Department of Evolutionary Ecology and Genetics, Christian-Albrechts University, Kiel, Germany.
Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston TX.
G3 (Bethesda). 2020 Sep 2;10(9):3025-3039. doi: 10.1534/g3.120.401309.
The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships in host-microbiome systems. Yet the available communities suffer from several drawbacks, such as artificial (thus non-natural) choice of microbes, microbe-host mismatch (, human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified natural microbiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of the model system, strains included are readily culturable, they all colonize the worm gut individually, and comprise a robust community that distinctly affects nematode life-history. Several tools have additionally been developed for the CeMbio strains, including diagnostic PCR primers, completely sequenced genomes, and metabolic network models. With CeMbio, we provide a versatile resource and toolbox for the in-depth dissection of naturally relevant host-microbiome interactions in .
通过测序研究微生物组，揭示了微生物群落组成与相应宿主物种的各种生活史特征之间存在大量相关性。然而，即使在简单的生物体中，从相关性推断因果关系通常也受到微生物组组成复杂性的阻碍。合成群落为推断宿主-微生物组系统中的因果关系提供了一种有效的方法。然而，现有的群落存在几个缺点，例如微生物的人为（因此非自然）选择、微生物-宿主不匹配（例如，无菌小鼠中的人类微生物）或缺乏遗传可操作性的宿主。在这里，我们介绍了 CeMbio，这是一种简化的天然微生物组，源自我们之前对这种线虫天然微生物组的荟萃分析。CeMbio 资源适用于该模型系统的所有强度，包括的菌株都容易培养，它们都可以单独定植在蠕虫肠道中，并构成一个稳健的群落，明显影响线虫的生活史。此外，还为 CeMbio 菌株开发了几种工具，包括诊断性 PCR 引物、完全测序的基因组和代谢网络模型。通过 CeMbio，我们提供了一个多功能的资源和工具包，用于深入剖析线虫中自然相关的宿主-微生物组相互作用。
