Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt
Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt
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DOI：
10.1007/978-1-4939-8728-3_11
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发表时间：
2018-01-01
期刊：
影响因子：
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通讯作者：
Langille, Morgan G. I.
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文献类型：
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作者：
Douglas, Gavin M.;Beiko, Robert G.;Langille, Morgan G. I.
标记基因测序是一种经济高效的微生物群落分类分析方法。与宏基因组方法不同，标记基因测序不提供有关群落成员基因组中存在的功能基因的直接信息。然而，通过利用已测序基因组数量的快速增长，可以根据标记基因与参考基因组的序列相似性来推断哪些功能可能与标记基因相关。 PICRUSt 工具就是基于这个想法，可以根据输入标记基因预测功能类别丰度。简而言之，该方法需要参考系统发育，其提示对应于具有参考基因组的类群以及缺乏测序基因组的类群。然后使用改进的祖先状态重建（ASR）方法来推断没有参考基因组的类群的功能类别计数。预测被写入预先计算的文件中，这些文件可以与其他数据集交叉引用，以快速生成社区功能潜力的预测。本章将深入描述这些方法并描述如何使用 PICRUSt。
Marker-gene sequencing is a cost-effective method of taxonomically profiling microbial communities. Unlike metagenomic approaches, marker-gene sequencing does not provide direct information about the functional genes that are present in the genomes of community members. However, by capitalizing on the rapid growth in the number of sequenced genomes, it is possible to infer which functions are likely associated with a marker gene based on its sequence similarity with a reference genome. The PICRUSt tool is based on this idea and can predict functional category abundances based on an input marker gene. In brief, this method requires a reference phylogeny with tips corresponding to taxa with reference genomes as well as taxa lacking sequenced genomes. A modified ancestral state reconstruction (ASR) method is then used to infer counts of functional categories for taxa without reference genomes. The predictions are written to pre-calculated files, which can be cross-referenced with other datasets to quickly generate predictions of functional potential for a community. This chapter will give an in-depth description of these methods and describe how PICRUSt should be used.