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d42_OMM11-SW160_HILICMSpos_20240320.cefftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10327/FILES/RAW_FILES/Batch3/DS012C_FL_OLD-C6_2_HILICMSpos_20240917.d.zipftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10327/FILES/DERIVED_FILES/Batch1/DS012A_EGH-44_feces d30_OMM11-SW160_HILICMSpos_20231016.cefftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10327/FILES/DERIVED_FILES/Batch1/DS012A_EGH-37_feces d30_OMM11-KB1_HILICMSpos_20231016.cefftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10327/FILES/DERIVED_FILES/Batch3/DS012C_Cecum_OMM12_Munich_3_HILICMSpos_20240917.cefftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10327/FILES/DERIVED_FILES/Batch1/DS012A_EGH-54_feces d30_OMM11-SW160_HILICMSpos_20231016.cefftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10327/FILES/DERIVED_FILES/Batch3/DS012C_FL_NEW_C12_1_HILICMSpos_20240917.cefftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10327/FILES/RAW_FILES/Batch3/DS012C_2805-1_OMM11-KB1_STmM2702_d42_HILICMSpos_20240917.d.zipftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10327/FILES/DERIVED_FILES/Batch3/DS012C_FL_NEW_C7_2_HILICMSpos_20240917.cefftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10327/FILES/RAW_FILES/Batch2/DS012A_EGH-15_cecum d42_OMM11-KB1_HILICMSpos_20240320.d.zipftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10327/FILES/RAW_FILES/Batch3/DS012C_2942-1_OMM11-KB1_STmM2702_d42_HILICMSpos_20240917.d.zipftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10327/FILES/DERIVED_FILES/Batch3/DS012C_FL_OLD-C6_2_HILICMSpos_20240917.cefftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10327/FILES/DERIVED_FILES/Batch1/DS012A_EGH-14_cecum d42_OMM11-KB1_HILICMSpos_20231016.cefprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS10327<p>Fructoselysine&nbsp;was identified by level-1 annotation. Commercial standards have been solubilized and acquired using the same chromatography system as the samples.</p><p>Annotation was made based on retention time, high-resolution MS and MS/MS spectra in 3 collision energies: 10, 20 and 40 eV.</p>MetaboLightsPublicLiquid Chromatography MS - positive - hilic<p>Chromatographic separation was performed by normal-phased chromatography (InfinityLab Poroshell 120 HILIC-Z, 2.1 x 150 mm, 2.7-micron pore size) using an Agilent 1200 Infinity UHPLC system and mobile phases A: H2O + 5 mM Ammonium formate + 0.1% formic acid and B: acetonitrile + 5 mM Ammonium formate + 0.1% formic acid. The column compartment was kept at 25 °C. In total 5 µL of the sample was injected at 98% B and 0.250 mL/min flow followed by: 98% B until min 3, a gradient to 70% B until min 11, a gradient to 60% B until min 12, a gradient to 5% B to min 16, remaining at 5% until min 18 before re-equilibration to 98% until min 20. Flow remained at 0.250 mL/min.</p>Gut microbiota within-host evolution enforces colonization resistance against enteric infection. 10.64898/2026.03.27.714693.Denise SelegatoEMBL Heidelbegblank sampleanimal food productreference compoundPooled Samplececumsample preparation blankfecespure substancereference compound mixmass spectrometry assay<p>For metabolite extraction, 20 µL of the homogenized supernatants were plated in a 96-well plate with 100 µL of ACN:MeOH solvent mixture in a 1:1 ratio, and 0.8 µM of the internal standards (phenylalanine-d5, tryptophan-d5, ibuprofen-d4, tolfenamic acid-d4, estriol-d3, diclofenac-d4, warfarin-d5, oxfendazole-d3, chloramphenicol-d5, nafcillin-d5 and caffeine-d9, each to a final concentration of 80 nM). Following, samples were frozen at -20 °C for 1 h to allow proteins to precipitate and centrifuged at 4500 rpm, 15 min at 4 °C. The remaining supernatant was finally aliquoted in a 96-well microtiter plates with 50 µL of samples and 50 µL of water and an additional centrifugation step at 4500 rpm for 15 min and 4 °C.</p>Mus musculusanimal food productreference compoundsolvent blanksample preparation blankPooled samplereference compound mixhttps://www.ebi.ac.uk/metabolights/MTBLS10327Marta Salvado Silva. Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU, Munich, Germany. Pettenkoferstrasse 9a, 80336, München, Germany. salvado@mvp.lmu.de. +49 89 2180 72861.Denise Selegato. Zimmermann Group, Molecular Systems Biology Unit, European Molecular Biology Laboratory. European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany. denise.selegato@embl.de. +49 1733857809.Michael Zimmermann. Zimmermann Group, European Molecular Biology Laboratory (EMBL) Heidelberg. European Molecular Biology Laboratory Meyerhofstraße 1 69117 Heidelberg Germany. michael.zimmermann@embl.de. +49 (0)6221 387 8740.Bärbel Stecher. Pettenkoferstrasse 9a, 80336, München, Germany. +49 89 2180-72948. stecher@mvp.lmu.de. Stecher@mvp.lmu.de.Simon Woelfel. Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU, Munich, Germany. Pettenkoferstrasse 9a, 80336, München, Germany. woelfel@mvp.lmu.de. +49 89 2180 951.