Raw data, processed data, and scripts for Anti-diarrheal drug loperamide induces dysbiosis in zebrafish microbiota via bacterial inhibition
This repository contains the scripts, processed sequencing artifacts, and the Rmd script files to reproduce the figures in the manuscript. The raw sequences generated for this study can be found in the NCBI Short Read Archive under BioProject no. PRJNA908751. The corresponding accession numbers for each 16S rRNA amplicon sample are detailed in PRJNA908751_NCBI_info.xlsx.
Stevick, R.J., Audrain, B., Bedu, S., Dray, N., Ghigo, J-M. & Pérez-Pascual, D. (2023) Anti-diarrheal drug loperamide induces dysbiosis in zebrafish microbiota via targeted bacterial inhibition. ...
- LoperamideStraininfo.xlsx - metadata for the strains used in the study
- figures/ - general figures
This folder contains scripts used to perform QIIME2 analysis on the 16S rRNA amplicon data, the QIIME2 output artifacts, and the Rmd script to reproduce the figures in the manuscript.
- scripts/ - QIIME2 bash script and Rmd files
- output/ - QIIME2 artifacts and processed files
- metadata/
- figures/
This folder contains all the raw data files and the scripts to reproduce the figures and statistics in the manuscript.
This folder contains all the raw data files and the scripts to reproduce the figures and statistics in the manuscript.
| Fig | Description | Code | Figure |
|---|---|---|---|
| 1 | Experimental schematic | Made using BioRender |  |
| 2 | Conventional microbiota changes | Loperamide16Samplicon_analysis.Rmd |  |
| 3 | Bacterial survival | WaterSurvivalCFUs_loperamide.Rmd |  |
| 4 | Mono-colonization | ZebrafishMonoCFUs_loperamide.Rmd |  |
| 5 | Mix-colonization | ZebrafishMixCFUs_loperamide.Rmd |  |
| 6 | Alpha-diversity comparison | ZebrafishMixCFUs_loperamide.Rmd |  |
| Supp Fig | Description | Code | Figure |
|---|---|---|---|
| S1 | QC and rarefaction curves | Loperamide16Samplicon_analysis.Rmd |  |
| S2 | Sequencing controls | Loperamide16Samplicon_analysis.Rmd |  |
| S3 | Phylum barplot | Loperamide16Samplicon_analysis.Rmd |  |
| S4 | Genus barplot and venn diagram | Loperamide16Samplicon_analysis.Rmd |  |
| S5 | All samples beta-diversity | Loperamide16Samplicon_analysis.Rmd |  |
| S6 | Zebrafish growth | LoperamideFishMeasurements.Rmd |  |
| S7 | Bacterial growth | LoperamideGrowthCurves.Rmd |  |
| S8 | Compare Mono vs Water | ZebrafishMonoCFUs_loperamide.Rmd |  |
| S9 | Compare Mix vs Mono | ZebrafishMixCFUs_loperamide.Rmd |  |
