Thank you for visiting nature. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser or turn off compatibility mode in Internet Explorer. In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. 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 bacterial species is mined for markers showing specificity at different phylogenetic levels. Using a univariate statistical analysis method, we determine 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 as faecal samples.
To demonstrate the MS method-agnostic nature, samples are analysed using spatial metabolomics and traditional bulk-based metabolomics approaches. Rapid and reliable detection and identification of bacteria are crucial for clinical diagnosis, personalised medicine, and prevention of treatment resistance 1.
Additionally, these techniques are limited by the availability of commercial culturing media to detect unknown and difficult-to-cultivate bacterial species 2 , 3 , 5. However, while the identification process itself is faster, MALDI-MS-based analysis suffers from the same time-consuming isolation step as traditional approaches.
