Synthesis-driven reverse metabolomics reveals 3-hydroxy N-acyl amides as gut microbial molecules
9 affiliations
- 1Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
- 2Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, California, USA
- 3Department of Chemistry and Biochemistry, University of California San Diego, Gilman Drive, La Jolla, California, USA
- 4Department of Psychiatry, University of California San Diego, Gilman Drive, La Jolla, California, USA
- 5Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- 6Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- 7Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- 8Program in Materials Science and Engineering, University of California, San Diego, Gilman Drive, La Jolla, California, USA
- 9Soil Health Center, Scripps Institution of Oceanography, University of California San Diego, Gilman Drive, La Jolla, California, USA
Abstract
3-Hydroxy N-acyl amides are bioactive lipids with reported anti-obesity and glucose-regulating effects, yet they are rarely detected in untargeted metabolomics studies because they are largely absent from existing spectral reference libraries. To address this gap, we synthesized an MS/MS spectral resource comprising 436 structurally diverse 3-hydroxy N-acyl amides, spanning 3- to 18-carbon chains with a wide range of amine headgroups, such as ornithine, valine, and dopamine. Using a synthesis-driven reverse metabolomics approach, we found 161,626 spectral matches across 54,744 publicly available files in untargeted metabolomics data sets, revealing widespread occurrences in biological samples, including human-derived specimens. Of these molecules detected through MS/MS spectral matching, 334 represent newly reported biological entities. We further confirmed their presence in human saliva, stool, and skin using retention time and ion mobility measurements. Frequent detection in microbial data sets and validation in communities of human-derived gut bacteria support microbial production. Several metabolites also showed altered abundance in individuals with diabetes mellitus, showing that this lipid class is modulated in human metabolic disease. Together, these findings establish 3-hydroxy N-acyl amides as a distinct and biologically relevant lipid class, and the accompanying MS/MS spectral resource will enable their broader recognition and study in untargeted metabolomics data.
IMPORTANCE: Microbe-host interactions lead to the production of metabolites that play an important role in human health and disease, though the annotation of such metabolites remains scarce. We created a re-usable MS/MS spectral library of an underrepresented class of compounds—3-hydroxy N-acyl amides. Our study characterized the presence of over 400 3-hydroxy N-acyl amides among thousands of public untargeted metabolomics datasets. We found over 100,000 instances of these metabolites within microbial, plant, and animal data, and used orthogonal validation methods to confirm nine previously unreported molecules within human feces, saliva, and skin samples. We cultured communities of human-derived gut bacteria and found evidence of bacterial production of four 3-hydroxy N-acyl amides. Our results suggest that these metabolites play important roles in human metabolism and disease, and sharing this curated resource enables the detection of these metabolites in future studies.
Related
- Metabolomics in microbiology: interrogating microbial physiology and interactions
- Whole blood metabolomics reveals coordinated redox-one-carbon axis disruption in NSCLC: a pilot study in an Indian cohort
- A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer’s disease mouse models
- Combined metabolomics and microbiota analysis reveals the therapeutic effect of indole-3-propionic acid on ovariectomy-induced osteoporosis
- Integrated Serum and Spatial Metabolomics Reveals Compartmentalized Metabolic Reprogramming and Ferroptosis Susceptibility in Nasopharyngeal Carcinoma
BibTeX
@article{deleray2026synthesisdriven,
title = {{Synthesis-driven reverse metabolomics reveals 3-hydroxy N-acyl amides as gut microbial molecules}},
author = {Victoria Deleray and Vincent Charron-Lamoureux and Kyle Vittali and Helena Mannochio-Russo and Crystal X. Wang and Corinn Walker and Karsten Zengler and Dionicio Siegel and Pieter C. Dorrestein},
journal = {mSystems},
year = {2026},
month = sep,
doi = {10.1128/msystems.00839-26},
url = {https://doi.org/10.1128/msystems.00839-26},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Synthesis-driven reverse metabolomics reveals 3-hydroxy N-acyl amides as gut microbial molecules
AU - Victoria Deleray
AU - Vincent Charron-Lamoureux
AU - Kyle Vittali
AU - Helena Mannochio-Russo
AU - Crystal X. Wang
AU - Corinn Walker
AU - Karsten Zengler
AU - Dionicio Siegel
AU - Pieter C. Dorrestein
PY - 2026
DA - 2026/09/24
JO - mSystems
DO - 10.1128/msystems.00839-26
UR - https://doi.org/10.1128/msystems.00839-26
AB - 3-Hydroxy N-acyl amides are bioactive lipids with reported anti-obesity and glucose-regulating effects, yet they are rarely detected in untargeted metabolomics studies because they are largely absent from existing spectral reference libraries. To address this gap, we synthesized an MS/MS spectral resource comprising 436 structurally diverse 3-hydroxy N-acyl amides, spanning 3- to 18-carbon chains with a wide range of amine headgroups, such as ornithine, valine, and dopamine. Using a synthesis-driven reverse metabolomics approach, we found 161,626 spectral matches across 54,744 publicly available files in untargeted metabolomics data sets, revealing widespread occurrences in biological samples, including human-derived specimens. Of these molecules detected through MS/MS spectral matching, 334 represent newly reported biological entities. We further confirmed their presence in human saliva, stool, and skin using retention time and ion mobility measurements. Frequent detection in microbial data sets and validation in communities of human-derived gut bacteria support microbial production. Several metabolites also showed altered abundance in individuals with diabetes mellitus, showing that this lipid class is modulated in human metabolic disease. Together, these findings establish 3-hydroxy N-acyl amides as a distinct and biologically relevant lipid class, and the accompanying MS/MS spectral resource will enable their broader recognition and study in untargeted metabolomics data. IMPORTANCE: Microbe-host interactions lead to the production of metabolites that play an important role in human health and disease, though the annotation of such metabolites remains scarce. We created a re-usable MS/MS spectral library of an underrepresented class of compounds—3-hydroxy N-acyl amides. Our study characterized the presence of over 400 3-hydroxy N-acyl amides among thousands of public untargeted metabolomics datasets. We found over 100,000 instances of these metabolites within microbial, plant, and animal data, and used orthogonal validation methods to confirm nine previously unreported molecules within human feces, saliva, and skin samples. We cultured communities of human-derived gut bacteria and found evidence of bacterial production of four 3-hydroxy N-acyl amides. Our results suggest that these metabolites play important roles in human metabolism and disease, and sharing this curated resource enables the detection of these metabolites in future studies.
SN - 2379-5077
ER -