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 (e.g., human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified natural Caenorhabditis elegans microbiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of the C. elegans 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 C. elegans.

通过测序对微生物组进行的研究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的大量相关性。然而，即使在简单的生物体中，微生物组的复杂组成也常常阻碍从相关性推断因果关系。合成群落提供了一种推断宿主微生物系统中因果关系的有效方法。然而，现有的群落存在一些缺点，例如微生物的人工（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）或宿主缺乏遗传易处理性。在这里，我们介绍 CeMbio，这是一种简化的天然秀丽隐杆线虫微生物群，源自我们之前对该线虫天然微生物组的荟萃分析。CeMbio 资源适用于线虫模型系统的所有优势，所包含的菌株易于培养，它们都单独定植于蠕虫肠道，并构成一个强大的群落，明显影响线虫的生活史。另外还为 CeMbio 菌株开发了多种工具，包括诊断 PCR 引物、完全测序的基因组和代谢网络模型。通过 CeMbio，我们提供了多功能资源和工具箱，用于深入剖析线虫中自然相关的宿主-微生物组相互作用。