Abstract
BackgroundHuman-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.ResultsHere, 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.ConclusionsCurrent 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.
Highlights
Human-targeted drugs may exert off-target effects or can be repurposed to modulate the gut microbiota
After 24 h, the cultured microbiomes are prepared for metaproteomic analysis using a microplate-based metaproteomic sample processing workflow (Supplementary Figure S1) adapted from our single-tube protocol [28]
Effects of compounds on microbiome abundance and composition We examined the effect of the 43 compounds on the overall abundance of each individual microbiome by comparing the total peptide intensity (Fig. 2a)
Summary
Human-targeted drugs may exert off-target effects or can be repurposed to modulate the gut microbiota. The size and complexity of these culturing systems limit the number of individual microbiomes and drugs that can be examined [11], and may not be suitable for high-throughput drug screening purpose. A recent study examined the effects of approved drugs on the biomass of forty individually cultured bacterial strains in a high-throughput manner [13] This approach highlighted the importance of biomass in identifying antibacterial effects. It did not take into account the complexity of a microbial community that could lead to different microbial responses Approaches such as optical density measurement [13], flow cytometry [14], and quantitative realtime PCR [15] can be used to compare microbiome biomass. There has been no report of an in vitro gut microbiome-based drug screening approach that could assess both biomass responses and functional alterations in a single analytical test
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