Plot Shannon-Wiener rarefaction curves(Shannon-Wie

Shannon-Wiener [1]是反映样本中微生物多样性的指数,利用各样本的测序量在不同测序深度时的微生物多样性指数构建曲线,以此反映各样本在不同测序数量时的微生物多样性。当曲线趋向平坦时,说明测序数据量足够大,可以反映样本中绝大多数的微生物信息。

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Shannon Wiener曲线图:

     

注:横坐标:随机抽取的测序数据量;纵坐标:对应的Shannon多样性指数。

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] Yu Wang, Hua-Fang Sheng, et al. Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags. Appl. Environ. Microbiol. 2012, 78(23):8264. DOI: 10.1128/AEM.01821-12.

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.