Escherichia coli and Shigella spp. causing illnesses in humans represent a genotypically and phenotypically diverse group of pathogens. Although E. coli diversity has been studied by comparative genomics, the intra‐species variation at the proteome level is currently unknown. The proteomes of 16 pathogenic E. coli, 2 non‐pathogenic E. coli, and 5 Shigella strains originating from 18 phylogenetic lineages are investigated. By applying label‐free quantitative proteomics on trypsin‐digested cell extracts from bacteria grown on blood agar, 4018 proteins are detected, 3285 of which arequantified, and 261 represented virulence factors. Of 753 proteins quantified in all strains, the levels of 153 vary substantially between strains and are functionally associated mostly with stress response and peripheral metabolism. The levels of proteins associated with the central metabolism vary considerably less than the levels of proteins from other metabolic pathways. Hierarchical clustering analysis based on the protein levels results in strains grouping that differ from that obtained by gene‐based phylogenetic analysis. Finally, strains of some E. coli pathotypes have more similar protein profiles even when the strains are not genetically closely related. The results suggest that the degree of genetic relatedness may not necessarily be a good predictor of E. coli phenotypic characteristics.

中文翻译：

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致病性大肠杆菌和志贺氏菌的不同代谢特征。由无标记定量蛋白质组学测定

大肠杆菌和志贺氏菌属。导致人类疾病的病原体代表了一组基因型和表型多样的病原体。尽管已经通过比较基因组学研究了大肠杆菌的多样性，但蛋白质组水平的种内变异目前尚不清楚。16 种致病性大肠杆菌、2 种非致病性大肠杆菌和 5 种志贺氏菌的蛋白质组研究了源自 18 个系统发育谱系的菌株。通过对血琼脂上生长的细菌的胰蛋白酶消化细胞提取物应用无标记定量蛋白质组学，检测到 4018 种蛋白质，其中 3285 种被量化，261 种代表毒力因子。在所有菌株中量化的 753 种蛋白质中，153 种蛋白质的水平在菌株之间差异很大，并且在功能上主要与应激反应和外周代谢相关。与来自其他代谢途径的蛋白质水平相比，与中央代谢相关的蛋白质水平变化要小得多。基于蛋白质水平的分层聚类分析导致菌株分组与通过基于基因的系统发育分析获得的不同。最后，一些大肠杆菌菌株即使菌株在遗传上没有密切关系，致病型也具有更多相似的蛋白质谱。结果表明，遗传相关程度不一定是大肠杆菌表型特征的良好预测指标。