: Start: 1% B, 2 min: 1% B, 20 min: 100% B, 25 min: 100% B, 30 min: 1% B. Whole metabolome samples were analyzed by quadrupole time-of-flight mass spectrometry on a Bruker Daltonics maXis HD QTof instrument using electrospray ionization in positive and negative modes. Raw data of the metabolome study were exported as mzXML.data and analysed using XCMSonline \[<https://xcmsonline.scripps.edu/>\] and Bruker Daltonics DataAnalysis software. Standard parameters for XCMSonline were used for further data analysis if not specified otherwise. Feature detection was performed using the CentWave algorithm and a maximum tolerated m/z deviation in consecutive scans at 5 ppm. Retention time correction was performed using the obiwarb algorithm (1 m/z step wise). Accurate masses were obtained by internal calibration using a sodium formiate cluster and lock mass calibration.

Statistically significant regulated features were searched against the METLIN (<https://metlin.scripps.edu/>) metabolite database and the *E. coli* metabolome database (ECMDB, <http://ecmdb.ca/>). Metabolite identifications were achieved by matching the retention time, MS and MS/MS fragmentation pattern of each feature of interest to an in-house library of 600 metabolites as pure chemical standards. For lipids, one chemical standard per lipid class was used as the basis for assigning the MS2 spectra and/or comparison to online databases. Metabolites which were identified by pure chemical standards are marked as red in the Supplementary Dataset [S1](#MOESM4){ref-type="media"}. Features which could not be identified with the in-house library were putatively identified by matching the exact mass and MS/MS fragmentation pattern to open-source MS/MS libraries like ECMDB and METLIN DB, or to theoretical MS/MS fragmentation patterns generated by MetFrag \[http://msbi.ipb-halle.de/MetFrag/\].

Derivatisation of GC-MS samples {#Sec10}
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The polar phases of GC-MS samples were derivatized with 40 µl methoxyamine/pyridine sol