0       5       0       0       0       0       0

其他参数默认。

输出:

各样本稀释性曲线图:

        注:横坐标:随机抽取的测序数据量;纵坐标:观测到的OTU数量。

       

       

分析模块引用了mothurv.1.35.0)的rarefaction.single命令,利用R语言(v2.12.1)制作曲线图。

相关文献如下所示:

[1]Katherine R Amato. et al. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. The ISME Journal (2013) 7, 1344–1353; doi:10.1038/ismej.

Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

The original tools:

Schloss, PD & Handelsman, J. (2006) Introducing SONS, a tool for OTU-based comparisons of membership and structure between microbial communities. Applied and Environmental Microbiology. 72:6773-9.

Schloss, PD & Handelsman, J. (2006). Introducing TreeClimber, a test to compare community structures. Applied and Environmental Microbiology. 72: 2379-84.

Schloss, PD & Handelsman, J. (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Applied and Environmental Microbiology. 71:1501-6.

Schloss, PD, Larget, BR, & Handelsman J. (2004). Integration of microbial ecology and statistics: a test to compare gene libraries. Applied and Environmental Microbiology. 70:5485-92.