Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset.
Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset.
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DOI：
10.1186/2042-5783-1-4
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发表时间：
2011-06-14
期刊：
影响因子：
--
通讯作者：
Gilbert JA
中科院分区：
文献类型：
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作者：
Larsen PE;Collart FR;Field D;Meyer F;Keegan KP;Henry CS;McGrath J;Quinn J;Gilbert JA
世界上的海洋是各种微生物的家园，它们的代谢活动有助于推动地球的地球化学循环。宏基因组分析彻底改变了我们对这些社区的访问，提供了微生物群落相互作用的系统规模视角。然而，虽然宏基因组测序可以提供环境之间或随着时间的推移特定基因和分类群丰度的相对变化的有用估计，但这并没有调查不同代谢物的生产或消耗的相对变化。我们提出了一种方法，预测相对代谢周转率（PRMT），定义并实现从宏基因组推断的代谢空间的探索。我们对西英吉利海峡时间序列研究的宏基因组数据的分析表明，预测的相对代谢周转与测量环境参数丰度的季节性变化以及观察到的细菌种群结构的季节性变化之间存在相当大的相关性。PRMT方法成功地应用于宏基因组数据，探索西英吉利海峡微生物代谢组，以产生特定的，生物学上可检验的假设。产生的假说将有机磷酸盐的利用与Gammaproteobacteria、Plantcomycetes和Betaproteobacteria联系起来，将几丁质降解与放线菌联系起来，并将潜在的小分子生物合成途径与LentiSphaeora、Chlamyphaeora和Crenarchaeota联系起来。PRMT方法可以作为一种通用工具，用于分析额外的宏基因组或转录组数据集。
The world's oceans are home to a diverse array of microbial life whose metabolic activity helps to drive the earth's biogeochemical cycles. Metagenomic analysis has revolutionized our access to these communities, providing a system-scale perspective of microbial community interactions. However, while metagenome sequencing can provide useful estimates of the relative change in abundance of specific genes and taxa between environments or over time, this does not investigate the relative changes in the production or consumption of different metabolites. We propose a methodology, Predicted Relative Metabolic Turnover (PRMT) that defines and enables exploration of metabolite-space inferred from the metagenome. Our analysis of metagenomic data from a time-series study in the Western English Channel demonstrated considerable correlations between predicted relative metabolic turnover and seasonal changes in abundance of measured environmental parameters as well as with observed seasonal changes in bacterial population structure. The PRMT method was successfully applied to metagenomic data to explore the Western English Channel microbial metabalome to generate specific, biologically testable hypotheses. Generated hypotheses linked organic phosphate utilization to Gammaproteobactaria, Plantcomycetes, and Betaproteobacteria, chitin degradation to Actinomycetes, and potential small molecule biosynthesis pathways for Lentisphaerae, Chlamydiae, and Crenarchaeota. The PRMT method can be applied as a general tool for the analysis of additional metagenomic or transcriptomic datasets.