Direct and indirect effects of pesticide exposure on farmland raptor gut microbiota
Data files
Jun 09, 2025 version files 1.72 GB
Abstract
Recent studies in humans have shown that certain pesticides could affect the composition and functions of gut microbiota, an essential modulator of vertebrate physiology, leading to potential dysbiosis. However, this relationship remains largely unknown in wild birds despite the implications of pesticides in the current decline of farmland species. The present study sought to fill this gap by providing data on the association between pesticide concentrations in blood and gut microbiota characteristics in relation to individual traits in a farmland raptor, the Montagu’s Harrier (Circus pygargus). Results showed that females with higher body condition and higher pesticide load harboured a higher gut bacterial richness and diversity, while the relationship was opposite in males with higher body condition. Regarding taxonomic composition, Proteobacteria were the main phylum found in all nestlings. Differences in certain phylum and genus abundance according to pesticide load were found, with more Bacteroidota, Leifsonia, and less Bulkholderia in nestlings with higher pesticide concentrations in their blood. Thus, this study highlights differences in microbiota and contamination by several pesticides according to the phenotypic characteristics of a wild raptor, and shows that farmland birds can represent relevant biosentinels for assessing the health/proper functioning of ecosystems (One Health approach).
https://doi.org/10.5061/dryad.r7sqv9snf
Description of the data and file structure
Files and variables
File: Harrier_microbiome_raw_sequencing_data.zip
Description: This compressed folder contains 6 compressed fastq files corresponding to the raw pre-processed sequencing data produced by Illumina sequencing. The prefixes phytobird1, phytobird2, and phytobird3 correspond to the 3 PCR replicates of each sample performed in 3 different libraries. The suffixes R1.fastq and R2.fastq correspond to the 2 paired-end readings of each sequence.
The folder also contains 3 ngsfilter.tab files corresponding to each of the 3 libraries. Each of these files contains the following variables:
- Column A: project name
- Column B: Sample ID name, Harrier samples contain the letters "BU". Identification codes BLK... and Vide... correspond to empty wells and non-existent tag combinations used for evaluating the level of tag-switching. All other codes correspond to samples from other unrelated projects.
- Column C: Unique tag combination for each sample used for demultiplexing sequences (assigning sequences to the right sample)
- Column D: Forward Primer
- Column E: Reverse Primer
- Column F: PCR metadata summary, indicating PCR id, sample id, PCR type (sample or control), control type (positive, negative, extraction, sequencing), DNA extraction date, PCR replicate, bird id number, forward tag row number, reverse tag column number, PCR plate position
File: phytobird_merged_R1R2_good_demultiplexed_derepl_basicfilt_cl_agg.fasta
Description: This fasta file corresponds to the harrier microbiome sequencing data after bioinformatic processing - i.e., merged PCR replicates, paired-end assembly, sequence quality filtering, demultiplexing, dereplication, basic filtering, and clustering. Taxonomic affiliation was performed at a later stage using the SILVA database.
Microbial samples were collected by performing cloacal lavages on 22 Montagu's Harrier (Circus pygargus) nestlings. Samples were then analysed using a standard 16S amplicon metabarcoding sequencing method, with paired-end Illumina sequencing.