Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples
Abstract
Increasing appreciation of the gut microbiome's role in health motivates understanding the molecular composition of human feces. To analyze such complex samples, we developed a platform coupling targeted and untargeted metabolomics. The approach is facilitated through split flow from one UPLC, joint timing triggered by contact closure relays, and a script to retrieve the data. It is designed to detect specific metabolites of interest with high sensitivity, allows for correction of targeted information, enables better quantitation thus providing an advanced analytical tool for exploratory studies. Procrustes analysis revealed that untargeted approach provides a better correlation to microbiome data, associating specific metabolites with microbes that produce or process them. With the subset of over one hundred human fecal samples from the American Gut project, the implementation of the described coupled workflow revealed that targeted analysis using combination of single transition per compound with retention time misidentifies 30% of the targeted data and could lead to incorrect interpretations. At the same time, the targeted analysis extends detection limits and dynamic range, depending on the compounds, by orders of magnitude. A software application has been developed as a part of the workflow to allows for quantitative assessments based on calibration curves. Using this approach, we detect expected microbially modified molecules such as secondary bile acids and unexpected microbial molecules including Pseudomonas-associated quinolones and rhamnolipids in feces, setting the stage for metabolome-microbiome-wide association studies (MMWAS).
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Changes in the microbiome often result in altered metabolic profiles, impacting the availability and diversity of nutrients and microbial metabolites.
“changes in the microbiome often result in altered metabolic profiles, impacting the availability and diversity of nutrients and microbial metabolites (Dodd et al., 2017; Melnik et al., 2017; Sharon et al., 2014; Wikoff et al., 2009).”
From Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice (2019) · cites this paper as Melnik et al., 2017
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- Authors
- Melnik, A. V., da Silva, R. R., Hyde, E. R., Aksenov, A. A., Vargas, F., Bouslimani, A., Protsyuk, I., Jarmusch, A. K., Tripathi, A., Alexandrov, T., Knight, R., & Dorrestein, P. C.
- Affiliations
- University of California San Diego (US)
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- European Molecular Biology Laboratory (DE)
- Corresponding author
- Alexandrov, Theodore
- Knight, Rob
- Dorrestein, Pieter C.
- ORCID
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2017-07-06
- Volume
- 89
- Issue
- 14
- Pages
- 7549-7559
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- OpenAlex
- W2666871553
- Cited by
- 87
- References
- 47
- Citations by year
- 2025: 10 · 2024: 13 · 2023: 7 · 2022: 9 · 2021: 12 · 2020: 16 · 2019: 10 · 2018: 7 · 2017: 2
- FWCI
- 3.91
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Analytical Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Horizon 2020 Framework Programme (634402)
- National Institute of General Medical Sciences (5P41GM103484-07, GMS10RR029121)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Keywords
- targeted metabolomics, untargeted metabolomics, human fecal samples, gut microbiota, Procrustes analysis, secondary bile acids, rhamnolipids, American Gut Project, calibration curve, microbial metabolites
- MeSH terms
- Feces, Humans, Mass Spectrometry, Molecular Structure, Metabolome
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