Taxonomic and mechanistic insights into gut microbiota bioaccumulation of entacapone using bioorthogonal drug labelling
Taxonomic and mechanistic insights into gut microbiota bioaccumulation of entacapone using bioorthogonal drug labelling
Aim: the gut microbiota plays a key role in shaping individual responses to drugs, but current tools have limited potential to probe drug-microbe interactions within the complex, individualised gut environment. This study employed bioorthogonal labelling to track and identify gut microbial taxa and molecular mechanisms involved in the bioaccumulation of entacapone, a Parkinson’s disease drug.
Methods: we synthesised alkyne-tagged derivatives of entacapone and evaluated their suitability as molecular probes in ex vivo incubations with faecal communities or different Escherichia coli (E. coli) strains. Following incubation, tagged drugs were conjugated to a fluorescently labelled azide via click chemistry. Labelled cells were visualised, quantified, sorted via fluorescence-activated cell sorting (FACS), and identified via 16S ribosomal RNA (rRNA) gene amplicon sequencing.
Results: entacapone alkyne derivatives retained the biological activity and effects of the original drug on the microbiota, significantly reducing microbial loads and shifting community composition across the three donors tested. Conjugation of alkyne-entacapone with a labelled azide revealed that between 80% to 96% of all microbial cells in a donor’s faecal sample accumulate entacapone. Nearly all taxa detected in incubations were recovered in labelled FACS fractions, confirming widespread uptake of the drug. Finally, we demonstrate that different E. coli strains exhibit varying levels of entacapone accumulation and identify a siderophore transporter that plays a role in this process.
Conclusion: our findings reveal that entacapone is widely bioaccumulated by the gut microbiota across three donors and identify a key molecular mediator of this accumulation. This study expands the toolkit for investigating drug-microbiome interactions and holds significant potential to advance our understanding of drug-microbiome dynamics and therapeutic outcomes.
Faecal microbiota, Pharmaceuticals, bioorthogonal labelling, drug accumulation, siderophore transporter, faecal microbiota
Guantai, Linda M.
70ee8990-43de-4275-ad39-2e802a90f68a
Bavinton, Clementine E.
8b0b0a3f-03ab-49ea-8cef-e92b87604898
Shazzad, Juwairiyah B.
72cd905f-fbad-4912-8e2d-38db082686f4
Mahajan, Sumeet
b131f40a-479e-4432-b662-19d60d4069e9
Thompson, Sam
99b7e34e-fe24-401c-b7b0-64e56cbbbcb1
Pereira, Fatima C.
a9396948-26f9-4f13-8f83-a22fec1dd0e0
20 November 2025
Guantai, Linda M.
70ee8990-43de-4275-ad39-2e802a90f68a
Bavinton, Clementine E.
8b0b0a3f-03ab-49ea-8cef-e92b87604898
Shazzad, Juwairiyah B.
72cd905f-fbad-4912-8e2d-38db082686f4
Mahajan, Sumeet
b131f40a-479e-4432-b662-19d60d4069e9
Thompson, Sam
99b7e34e-fe24-401c-b7b0-64e56cbbbcb1
Pereira, Fatima C.
a9396948-26f9-4f13-8f83-a22fec1dd0e0
Guantai, Linda M., Bavinton, Clementine E., Shazzad, Juwairiyah B., Mahajan, Sumeet, Thompson, Sam and Pereira, Fatima C.
(2025)
Taxonomic and mechanistic insights into gut microbiota bioaccumulation of entacapone using bioorthogonal drug labelling.
Microbiome Research Reports, 4 (4), [41].
(doi:10.20517/mrr.2025.73).
Abstract
Aim: the gut microbiota plays a key role in shaping individual responses to drugs, but current tools have limited potential to probe drug-microbe interactions within the complex, individualised gut environment. This study employed bioorthogonal labelling to track and identify gut microbial taxa and molecular mechanisms involved in the bioaccumulation of entacapone, a Parkinson’s disease drug.
Methods: we synthesised alkyne-tagged derivatives of entacapone and evaluated their suitability as molecular probes in ex vivo incubations with faecal communities or different Escherichia coli (E. coli) strains. Following incubation, tagged drugs were conjugated to a fluorescently labelled azide via click chemistry. Labelled cells were visualised, quantified, sorted via fluorescence-activated cell sorting (FACS), and identified via 16S ribosomal RNA (rRNA) gene amplicon sequencing.
Results: entacapone alkyne derivatives retained the biological activity and effects of the original drug on the microbiota, significantly reducing microbial loads and shifting community composition across the three donors tested. Conjugation of alkyne-entacapone with a labelled azide revealed that between 80% to 96% of all microbial cells in a donor’s faecal sample accumulate entacapone. Nearly all taxa detected in incubations were recovered in labelled FACS fractions, confirming widespread uptake of the drug. Finally, we demonstrate that different E. coli strains exhibit varying levels of entacapone accumulation and identify a siderophore transporter that plays a role in this process.
Conclusion: our findings reveal that entacapone is widely bioaccumulated by the gut microbiota across three donors and identify a key molecular mediator of this accumulation. This study expands the toolkit for investigating drug-microbiome interactions and holds significant potential to advance our understanding of drug-microbiome dynamics and therapeutic outcomes.
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Accepted/In Press date: 17 November 2025
e-pub ahead of print date: 20 November 2025
Published date: 20 November 2025
Keywords:
Faecal microbiota, Pharmaceuticals, bioorthogonal labelling, drug accumulation, siderophore transporter, faecal microbiota
Identifiers
Local EPrints ID: 508725
URI: http://eprints.soton.ac.uk/id/eprint/508725
ISSN: 2771-5965
PURE UUID: 95fd7408-e4bc-4535-90a6-133f560821a8
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Date deposited: 02 Feb 2026 17:41
Last modified: 03 Feb 2026 03:07
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Contributors
Author:
Linda M. Guantai
Author:
Clementine E. Bavinton
Author:
Juwairiyah B. Shazzad
Author:
Fatima C. Pereira
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