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Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach

机译：宏基因组学知识与综合系统生态学方法推定的细菌相互作用

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Abstract Following the trend of studies that investigate microbial ecosystems using different metagenomic techniques, we propose a new integrative systems ecology approach that aims to decipher functional roles within a consortium through the integration of genomic and metabolic knowledge at genome scale. For the sake of application, using public genomes of five bacterial strains involved in copper bioleaching: Acidiphilium cryptum , Acidithiobacillus ferrooxidans , Acidithiobacillus thiooxidans , Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans , we first reconstructed a global metabolic network. Next, using a parsimony assumption, we deciphered sets of genes, called Sets from Genome Segments (SGS), that (1) are close on their respective genomes, (2) take an active part in metabolic pathways and (3) whose associated metabolic reactions are also closely connected within metabolic networks. Overall, this SGS paradigm depicts genomic functional units that emphasize respective roles of bacterial strains to catalyze metabolic pathways and environmental processes. Our analysis suggested that only few functional metabolic genes are horizontally transferred within the consortium and that no single bacterial strain can accomplish by itself the whole copper bioleaching. The use of SGS pinpoints a functional compartmentalization among the investigated species and exhibits putative bacterial interactions necessary for promoting these pathways.
机译：摘要跟随使用不同宏基因组学技术研究微生物生态系统的研究趋势，我们提出了一种新的集成系统生态学方法，旨在通过在基因组规模上整合基因组和代谢知识来破译财团中的功能角色。为了便于应用，我们使用了五个涉及铜生物浸出的细菌菌株的公共基因组：嗜酸隐孢子虫，酸性氧化铁硫杆菌，氧化硫硫酸杆菌，铁钩端螺旋体和热硫氧化硫杆菌，我们首先重建了一个全球代谢网络。接下来，使用简约假设，我们破译了称为基因组区段（SGS）的基因集，这些基因集（1）分别位于各自的基因组上，（2）活跃于代谢途径，（3）其相关代谢代谢网络中的反应也密切相关。总体而言，此SGS范例描绘了基因组功能单元，这些功能单元强调了细菌菌株在催化代谢途径和环境过程中的各自作用。我们的分析表明，只有少数功能代谢基因在财团内水平转移，并且没有任何细菌菌株能够独自完成整个铜的生物浸出。 SGS的使用可精确指出所研究物种之间的功能区分开，并显示出促进这些途径所必需的假定细菌相互作用。

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