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 structureProject: How to do Diet DNA Metabarcoding from Animal Faecal SamplesDate: 30/08/2025Authors: Rachel D. McConnell and Crinan Jarrett, Diogo F. Ferreira, Luke L. Powell, Alma L.S. Quiñones, Davide M. Dominoni, Andreanna J. WelchPurpose: 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.Files and variablesFile: Statistical_Analysis_Files.zipDescription: This folder contains the bird and bat dietary ASV Table "16Farms_ASV_Table.csv" and themetadata 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&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".File: NCBI_Database.zipDescription: 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".File: ZBJ_Sequence_Files_1.zipDescription: This file contains dietary DNA from birds and bats sampled in Cameroon.File: QIIME2_Workflow_Script.txtDescription: 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.File: Taxonomy.zipDescription: This folder contains the Qiime2 outputs from the taxonomic assignment of the 16Farms data.File: cutadapters.txtDescription: This is the report created from using cutadapt to remove the adapters from the ZBJ dietary sequences.File: cutZBJ.qzvDescription: This is the Qiime2 visualisation file of the dietary sequences following the removal of the ZBJ primers.File: cutZBJ.txtDescription: This is the report created from using cutadapt to remove the primers from the ZBJ dietary sequences.File: manifest.tsvDescription: This file contains the file paths of the dietary data required for import into Qiime2.Variablessample-id:forward-absolute-filepath:reverse-absolute-filepath:File: ZBJ_featuretable.qzaDescription: The file contains information on the number of times each ASV is present in each sample.File: ZBJ_featuretable.qzvDescription: This is a Qiime2 visualisation file of the feature table containing information on the ASV count in each sample.File: ZBJ_rep_seqs.qzaDescription: This file contains the representative unique ASV sequences present in the ZBJ dietary data.File: ZBJ_rep_seqs.qzvDescription: This file contains a Qiime2 visualisation of the representative ASV sequences present in the ZBJ dietary data.File: ZBJ_stats.qzaDescription: This file summarises the number of reads that were retained after each DADA2 filtering step.File: ZBJ_stats.qzvDescription: This is a Qiime2 visualisation file containing a table of the number of reads retained after each DADA2 filtering step for each sample.File: cutZBJ.qzaDescription: This is the Qiime2 file containing the ZBJ dietary sequences with the primers removed.File: ZBJ_Sequence_Files_2.zipDescription: This file contains dietary DNA from birds and bats sampled in Cameroon.Code/softwareThe software used to generate this data includes:High performance computingMiniconda3Qiime2-amplicon-2025.7R version 4.3.1Microsoft Excel