/Gut-microbiota-of-the-threatened-takahe-biogeographic-patterns-and-conservation-implications

Comparative gut bacterial community analysis in the threatened Aotearoa New Zealand takahē.

16S rRNA statistical analyses for takahē gut microbiota

RStudio Statistical analyses associated with the paper Gut microbiota of the threatened takahe: biogeographic patterns and conservation implications published in Animal Microbiome 2022.

Amplicon sequence data (demultiplexed, paired-end reads) were sequenced on the Illumina MiSeq platform at Auckland Genomics Ltd and are available in the NCBI SRA repository Bioproject accession number PRJNA737580.

General notes

This pipeline utilises amplicon sequence variants (ASVs) produced using the R package DADA2. Please refer to the publication for specific parameters employed for this dataset and appropriate references.

This pipeline also contains modified versions of scripts published by Bodkhe et al. 2019 available here.