biostudies-literatureChen WCancer Research UKDeutsche Forschungsgemeinschaft (German Research Foundation)National Institute for Health Research (NIHR)China Scholarship Council (CSC)165https://www.ebi.ac.uk/biostudies/studies/S-EPMC11697447biostudies-literatureUnknown16(1)Fast and reliable identification of bacteria directly in clinical samples is a critical factor in clinical microbiological diagnostics. Current approaches require time-consuming bacterial isolation and enrichment procedures, delaying stratified treatment. Here, we describe a biomarker-based strategy that utilises bacterial small molecular metabolites and lipids for direct detection of bacteria in complex samples using mass spectrometry (MS). A spectral metabolic library of 233 bacterial species is mined for markers showing specificity at different phylogenetic levels. Using a univariate statistical analysis method, we determine 359 so-called taxon-specific markers (TSMs). We apply these TSMs to the in situ detection of bacteria using healthy and cancerous gastrointestinal tissues as well aNature communicationsUniversal, untargeted detection of bacteria in tissues using metabolomics workflows.PMC11697447P64610505372148ICL BRC Molecular Phenomics202208320033C52720/A25038CRC1182Ramonaite TJanßen KPKinross JQiu MLiebeke MGoldin RDRebec MZborovsky LMcKenzie JSChen WPaizs PStrittmatter NSadowski MMejias-Luque RTakats ZfalseUniversal, untargeted detection of bacteria in tissues using metabolomics workflows.Fast and reliable identification of bacteria directly in clinical samples is a critical factor in clinical microbiological diagnostics. Current approaches require time-consuming bacterial isolation and enrichment procedures, delaying stratified treatment. Here, we describe a biomarker-based strategy that utilises bacterial small molecular metabolites and lipids for direct detection of bacteria in complex samples using mass spectrometry (MS). A spectral metabolic library of 233 bacterial species is mined for markers showing specificity at different phylogenetic levels. Using a univariate statistical analysis method, we determine 359 so-called taxon-specific markers (TSMs). We apply these TSMs to the in situ detection of bacteria using healthy and cancerous gastrointestinal tissues as well a2025-01-01T00:00:00Z2025 Jan2025-04-04T12:02:22.918Z2025-04-04T12:02:22.918ZS-EPMC116974473974703910.1038/s41467-024-55457-7