Microbial communities play essential and preponderant roles in all ecosystems. Understanding the rules that govern microbial community assembly will have a major impact on our ability to manage microbial ecosystems, positively impacting, for instance, human health and agriculture. Here, I present a phylogenetically constrained community assembly principle grounded on the well-supported facts that deterministic processes have a significant impact on microbial community assembly, that microbial communities show significant phylogenetic signal, and that microbial traits and ecological coherence are, to some extent, phylogenetically conserved. From these facts, I derive a few predictions which form the basis of the framework. Chief among them is the existence, within most microbial ecosystems, of phylogenetic core groups (PCGs), defined as discrete portions of the phylogeny of varying depth present in all instances of the given ecosystem, and related to specific niches whose occupancy requires a specific phylogenetically conserved set of traits. The predictions are supported by the recent literature, as well as by dedicated analyses. Integrating the effect of ecosystem patchiness, microbial social interactions, and scale sampling pitfalls takes us to a comprehensive community assembly model that recapitulates the characteristics most commonly observed in microbial communities. PCGs' identification is relatively straightforward using high-throughput 16S amplicon sequencing, and subsequent bioinformatic analysis of their phylogeny, estimated core pan-genome, and intra-group co-occurrence should provide valuable information on their ecophysiology and niche characteristics. Such a priori information for a significant portion of the community could be used to prime complementing analyses, boosting their usefulness. Thus, the use of the proposed framework could represent a leap forward in our understanding of microbial community assembly and function.

中文翻译：

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微生物群落系统发育限制组装的概念框架。

微生物群落在所有生态系统中都发挥着重要且重要的作用。了解微生物群落组装的规则将对我们管理微生物生态系统的能力产生重大影响，例如对人类健康和农业产生积极影响。在这里，我提出了一个系统发育约束的群落组装原则，该原则基于有充分支持的事实，即确定性过程对微生物群落组装具有重大影响，微生物群落显示出显着的系统发育信号，并且微生物特征和生态一致性在某种程度上是，系统发育上保守。从这些事实中，我得出了一些预测，这些预测构成了该框架的基础。其中最主要的是大多数微生物生态系统中存在系统发育核心群（PCG），其定义为存在于给定生态系统的所有实例中的不同深度的系统发育的离散部分，并且与特定的生态位相关，其占据需要特定的系统发育一组保守的性状。这些预测得到了最新文献以及专门分析的支持。整合生态系统斑块、微生物社会相互作用和规模抽样陷阱的影响，我们得到了一个全面的群落组装模型，该模型概括了微生物群落中最常见的特征。使用高通量 16S 扩增子测序，PCG 的鉴定相对简单，随后对其系统发育、估计的核心泛基因组和组内共现进行的生物信息学分析应提供有关其生态生理学和生态位特征的有价值的信息。社区很大一部分人的此类先验信息可用于启动补充分析，从而提高其有用性。因此，所提出的框架的使用可能代表我们对微生物群落组装和功能的理解的飞跃。