RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs
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Abstract
Background: Human-targeted drugs may exert off-target effects or can be repurposed to modulate the gut microbiota. However, our understanding of such effects is limited due to a lack of rapid and scalable assay to comprehensively assess microbiome responses to drugs. Drugs and other compounds can drastically change the overall abundance, taxonomic composition, and functions of a gut microbiome. Results: Here, we developed an approach to screen compounds against individual microbiomes in vitro, using metaproteomics to both measure absolute bacterial abundances and to functionally profile the microbiome. Our approach was evaluated by testing 43 compounds (including 4 antibiotics) against 5 individual microbiomes. The method generated technically highly reproducible readouts, including changes of overall microbiome abundance, microbiome composition, and functional pathways. Results show that besides the antibiotics, the compounds berberine and ibuprofen inhibited the accumulation of biomass during in vitro growth of the microbiota. By comparing genus and species level-biomass contributions, selective antibacterial-like activities were found with 35 of the 39 non-antibiotic compounds. Seven of the compounds led to a global alteration of the metaproteome, with apparent compound-specific patterns of functional responses. The taxonomic distributions of altered proteins varied among drugs, i.e., different drugs affect functions of different members of the microbiome. We also showed that bacterial function can shift in response to drugs without a change in the abundance of the bacteria. Conclusions: Current drug-microbiome interaction studies largely focus on relative microbiome composition and microbial drug metabolism. In contrast, our workflow enables multiple insights into microbiome absolute abundance and functional responses to drugs. The workflow is robust, reproducible, and quantitative and is scalable for personalized high-throughput drug screening applications.
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Synthetic gut microbiome: Advances and challenges
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Evaluating live microbiota biobanking using an ex vivo microbiome assay and metaproteomics
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iMetaLab Suite: A one‐stop toolset for metaproteomics
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Self-citationMAGNETO: An Automated Workflow for Genome-Resolved Metagenomics
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Mining bacterial NGS data vastly expands the complete genomes of temperate phages
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miniBUSCO: a faster and more accurate reimplementation of BUSCOPreprint
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Advances in the clinical use of metaproteomics
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A new and widespread group of fish apicomplexan parasites
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Prophages in the infant gut are largely induced, and may be functionally relevant to their hostsPreprint
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- Authors
- Li, L., Ning, Z., Zhang, X., Mayne, J., Cheng, K., Stintzi, A., & Figeys, D.
- Affiliations
- University of Ottawa (CA)
- Canadian Institute for Advanced Research (CA)
- Corresponding author
- Stintzi, Alain
- Figeys, Daniel
- Venue
- Microbiome
- Published
- 2020-03-11
- Volume
- 8
- Issue
- 1
- Pages
- 33-33
- ISSN
- 2049-2618 (ISSN-L)
- PMC
- PMC7066843
- OpenAlex
- W3010746544
- Cited by
- 328
- References
- 78
- Citations by year
- 2026: 28 · 2025: 60 · 2024: 60 · 2023: 60 · 2022: 53 · 2021: 49 · 2020: 14 · 2019: 3 · 2018: 1
- FWCI
- 14.28
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Microbiome (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- UEA Digital Repository (University of East Anglia) (acceptedVersion)
- uO Research (University of Ottawa) (submittedVersion, public-domain)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Genome Canada (OGI-114 and OGI-149)
- Canadian Institutes of Health Research (ECD-144627)
- Natural Sciences and Engineering Research Council of Canada (210034)
- Ontario Ministry of Economic Development and Innovation (REG1-4450)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- gut microbiota, drug-microbiome interactions, metaproteomics, antibiotic effects on microbiota, selective antibacterial activity, bacterial biomass, berberine, ibuprofen, drug repurposing, personalized drug screening
- MeSH terms
- Proof of Concept Study, Adult, Anti-Bacterial Agents, Bacteria, Nonprescription Drugs, Feces, Female, Humans, Male, RNA, Ribosomal, 16S, Colony Count, Microbial, Proteomics, Prescription Drugs, Microbiota
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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