Mass spectrometry based targeted metabolomics precisely characterized new functional metabolites that regulate biofilm formation in Escherichia coli

Highlights: • LC/TQ based targeted metabolomics method was optimized to determine 100+ key microbial metabolites. • Iron was characterized to regulate biofilm formation through the mediation of bacterial metabolism. • Five functional metabolites were identified to confer functional regulation on the biofilm formation in E. coli. Biofilms are broadly formed by diverse microorganisms under stressful environments that are basically surrounded by an EPS matrix, which enable bacterial cells to confer the resistance to the biocides, antibiotics and other invasions. Yet, biofilms cause harmful impacts in various fields, including clinical infections, food contaminations and environmental pollution. However, the mechanism of biofilm formation remains incompletely elucidated, and currently, we lack an efficient strategy to tackle these tough problems by eradicating biofilms. In the present study, we sought to decipher the mechanism of biofilm formation in Escherichia coli from metabolic perspective. By exposing bacterial cells to various concentrations of iron, we found that iron can regulate biofilm formation, and the phenotypic changes were obviously dependent on iron concentration. A functional metabolome assay was further implemented to investigate the regulatory mechanism of iron on biofilm formation; we verified that siderophores mostly account for the transportation of iron into bacterial cells. Then, the bioavailable iron was recruited by bacterial cells to direct the levels of five functional metabolites (l-tryptophan, 5′-MTA, spermidine, CMP and L-leucine), which were identified as new effectors that directly regulate biofilm formation. Taken together, this study is the first to identify five functional metabolites to efficiently regulate biofilm formation, which can be targeted to tackle the harmful impacts associated with biofilm formation in different niches.