In the current study, metabolic genes and networks that influence the persistence of pathogenic Escherichia coli O104:H4 strain C227/11Φcu in agricultural soil microenvironments at low temperature were investigated. The strain was incubated in alluvial loam (AL) and total RNA was prepared from samples at time point 0, and after 1 and 4 weeks. Differential transcriptomic analysis was performed by RNA sequencing analysis and values obtained at weeks 1 and 4 were compared to those of time point 0. We found differential expression of more than 1500 genes for either time point comparison. The two lists of differentially expressed genes were then subjected to gene set enrichment of Gene Ontology terms. In total, 17 GO gene sets and 3 Pfam domains were found to be enriched after 1 week. After 4 weeks, 17 GO gene sets and 7 Pfam domains were statistically enriched. Especially stress response genes and genes of the primary metabolism were particularly affected at both time points. Genes and gene sets for uptake of carbohydrates, amino acids were strongly upregulated, indicating adjustment to a low nutrient environment. The results of this transcriptome analysis show that persistence of C227/11Φcu in soils is associated with a complex interplay of metabolic networks.

中文翻译：

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低温土壤微环境中大肠杆菌 O104:H4 菌株 C227/11Φcu 代谢基因的广泛时间依赖性转录活性

在当前的研究中，研究了影响致病性大肠杆菌O104:H4菌株C227/11Φcu在低温农业土壤微环境中持久存在的代谢基因和网络。将菌株在冲积壤土 (AL) 中孵育，并在时间点 0 以及 1 周和 4 周后从样品中制备总 RNA。通过 RNA 测序分析进行差异转录组分析，并将第 1 周和第 4 周获得的值与时间点 0 的值进行比较。我们发现任一时间点比较都有超过 1500 个基因的差异表达。然后对差异表达基因的两个列表进行基因本体术语的基因集富集。总共发现 17 个 GO 基因集和 3 个 Pfam 结构域在 1 周后富集。4 周后，17 个 GO 基因集和 7 个 Pfam 结构域在统计上得到富集。尤其是应激反应基因和初级代谢基因在这两个时间点都受到特别影响。摄取碳水化合物、氨基酸的基因和基因组强烈上调，表明对低营养环境的调整。该转录组分析的结果表明，C227/11Φcu 在土壤中的持久存在与代谢网络的复杂相互作用有关。