Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA.
ISME J. 2018 Aug;12(8):2011-2023. doi: 10.1038/s41396-018-0145-6. Epub 2018 May 24.
The advent of high-throughput 'omics approaches coupled with computational analyses to reconstruct individual genomes from metagenomes provides a basis for species-resolved functional studies. Here, a mutual information approach was applied to build a gene association network of a commensal consortium, in which a unicellular cyanobacterium Thermosynechococcus elongatus BP1 supported the heterotrophic growth of Meiothermus ruber strain A. Specifically, we used the context likelihood of relatedness (CLR) algorithm to generate a gene association network from 25 transcriptomic datasets representing distinct growth conditions. The resulting interspecies network revealed a number of linkages between genes in each species. While many of the linkages were supported by the existing knowledge of phototroph-heterotroph interactions and the metabolism of these two species several new interactions were inferred as well. These include linkages between amino acid synthesis and uptake genes, as well as carbohydrate and vitamin metabolism, terpenoid metabolism and cell adhesion genes. Further topological examination and functional analysis of specific gene associations suggested that the interactions are likely to center around the exchange of energetically costly metabolites between T. elongatus and M. ruber. Both the approach and conclusions derived from this work are widely applicable to microbial communities for identification of the interactions between species and characterization of community functioning as a whole.
高通量“组学”方法的出现，加上对宏基因组进行重建以获得个体基因组的计算分析，为基于物种解析的功能研究提供了基础。在这里，应用互信息方法构建了一个共生联合体的基因关联网络，其中单细胞蓝细菌Thermosynechococcus elongatus BP1 支持好氧异养菌 Meiothermus ruber 菌株 A 的生长。具体来说，我们使用相关关系的上下文似然（CLR）算法，根据代表不同生长条件的 25 个转录组数据集生成基因关联网络。由此产生的种间网络揭示了每个物种中基因之间的许多联系。虽然许多联系得到了光养生物-异养生物相互作用的现有知识和这两个物种代谢的支持，但也推断出了一些新的相互作用。这些包括氨基酸合成和摄取基因之间的联系，以及碳水化合物和维生素代谢、萜类代谢和细胞黏附基因之间的联系。对特定基因关联的进一步拓扑学检查和功能分析表明，这些相互作用可能集中在 Thermosynechococcus elongatus 和 Meiothermus ruber 之间交换能量密集型代谢物上。这种方法和由此得出的结论广泛适用于微生物群落，可用于识别物种之间的相互作用，并描述整个群落的功能。
