Although enteric bacteria normally reside within the animal intestine, the ability to persist extraintestinally is an essential part of their overall lifestyle, and it might contribute to transmission between hosts. Despite this potential importance, few genetic determinants of extraintestinal growth and survival have been identified, even for the best-studied model, Escherichia coli. In this work, we thus used a genome-wide library of barcoded transposon insertions to systematically identify functional clusters of genes that are crucial for E. coli fitness in lake water. Our results revealed that inactivation of pathways involved in maintaining outer membrane integrity, nucleotide biosynthesis, and chemotaxis negatively affected E. coli growth or survival in this extraintestinal environment. In contrast, inactivation of another group of genes apparently benefited E. coli growth or persistence in filtered lake water, resulting in higher abundance of these mutants. This group included rpoS, which encodes the general stress response sigma factor, and genes encoding several other global transcriptional regulators and RNA chaperones, as well as several poorly annotated genes. Based on this co-enrichment, we identified these gene products as novel positive regulators of RpoS activity. We further observed that, despite their enhanced growth, E. coli mutants with inactive RpoS had reduced viability in lake water, and they were not enriched in the presence of the autochthonous microbiota. This highlights the duality of the general stress response pathway for E. coli growth outside the host.

中文翻译：

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控制大肠杆菌生长和在湖水中持久存在的遗传决定因素的全基因组筛选


尽管肠道细菌通常存在于动物肠道内，但在肠外持续存在的能力是其整体生活方式的重要组成部分，并且可能有助于宿主之间的传播。尽管具有这种潜在的重要性，但即使对于研究最充分的模型大肠杆菌，也很少确定肠外生长和存活的遗传决定因素。因此，在这项工作中，我们使用了条形码转座子插入的全基因组文库来系统地识别对湖水中的大肠杆菌适应性至关重要的基因功能簇。我们的结果表明，维持外膜完整性、核苷酸生物合成和趋化性相关途径的失活会对大肠杆菌在肠外环境中的生长或存活产生负面影响。相比之下，另一组基因的失活显然有利于大肠杆菌的生长或在过滤湖水中的持久性，从而导致这些突变体的丰度更高。该组包括编码一般应激反应 sigma 因子的 rpoS、编码其他几种全局转录调节因子和 RNA 伴侣的基因，以及一些注释不明确的基因。基于这种共富集，我们确定这些基因产物是 RpoS 活性的新型正调节因子。我们进一步观察到，尽管 RpoS 失活的大肠杆菌突变体生长增强，但它们在湖水中的生存能力降低，并且它们在本地微生物群存在的情况下并未富集。这凸显了大肠杆菌在宿主外生长的一般应激反应途径的双重性。