• 四种研究方法依次是:比较方法用来分析进化上不同起源的微生物之间的多种表型差异;
  • 祖传表型推断基于物种进化史和亲缘关系推断共祖群体的共有表型;
  • 系统发育参数通过构建具有生物学意义的变量简化或概括群落特征;
  • 还可结合亲缘关系描述样本间距,用于样本聚类、拟合等;
  • 此类分析基于物种间的系统发生关系,受所选基因、基因水平转移等因素影响很大;
  • 必须小心选择研究问题和研究假设,具体可参考作者在线提供的实战教程。
复杂菌群中的个体并非是孤立存在的,而是具有一定亲缘关系的。因此,在分析菌群表型时理应将物种之间的系统发育信息考虑进来。Nature Microbiology上的这篇综述总结出4种不同的研究问题和分析方法,更在网站上在线提供了具体分析流程,是进行菌群数据系统发育分析时非常有价值的参考材料。

Methods for phylogenetic analysis of microbiome data



2018-05-24, Review

Abstract & Authors:展开

How does knowing the evolutionary history of microorganisms affect our analysis of microbiological datasets? Depending on the research question, the common ancestry of microorganisms can be a source of confounding variation, or a scaffolding used for inference. For example, when performing regression on traits, common ancestry is a source of dependence among observations, whereas when searching for clades with correlated abundances, common ancestry is the scaffolding for inference. The common ancestry of microorganisms and their genes are organized in trees—phylogenies—which can and should be incorporated into analyses of microbial datasets. While there has been a recent expansion of phylogenetically informed analytical tools, little guidance exists for which method best answers which biological questions. Here, we review methods for phylogeny-aware analyses of microbiome datasets, considerations for choosing the appropriate method and challenges inherent in these methods. We introduce a conceptual organization of these tools, breaking them down into phylogenetic comparative methods, ancestral state reconstruction and analysis of phylogenetic variables and distances, and provide examples in Supplementary Online Tutorials. Careful consideration of the research question and ecological and evolutionary assumptions will help researchers choose a phylogeny and appropriate methods to produce accurate, biologically informative and previously unreported insights.

First Authors:
Alex D Washburne,James T Morton

Correspondence Authors:
Alex D Washburne

All Authors:
Alex D Washburne,James T Morton,Jon Sanders,Daniel Mcdonald,Qiyun Zhu,Angela M Oliverio,Rob Knight