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Integration of Microbial Ecology and Statistics: a Test To Compare Gene Libraries

机译：微生物生态学和统计学的整合：比较基因库的测试

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Libraries of 16S rRNA genes provide insight into the membership of microbial communities. Statistical methods help to determine whether differences in library composition are artifacts of sampling or are due to underlying differences in the communities from which they are derived. To contribute to a growing statistical framework for comparing 16S rRNA libraries, we present a computer program, ∫-LIBSHUFF, which calculates the integral form of the Cramér-von Mises statistic. This implementation builds upon the LIBSHUFF program, which uses an approximation of the statistic and makes a number of modifications that improve precision and accuracy. Once ∫-LIBSHUFF calculates the P values, when pairwise comparisons are tested at the 0.05 level, the probability of falsely identifying a significant P value is 0.098 for a study with two libraries, 0.265 for three libraries, and 0.460 for four libraries. The potential negative effects of making the multiple pairwise comparisons necessitate correcting for the increased likelihood that differences between treatments are due to chance and do not reflect biological differences. Using ∫-LIBSHUFF, we found that previously published 16S rRNA gene libraries constructed from Scottish and Wisconsin soils contained different bacterial lineages. We also analyzed the published libraries constructed for the zebrafish gut microflora and found statistically significant changes in the community during development of the host. These analyses illustrate the power of ∫-LIBSHUFF to detect differences between communities, providing the basis for ecological inference about the association of soil productivity or host gene expression and microbial community composition.
机译：16S rRNA基因文库提供了微生物群落成员的见解。统计方法有助于确定图书馆组成的差异是抽样的产物还是归因于其来源社区的根本差异。为了为不断发展的用于比较16S rRNA文库的统计框架做出贡献，我们提出了一个计算机程序∫-LIBSHUFF，它计算Cramér-vonMises统计信息的积分形式。此实现建立在LIBSHUFF程序的基础上，该程序使用了统计量的近似值，并进行了许多修改，以提高精度和准确性。一旦∫-LIBSHUFF计算出P值，当在0.05水平上进行成对比较测试时，对于具有两个文库的研究，错误地识别出明显的P值的可能性为0.098，对于三个文库，则为0.265，对于四个文库，则为0.460。进行多次成对比较的潜在负面影响必须纠正治疗之间差异是由于偶然因素而无法反映生物学差异的可能性增加。使用∫-LIBSHUFF，我们发现以前发布的从苏格兰和威斯康星州土壤构建的16S rRNA基因文库包含不同的细菌谱系。我们还分析了为斑马鱼肠道菌群构建的已发布文库，并在宿主发育过程中发现了社区中的统计学显着变化。这些分析说明了∫-LIBSHUFF能够检测群落之间的差异，为生态推断有关土壤生产力或宿主基因表达与微生物群落组成之间的关系提供了基础。

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