<p>To reduce data complexity for downstream untargeted metabolomics analysis, MS1 features were extracted in profile mode with MassHunter Profinder (Agilent, version 10.0) at a signal threshold of 5000. This data is simplified such that each peak in m/z dimension is represented by a single peak in the mass spectrum. Following, MassHunter Qualitative Analysis Software (Agilent, version 10.2), and Mass Profiler Professional (Agilent, version 15.1) were used to align the converted data, generating a table of molecular features, along with their relative abundances per sample. For this, the allowed tolerances used for mass and retention times were 0.002 amu / 20 ppm and 0.3 min / 2%, respectively. The feature quantification table was further processed in R 4.4.1 using RStudio/2023.06.1. For this, data was submitted to blank removal, imputation, normalization and scaling according to established protocols.</p><p><br></p><p>Statistical analysis and plotting were performed in R 4.4.1 using RStudio/2023.06.1. Statistical significance of feature intensity differences was assessed with ANOVA (aov functionin R), and p-values were FDR-corrected for multiple hypotheses testing using the Benjamini-Hochberg procedure (p.adjust function in R with fdr parameter). Significant metabolites were selected when their intensity had a log2(fold change) &gt; 1 between conditions and a corrected p-value &lt; 0.05.</p><p><br></p><p>For validation, MassHunter Quantitative Analysis Software (Agilent, version 7.0) was used for peak integration based on the retention time and accurate high-resolution mass extracted from fructoselysine standards. Integration allowed tolerance for mass of 0.002 amu or 20 ppm and tolerance for retention time of 0.3 min.</p>OriginTissueTreatmentTimepointCommunitydenise.selegato@embl.de<p>Cecum and colonic contents of mice were homogenized by bead beating with 200 µL of zirconia beads and 500 µL of water, followed by centrifugation at 15,000 x g, for 10 min at 4 °C.</p>Metabolomicsultra-performance liquid chromatography-mass spectrometryanimal food productMus musculusuntargeted analysisAgilent 6550 Q-TOFsolvent blankPooled samplemicrobiomeAgilent 1200 Infinity UHPLCsample preparation blankreference compound mixpure substancetargeted metabolitesexperimental sampleblank samplereference compounduntargeted metabolitescecumfecesultra-performance liquid chromatography-mass spectrometryanimal food productMus musculusuntargeted analysisAgilent 6550 Q-TOFsolvent blankPooled samplemicrobiomeAgilent 1200 Infinity UHPLCsample preparation blankreference compound mixpure substancetargeted metabolitesexperimental sampleblank samplereference compounduntargeted metabolitescecumfeces<p>The qTOF (Agilent 6550) was operated in positive scanning mode (50-1500 m/z) and electrospray ionization (ESI) with the following source parameters: VCap: 3000 V, nozzle voltage: 0 V, gas temp: 225 °C; drying gas 11 L/min; nebulizer: 40 psig; sheath gas temp 225 °C; sheath gas flow 10 L/min; fragmentor 300 V and Octopole RF Vpp 450 V. Online mass calibration was performed using a second ionization source and a constant flow of reference solution (121.0508 and 922.0097 m/z).</p><p><br></p><p>Tandem mass spectrometry analysis (LC-MS/MS) was performed for fructoselysine using the chromatographic separation and source parameters described above and the targeted-MS/MS mode of the instrument with a preferred inclusion list for parent ion with 20 ppm tolerance, Iso width set to narrow width and collision energy to either 10, 20 or 40 eV.</p>fructosyl-lysinefalseGut microbiota within-host evolution enforces colonization resistance against enteric infection<p>Limited resource availability in the gut promotes competitive interactions between bacteria, which drive adaptive within-host evolution. While the role of bacterial adaptive evolution of bacterial communities has been extensively studied, its functional implications for host physiology remain unknown. Here, we show that within-host evolution of the human commensal Enterococcus faecalis confers colonization resistance to enteric Salmonella enterica serovar Typhimurium (S. Typhimurium) infection. During gut colonization, E. faecalis evolves the ability to metabolize fructoselysine, an abundant Amadori rearrangement product generated by thermal food processing. The depletion of this diet-derived nutrient prevents S. Typhimurium colonization by restricting an essential resource. This protective mechanism was conserved across independent mouse colonies and arises via diverse evolutionary trajectories, including nucleotide polymorphisms, gene amplifications, and a horizontal gene transfer event. Additionally, analysis of E. faecalis isolates from human infants revealed that adaptation to fructoselysine availability occurs in a diet-dependent manner, with isolates from formula-fed infants utilizing fructoselysine, whereas those from breast-fed infants cannot. Conclusively, our results identify an inherent microbiome-driven self-healing mechanism, wherein bacterial evolution restores colonization resistance against enteric pathogens through nutrient depletion. Understanding these evolutionary dynamics will inform microbiome-targeted approaches to prevent and treat infectious diseases by harnessing adaptive bacterial metabolism.</p>2026-08-032025-03-28MTBLS10327