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.

To cite this work:

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. ...

This repository has been archived on Zenodo. Access or cite the most recent release:

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Contents

• LoperamideStraininfo.xlsx - metadata for the strains used in the study
• figures/ - general figures

16SampliconAnalysis

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/

inVitroAnalysis

This folder contains all the raw data files and the scripts to reproduce the figures and statistics in the manuscript.

• Growth curves
• Survival in water

inVivoAnalysis

This folder contains all the raw data files and the scripts to reproduce the figures and statistics in the manuscript.

• Mono-reconv CFUs
• Mix-reconv CFUs
• Fish growth and development

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Figure index

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

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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

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