Increasing Metagenomic Resolution of Microbiome Interactions Through Functional Phylogenomics and Bacterial Sub-Communities.
Increasing Metagenomic Resolution of Microbiome Interactions Through Functional Phylogenomics and Bacterial Sub-Communities.
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DOI：
10.3389/fgene.2016.00004
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发表时间：
2016
影响因子：
3.7
通讯作者：
Barona-Gómez F
中科院分区：
文献类型：
--
作者：
Cibrián-Jaramillo A;Barona-Gómez F
微生物组的基因组组成及其与环境的关系是生物学中一个令人兴奋的开放性问题。宏基因组学是发现以前未知的类群的有用工具，但其用于了解微生物组的功能和生态能力是有限的，直到在社区的背景下理解分类和功能。我们建议，这可以实现使用相结合的功能性基因组学和共培养为基础的实验策略，可以提高我们的能力来衡量亚社区的相互作用。功能基因组学可以识别和划分基因组，从而揭示隐藏的基因功能和具有独特进化信号的基因簇。我们可以使用一个基于亚群落种群的实验模型来测试这些基因组预测，这些亚群落种群代表了直接从环境样本中获得的多样性的一个子集。这些种群增加了对微生物组组装中驱动功能力的机制的检测，特别是来自关键类群的代谢物在群落相互作用中的作用。我们的综合方法利用宏基因组学的潜力来解决生态系统的生物学问题。
The genomic composition of the microbiome and its relationship with the environment is an exciting open question in biology. Metagenomics is a useful tool in the discovery of previously unknown taxa, but its use to understand the functional and ecological capacities of the microbiome is limited until taxonomy and function are understood in the context of the community. We suggest that this can be achieved using a combined functional phylogenomics and co-culture-based experimental strategy that can increase our capacity to measure sub-community interactions. Functional phylogenomics can identify and partition the genome such that hidden gene functions and gene clusters with unique evolutionary signals are revealed. We can test these phylogenomic predictions using an experimental model based on sub-community populations that represent a subset of the diversity directly obtained from environmental samples. These populations increase the detection of mechanisms that drive functional forces in the assembly of the microbiome, in particular the role of metabolites from key taxa in community interactions. Our combined approach leverages the potential of metagenomics to address biological questions from ecological systems.