Cairns Johannes, Jokela Roosa, Hultman Jenni, Tamminen Manu, Virta Marko, Hiltunen Teppo
Department of Microbiology, University of Helsinki, Helsinki, Finland.
Department of Biology, University of Turku, Turku, Finland.
Front Genet. 2018 Aug 14;9:312. doi: 10.3389/fgene.2018.00312. eCollection 2018.
Experimental microbial ecology and evolution have yielded foundational insights into ecological and evolutionary processes using simple microcosm setups and phenotypic assays with one- or two-species model systems. The fields are now increasingly incorporating more complex systems and exploration of the molecular basis of observations. For this purpose, simplified, manageable and well-defined multispecies model systems are required that can be easily investigated using culturing and high-throughput sequencing approaches, bridging the gap between simpler and more complex synthetic or natural systems. Here we address this need by constructing a completely synthetic 33 bacterial strain community that can be cultured in simple laboratory conditions. We provide whole-genome data for all the strains as well as metadata about genomic features and phenotypic traits that allow resolving individual strains by amplicon sequencing and facilitate a variety of envisioned mechanistic studies. We further show that a large proportion of the strains exhibit coexistence in co-culture over serial transfer for 48 days in the absence of any experimental manipulation to maintain diversity. The constructed bacterial community can be a valuable resource in future experimental work.
实验微生物生态学和进化利用简单的微观系统设置以及针对一或两种物种的模型系统进行的表型分析，已经对生态和进化过程产生了基础性的见解。现在，这些领域越来越多地纳入更复杂的系统，并探索观察结果的分子基础。为此，需要简化、易于管理且定义明确的多物种模型系统，这些系统可以使用培养和高通量测序方法轻松进行研究，从而弥合简单与更复杂的合成或自然系统之间的差距。在这里，我们通过构建一个可以在简单实验室条件下培养的完全合成的33种细菌菌株群落来满足这一需求。我们提供了所有菌株的全基因组数据以及有关基因组特征和表型性状的元数据，这些数据能够通过扩增子测序分辨各个菌株，并有助于开展各种设想的机理研究。我们进一步表明，在没有任何实验操作来维持多样性的情况下，很大一部分菌株在连续传代共培养48天的过程中表现出共存。构建的细菌群落可能会成为未来实验工作中的宝贵资源。
