Gene essentiality is altered during polymicrobial infections. Nevertheless, most studies rely on single-species infections to assess pathogen gene essentiality. Here, we use genome-scale metabolic models (GEMs) to explore the effect of coinfection of the diarrheagenic pathogen Vibrio cholerae with another enteric pathogen, enterotoxigenic Escherichia coli (ETEC). Model predictions showed that V. cholerae metabolic capabilities were increased due to ample cross-feeding opportunities enabled by ETEC. This is in line with increased severity of cholera symptoms known to occur in patients with dual infections by the two pathogens. In vitro coculture systems confirmed that V. cholerae growth is enhanced in cocultures relative to single cultures. Further, expression levels of several V. cholerae metabolic genes were significantly perturbed as shown by dual RNA sequencing (RNAseq) analysis of its cocultures with different ETEC strains. A decrease in ETEC growth was also observed, probably mediated by nonmetabolic factors. Single gene essentiality analysis predicted conditionally independent genes that are essential for the pathogen’s growth in both single-infection and coinfection scenarios. Our results reveal growth differences that are of relevance to drug targeting and efficiency in polymicrobial infections.

中文翻译：

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整合的代谢建模，培养和转录组学解释了在与产肠毒素的大肠杆菌共感染期间霍乱弧菌的毒力增强。

基因的重要性在微生物感染过程中发生了改变。尽管如此，大多数研究还是依靠单一物种感染来评估病原体基因的必要性。在这里，我们使用基因组规模的代谢模型（GEMs）来探讨腹泻性病原性霍乱弧菌与另一种肠病原性，肠毒素性大肠杆菌（ETEC）的共同感染效果。模型预测表明，由于ETEC提供了充足的交叉喂养机会，霍乱弧菌的代谢能力得到了提高。这与已知由两种病原体双重感染的患者中霍乱症状的严重程度增加相一致。体外共培养系统证实霍乱弧菌相对于单一培养，共培养的生长得到增强。此外，如通过与不同ETEC菌株共培养的双重RNA测序（RNAseq）分析所显示的，几个霍乱弧菌代谢基因的表达水平受到了显着干扰。还观察到ETEC生长下降，可能是由非代谢因素介导的。单基因必需性分析预测了在单次感染和合并感染情况下对于病原体生长必不可少的条件独立基因。我们的研究结果表明，增长差异与药物靶向性和微生物感染效率有关。