Data from: Drivers of host-pathogen community assemblies in European forests and urban green spaces (Part I to II)

ABSTRACT:

Major advances in the understanding of infectious diseases have been achieved in the last decades. However, the persistence and re-emergence of pathogens continues to raise public and veterinary health concerns, of which the recent COVID-19 pandemic may be one of the most dramatic examples. Understanding the impact of habitat alterations and concomitant biodiversity loss on pathogen transmission and emergence from wildlife remains challenging. Here, we aim to elucidate the interlinkages between biodiversity and rodent-borne diseases at local and European scales. We present recently collected host-pathogen data from 21 temperate forest sites and eight urban green spaces throughout five European countries, environments where rodents are abundant and human/domestic animals – wildlife interactions are likely to occur. 3766 specimens were analyzed during the period from 2020 to 2022 comprising 15 different small mammal species. Different organ tissues of each specimen were screened for bacteria by either 16S rRNA amplicon sequencing or specific PCR. The presence of antibodies to different families of viruses were screened using immunofluorescent assays. A multitude of pathogens of zoonotic potential from several genera including Bartonella, Borrelia, Mycoplasma, Anaplasma, Neoehrlichia, Leptospira, Orthohantavirus and Orthopoxvirus were detected at non-negligible prevalence in 11 different terrestrial mammal species. A shift in host community composition was observed along the anthropization gradient with more urban adapters in more anthropized sites. Parasite richness increased with an increase in host species diversity, following the “host-diversity begets parasite-diversity” hypothesis. The absence of some vector-transmitted parasites in urban areas suggest a shift in parasite community along the anthropization gradient. Host species and host intrinsic factors were dominant explanatory variables for endoparasitic Mycoplasma species and Sarcocystidae, while extrinsic environmental and climatic factors where influential in explaining variations in occurrences of several vector-transmitted pathogens. Apodemus sylvaticus and Clethrionomys glareolus were important connector host species in respectively urban green spaces and temperate forests. Increased host diversity, but not anthropization, correlated with a richer pathogen community. These results ultimately lead to an increased understanding of the complex host-pathogen system at the local landscape that can aid future management decisions and support the public health sector.

FILE DESCRIPTION:

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

This CSV 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, Sample_ID, Sample_type, and Extraction Kit for the 7761 PCR products multiplexed in 11 different Illumina MiSeq runs, corresponding to 3766 individuals performed in two technical replicates and 229 negative and positive controls.

File name: Sequencing_informations_spleen_samples.csv

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

These GZ 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 7761 multiplexed PCR products were indexed using both forward and reverse indices on 11 sequencing MiSeq runs. Information of the multiplexed samples (n=3766 in replicate) and positive (n= 50) & negative controls (n= 179) is provided in the following CSV file titled: Sequencing_informations_spleen_samples.csv

File names:

MiSeq_Reads_16S_Spleen_Run02.gz
MiSeq_Reads_16S_Spleen_Run04.gz
MiSeq_Reads_16S_Spleen_Run06.gz
MiSeq_Reads_16S_Spleen_Run07.gz
MiSeq_Reads_16S_Spleen_Run08.gz
MiSeq_Reads_16S_Spleen_Run10.gz
MiSeq_Reads_16S_Spleen_Run12.gz
MiSeq_Reads_16S_Spleen_Run14.gz
MiSeq_Reads_16S_Spleen_Run16.gz
MiSeq_Reads_16S_Spleen_Run18.gz
MiSeq_Reads_16S_Spleen_Run20.gz