Nutrient environment drives strain-specific remodelling of Escherichia coli lipidomes

ABSTRACT: Background/Objectives: Escherichia coli causes more than 2.8 million infections annually and is widely used as a model organism. Despite its importance, strain-level and handling differences in E. coli lipidomes remain poorly defined. Lipid composition can reveal membrane organization, metabolic state, and strain-specific features, but measured lipidomes depend strongly on experimental design. This study aimed to characterize the lipidomes of reference and pathogenic E. coli strains and to determine how sample handling and growth conditions influence their interpretation. Methods: Three E. coli strains (ATCC 25922, O127:H6, and O157:H7) were grown in minimal (M9) and rich (tryptic soy) media to late stationary phase. Lipids were extracted from bacterial pellets using direct extraction or a methanol-based quenching strategy and analyzed by reversed-phase LC–MS/MS. Statistical analysis included uni- and multivariate testing, along with evaluation of coordinated changes across lipid classes. Results: Methanol-based quenching altered lipid composition, increasing lysophospholipids and phosphatidylalcohols and shifting quinone balance, without improving reproducibility. Direct extraction minimized variability and preserved lipid composition. The growth medium defined the lipidome structure, with tryptic soy broth increasing phospholipid abundance while minimal medium constrained composition and increased remodelling-associated species. Pathogenic strains exhibited distinct lipidomic profiles, including increased cardiolipin and phosphatidic acid, elevated LPE/PE ratios, reduced diacylglycerol levels, and depletion of prenol lipids. Conclusions: The observed E. coli lipidome is defined by experimental design, with sample handling and growth medium constraining the measurable lipid space within which strain-specific differences emerge. These findings establish a context for the design and interpretation of lipidomics experiments across bacterial strains.

INSTRUMENT(S): Liquid Chromatography MS - negative - reverse-phase

PROVIDER: MTBLS14565 | MetaboLights | 2026-09-23

REPOSITORIES: MetaboLights