REFERENCES
1. Maier L, Pruteanu M, Kuhn M, et al. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature. 2018;555:623-8.
2. Pereira FC, Ge X, Kristensen JM, et al. The Parkinson’s disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration. Nat Microbiol. 2024;9:3165-83.
3. Walsh J, Griffin BT, Clarke G, Hyland NP. Drug-gut microbiota interactions: implications for neuropharmacology. Br J Pharmacol. 2018;175:4415-29.
4. Weersma RK, Zhernakova A, Fu J. Interaction between drugs and the gut microbiome. Gut. 2020;69:1510-9.
5. la Cuesta-Zuluaga J, Boldt L, Maier L. Response, resistance, and recovery of gut bacteria to human-targeted drug exposure. Cell Host Microbe. 2024;32:786-93.
6. Mayneris-Perxachs J, Moreno-Navarrete JM, Fernández-Real JM. The role of iron in host-microbiota crosstalk and its effects on systemic glucose metabolism. Nat Rev Endocrinol. 2022;18:683-98.
7. Yilmaz B, Li H. Gut Microbiota and Iron: The crucial actors in health and disease. Pharmaceuticals (Basel). 2018;11:98.
8. Wu H, Esteve E, Tremaroli V, et al. Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug. Nat Med. 2017;23:850-8.
9. van Kessel SP, Frye AK, El-Gendy AO, et al. Gut bacterial tyrosine decarboxylases restrict levels of levodopa in the treatment of Parkinson’s disease. Nat Commun. 2019;10:310.
10. Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Mapping human microbiome drug metabolism by gut bacteria and their genes. Nature. 2019;570:462-7.
11. Klünemann M, Andrejev S, Blasche S, et al. Bioaccumulation of therapeutic drugs by human gut bacteria. Nature. 2021;597:533-8.
12. Garcia-Santamarina S, Kuhn M, Devendran S, et al. Emergence of community behaviors in the gut microbiota upon drug treatment. Cell. 2024;187:6346-6357.e20.
13. Wilson ID, Nicholson JK. Gut microbiome interactions with drug metabolism, efficacy, and toxicity. Transl Res. 2017;179:204-22.
14. Vergalli J, Atzori A, Pajovic J, et al. The challenge of intracellular antibiotic accumulation, a function of fluoroquinolone influx versus bacterial efflux. Commun Biol. 2020;3:198.
15. Hatzenpichler R, Krukenberg V, Spietz RL, Jay ZJ. Next-generation physiology approaches to study microbiome function at single cell level. Nat Rev Microbiol. 2020;18:241-56.
16. Birch D, Christensen MV, Staerk D, Franzyk H, Nielsen HM. Fluorophore labeling of a cell-penetrating peptide induces differential effects on its cellular distribution and affects cell viability. Biochim Biophys Acta Biomembr. 2017;1859:2483-94.
17. Specht EA, Braselmann E, Palmer AE. A critical and comparative review of fluorescent tools for live-cell imaging. Annu Rev Physiol. 2017;79:93-117.
18. Scinto SL, Bilodeau DA, Hincapie R, et al. Bioorthogonal chemistry. Nat Rev Methods Primers. 2021;1:30.
19. Bird RE, Lemmel SA, Yu X, Zhou QA. Bioorthogonal chemistry and its applications. Bioconjug Chem. 2021;32:2457-79.
20. Valentini TD, Lucas SK, Binder KA, et al. Bioorthogonal non-canonical amino acid tagging reveals translationally active subpopulations of the cystic fibrosis lung microbiota. Nat Commun. 2020;11:2287.
21. Riva A, Rasoulimehrabani H, Cruz-Rubio JM, et al. Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting. Nat Commun. 2023;14:8210.
22. Nilsson I, Grove K, Dovala D, Uehara T, Lapointe G, Six DA. Molecular characterization and verification of azido-3,8-dideoxy-d-manno-oct-2-ulosonic acid incorporation into bacterial lipopolysaccharide. J Biol Chem. 2017;292:19840-8.
23. Deshpande PB, Randey AK, Dhameliya DR, Rathod BD, Luthra PK, inventor
24. Flanagan K, Gassner K, Lang M, et al. Human-derived microRNA 21 regulates indole and L-tryptophan biosynthesis transcripts in the gut commensal Bacteroides thetaiotaomicron. mBio. 2025;16:e0392824.
25. Caporaso JG, Lauber CL, Walters WA, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A. 2011;108 Suppl 1:4516-22.
26. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal. 2011;17:10-2.
27. Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581-3.
28. Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP. Bioconductor workflow for microbiome data analysis: from raw reads to community analyses. F1000Res. 2016;5:1492.
29. Schloss PD, Westcott SL, Ryabin T, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537-41.
30. Oksanen J, Blanchet FG, Kindt R, et al. vegan: Community Ecology Package [Internet]. Version 2.8-0. R package; 2025. Available from: https://CRAN.R-project.org/package=vegan (accessed 2025-10-24).
31. McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8:e61217.
32. Cole JR, Wang Q, Fish JA, et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42:D633-42.
33. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
34. Hatzenpichler R, Scheller S, Tavormina PL, Babin BM, Tirrell DA, Orphan VJ. In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry. Environ Microbiol. 2014;16:2568-90.
35. Tornøe CW, Christensen C, Meldal M. Peptidotriazoles on solid phase: [1,2,3]-triazoles by regiospecific copper(i)-catalyzed 1,3-dipolar cycloadditions of terminal alkynes to azides. J Org Chem. 2002;67:3057-64.
36. Yap BW, Sim CH. Comparisons of various types of normality tests. Journal of Statistical Computation and Simulation. 2011;81:2141-55.
37. Wang S, Healy D, Patangia D, et al. Assessment of absolute abundance in mother-infant gut microbiome using marine-sourced bacterial DNA spike-in and comparison with conventional quantification methods. Microbiome Res Rep. 2025;4:23.
38. Ding M, Chen H, Yu R, et al. Shared and non-shared sIgA-coated and -uncoated bacteria in intestine of mother-infant pairs. Int J Mol Sci. 2022;23:9873.
39. Fu SC, Lee CH, Hsieh YC, Wu PH, Lin SH, Wang H. A pilot study exploring the association of entacapone, gut microbiota, and the subsequent side effects in patients With Parkinson’s Disease. Front Cell Infect Microbiol. 2022;12:837019.
40. Vandeputte D, Kathagen G, D'hoe K, et al. Quantitative microbiome profiling links gut community variation to microbial load. Nature. 2017;551:507-11.
41. Presolski SI, Hong VP, Finn MG. Copper-catalyzed azide-alkyne click chemistry for bioconjugation. Curr Protoc Chem Biol. 2011;3:153-62.
42. Baba T, Ara T, Hasegawa M, et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2006;2:2006.0008.
43. Raymond KN, Dertz EA, Kim SS. Enterobactin: an archetype for microbial iron transport. Proc Natl Acad Sci. 2003;100:3584-8.
44. Yi W, Xiao P, Liu X, et al. Recent advances in developing active targeting and multi-functional drug delivery systems via bioorthogonal chemistry. Signal Transduct Target Ther. 2022;7:386.
45. Verhelst SHL, Bonger KM, Willems LI. Bioorthogonal reactions in activity-based protein profiling. Molecules. 2020;25:5994.
46. Pinto M, Silva TB, Sardão VA, et al. Cellular and mitochondrial toxicity of tolcapone, entacapone, and new nitrocatechol derivatives. ACS Pharmacol Transl Sci. 2024;7:1637-49.
47. Grün D, Zimmer VC, Kauffmann J, et al. Impact of oral COMT-inhibitors on gut microbiota and short chain fatty acids in Parkinson's disease. Parkinsonism Relat Disord. 2020;70:20-2.
48. Weis S, Schwiertz A, Unger MM, et al. Effect of Parkinson’s disease and related medications on the composition of the fecal bacterial microbiota. NPJ Parkinsons Dis. 2019;5:28.
49. Ruiz LM, Williams CL, Tamayo R. Enhancing bacterial survival through phenotypic heterogeneity. PLoS Pathog. 2020;16:e1008439.
50. Krismer J, Tamminen M, Fontana S, Zenobi R, Narwani A. Single-cell mass spectrometry reveals the importance of genetic diversity and plasticity for phenotypic variation in nitrogen-limited Chlamydomonas. ISME J. 2017;11:988-98.
51. Lindell AE, Zimmermann-Kogadeeva M, Patil KR. Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota. Nat Rev Microbiol. 2022;20:431-43.
52. Crudo F, Aichinger G, Mihajlovic J, et al.
53. Forsberg MM, Huotari M, Savolainen J, Männistö PT. The role of physicochemical properties of entacapone and tolcapone on their efficacy during local intrastriatal administration. Eur J Pharm Sci. 2005;24:503-11.
54. D'Onofrio A, Crawford JM, Stewart EJ, et al. Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chem Biol. 2010;17:254-64.
55. Kramer J, Özkaya Ö, Kümmerli R. Bacterial siderophores in community and host interactions. Nat Rev Microbiol. 2020;18:152-63.
56. Cohen Z, Kelly L. Bioaccumulation as a mechanism of microbiome/drug interactions. Trends Microbiol. 2022;30:99-101.
57. Ngo JT, Adams SR, Deerinck TJ, et al. Click-EM for imaging metabolically tagged nonprotein biomolecules. Nat Chem Biol. 2016;12:459-65.
58. Romano S, Savva GM, Bedarf JR, Charles IG, Hildebrand F, Narbad A. Meta-analysis of the Parkinson's disease gut microbiome suggests alterations linked to intestinal inflammation. NPJ Parkinsons Dis. 2021;7:27.
