DOI: 10.5061/dryad.r7sqv9snf
title: Direct and indirect effects of pesticide exposure on farmland raptor gut microbiota

description: 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).
description: Microbial samples were collected by performing cloacal lavages on
 22 Montagu's Harrier (<em>Circus pygargus</em>)
 nestlings. Samples were then analysed using a standard 16S amplicon
 metabarcoding sequencing method, with paired-end Illumina
 sequencing.
description: # Direct and indirect effects of pesticide exposure on farmland raptor gut
 microbiota
 [https://doi.org/10.5061/dryad.r7sqv9snf](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: ###### *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.