How to do Diet DNA Metabarcoding from Animal Faecal Samples

How to do Diet DNA Metabarcoding from Animal Faecal SamplesDescription of the data and file structure<b>Project:</b> How to do Diet DNA Metabarcoding from Animal Faecal Samples<b>Date</b>: 30/08/2025<b>Authors: Rachel D. McConnell and Crinan Jarrett, Diogo F. Ferreira, Luke L. Powell, Alma L.S. Quiñones, Davide M. Dominoni, Andreanna J. Welch</b><b>Purpose:</b> These data files may be used to run an example bioinformatics workflow and perform statistical analysis of metabarcoded Dietary DNA from birds and bats.The data is comprised of:ZBJ_Sequence_files containing dietary sequencing data from 277 samples collected from birds and bats across 16 farms in CameroonQiime2 bioinformatic output files including the final 16-farms-ASV tableAn NCBI COI ZBJ database and classifierStatistical Analysis including the bird and bat metadata, R scripts to clean and organise the diet data, perform basic generalised linear model, a multivariate analysis and a network analysis. The plots and results produced by the scripts are also included.<b>Files and variables</b><b>File: Statistical_Analysis_Files.zip</b><b>Description:</b> This folder contains the bird and bat dietary ASV Table "16Farms_ASV_Table.csv" and the<br>metadata files, "bird_and_bat_capturedata.csv" and "faeces_sample_database.xlsx". The folder also contains the R script used for statistical analysis. This includes "1.organize&amp;clean_metabarcoding.R" which contains a function to filter and organise the ASV table for statistical analysis, the file "2.glm_examples" which contains code to conduct GLMs and a multivariate analysis and the "3.building_analysing_networks" file which contains code to perform a network analysis of the dietary information. Missing values are indicated as "NA".<br><b>File: NCBI_Database.zip</b><b>Description:</b> This folder contains the COI reference sequences and taxonomy downloaded from NCBI using RESCRIPt and the output files generated from this tutorial https://forum.qiime2.org/t/using-rescripts-extract-seq-segments-to-extract-reference-sequences-without-pcr-primer-pairs/23618 (Robeson et al., 2021; Rognes et al., 2016). The COI classifier created from the ZBJ reference sequences and taxonomy produced by Qiime2 is also included, "zbj-ncbi-classifier.qza".<b>File: ZBJ_Sequence_Files_1.zip</b><b>Description:</b> This file contains dietary DNA from birds and bats sampled in Cameroon.<b>File: QIIME2_Workflow_Script.txt</b><b>Description:</b> A script of a Qiime2 Workflow to process ZBJ dietary DNA. The code removes the adapters and primers, performs error correction, merging of the double stranded DNA, the creation of ASVs and taxonomic assignment.<b>File: Taxonomy.zip</b><b>Description:</b> This folder contains the Qiime2 outputs from the taxonomic assignment of the 16Farms data.<b>File: cutadapters.txt</b><b>Description:</b> This is the report created from using cutadapt to remove the adapters from the ZBJ dietary sequences.<b>File: cutZBJ.qzv</b><b>Description:</b> This is the Qiime2 visualisation file of the dietary sequences following the removal of the ZBJ primers.<b>File: cutZBJ.txt</b><b>Description:</b> This is the report created from using cutadapt to remove the primers from the ZBJ dietary sequences.<b>File: manifest.tsv</b><b>Description:</b> This file contains the file paths of the dietary data required for import into Qiime2.<b>Variables</b>sample-id:forward-absolute-filepath:reverse-absolute-filepath:<b>File: ZBJ_featuretable.qza</b><b>Description:</b> The file contains information on the number of times each ASV is present in each sample.<b>File: ZBJ_featuretable.qzv</b><b>Description:</b> This is a Qiime2 visualisation file of the feature table containing information on the ASV count in each sample.<b>File: ZBJ_rep_seqs.qza</b><b>Description:</b> This file contains the representative unique ASV sequences present in the ZBJ dietary data.<b>File: ZBJ_rep_seqs.qzv</b><b>Description:</b> This file contains a Qiime2 visualisation of the representative ASV sequences present in the ZBJ dietary data.<b>File: ZBJ_stats.qza</b><b>Description:</b> This file summarises the number of reads that were retained after each DADA2 filtering step.<b>File: ZBJ_stats.qzv</b><b>Description:</b> This is a Qiime2 visualisation file containing a table of the number of reads retained after each DADA2 filtering step for each sample.<b>File: cutZBJ.qza</b><b>Description:</b> This is the Qiime2 file containing the ZBJ dietary sequences with the primers removed.<b>File: ZBJ_Sequence_Files_2.zip</b><b>Description:</b> This file contains dietary DNA from birds and bats sampled in Cameroon.<b>Code/software</b>The software used to generate this data includes:High performance computingMiniconda3Qiime2-amplicon-2025.7R version 4.3.1Microsoft Excel<br>