Data from: Longitudinal study of a rodent invasion reveals shifts in host pathogen interactions

ABSTRACT:

Invasive species can disrupt native epidemiological processes, potentially leading to the emergence of zoonotic pathogens. The relatively recent appearance and spread of the bank vole (Clethrionomys glareolus) in Ireland provides a unique model system to study these phenomena. The depauperate small mammal community in Ireland, combined with baseline data, allows us to identify the invasion gradient of C. glareolus and its effects on rodent-borne pathogens over time. A total of 498 C. glareolus and 584 Apodemus sylvaticus were sampled across nine sites in Ireland in 2016 and 2017, with six sites revisited in 2021 and 2022. 16S rRNA metabarcoding identified 10 putative pathogenic Operational Taxonomic Units (OTUs) present in these rodents, relating to four bacterial taxa, Bartonella spp., Mycoplasma coccoides, Mycoplasma haemomuris and Mycoplasma penetrans, and one family of protozoans, Sarcocystidae. Several epidemiological processes were found to be correlated with the C. glareolus invasion. C. glareolus in Ireland exhibited patterns consistent with the enemy release hypothesis, compared to native populations in France, and the native A. sylvaticus in Ireland. Likewise, a potential dilution effect, with reduced prevalence of M. haemomuris in A. sylvaticus at the C. glareolus invasion core compared to the invasion front, was observed. Finally, C. glareolus had increased prevalence of Sarcocystidae at the invasion front when compared to the invasion core, depending on the time and stage of invasion. These findings further our understanding of pathogen dynamics during biological invasions, demonstrating that invaders affect native host-pathogen communities differently as they advance through various stages of establishment.

FILE DESCRIPTION:

Information concerning the small mammal spleen samples and the positive and negative controls multiplexed in the 16Sv4 MiSeq sequencing runs

This XLSX file contains the Sequencing_run_ID, PCR_ID, PCR_replicate, Sequence file name (read 1 fastq file), Sequence file name (read 2 fastq file), Rodent_ID, Country, Sample_ID, Sample_type, Extraction Kit, the status “Used_in_this_study”, Comment and Zenodo link for the 6020 PCR products multiplexed in 7 different Illumina MiSeq runs, corresponding to 2466 individuals performed in two technical replicates and 1084 negative and positive controls. Note that only 1398 individuals from forest environments in France and Ireland were used in this study (see the column “Used_in_this_study”.

File name: Sequencing_informations_spleen_samples.xlsx

MiSeq raw sequences of the 16Sv4 rRNA gene from spleens of small mammal samples

These GZ and ZIP files contain the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each spleen rodent sample using the MiSeq platform. The 6020 multiplexed PCR products were indexed using both forward and reverse indices on 7 sequencing MiSeq runs. Information of the multiplexed samples (n=2466 in replicate) and positive (n= 14) & negative controls (n= 852) is provided in the following CSV file titled: Sequencing_informations_spleen_samples.xlsx . Note that only 1398 individuals from forest environments in France and Ireland were used in this study (see the column “Used_in_this_study” in the file “Sequencing_informations_spleen_samples.xlsx”.

File names and Zenodo links:

Run00: MiSeq_Reads_16S_Spleen_Run00.zip (this repository)
Run01: MiSeq_Reads_16S_Spleen_Run01.zip (this repository)
Run06: MiSeq_Reads_16S_Spleen_Run06.gz (https://zenodo.org/records/12518286/files/MiSeq_Reads_16S_Spleen_Run06.gz)
Run10: MiSeq_Reads_16S_Spleen_Run10.gz (https://zenodo.org/records/12518286/files/MiSeq_Reads_16S_Spleen_Run10.gz)
Run12: MiSeq_Reads_16S_Spleen_Run12.gz (https://zenodo.org/records/12518286/files/MiSeq_Reads_16S_Spleen_Run12.gz)
Run16: MiSeq_Reads_16S_Spleen_Run16.gz (https://zenodo.org/records/12518286/files/MiSeq_Reads_16S_Spleen_Run16.gz)
Run20: MiSeq_Reads_16S_Spleen_Run20.gz (https://zenodo.org/records/12518286/files/MiSeq_Reads_16S_Spleen_Run20.gz)
Run20’: MiSeq_Reads_16S_Spleen_Run20_AddSamples.zip (this repository)

Occurrence table of the 16v4 rRNA gene from spleen rodent samples after data filtering

This XLSX file contains the occurrences (presence: 1; absence: 0) after data filtering of each putative pathogenic Operational Taxonomic Unit (OTU) for each of the 1398 spleen rodent samples from Ireland and France analyzed in the study.

 File name: Spleen Prevalence forest only.xlsx