This repository contains open-source code, data, & text files.
Raw amplicon sequence files can be found at NCBI SRA BioProject PRJNA925886.
For information regarding the project, please visit: Scott, E., Brewer, M.S., Peralta, A.L. and Issa, F.A., 2023. The effects of social experience on host gut microbiome in male zebrafish (Danio rerio). The Biological Bulletin, 244(3), pp.177-189. https://doi.org/10.1086/729377
- Aim: This study examines the extent that social dominance during the first two weeks of social interactions influenced the composition of zebrafish gut microbiomes by comparing gut bacterial composition, diversity and abundance among socially dominant, submissive, social isolates, and control group-housed communal fish.
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analyses: An R Markdown file that includes R script written by Ariane Peralta, Michael Brewer, and Emily Scott.
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bin:
- MothurTools.R: An R script written by Dr. Mario E. Muscarella (website) containing functions used in the analysis of community sequence data.
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data: Files associated with amplicon data sets.
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figures: Figures (microbes-16S rRNA amplicon) generated according to R script located in R Markdown file.
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mothur: Files containing script for bioinformatic analysis of 16S rRNA gene sequences (Illumina MiSeq platform) using mothur pipeline.
This work was supported by the National Science Foundation grant (#1754513) to F.A.I. and grant (#1845845) to A.L.P..
Dr. Michael S. Brewer (website): Associate Professor, Department of Biology, East Carolina University
Dr. Fadi A. Issa (website): Associate Professor, Department of Biology, East Carolina University
Dr. Ariane Peralta (website): Associate Professor, Department of Biology, East Carolina University