ABSTRACT Rodents are major reservoirs of pathogens that can cause disease in humans and livestock. It is therefore important to know what pathogens naturally circulate in rodent populations, and to understand the factors that may influence their distribution in the wild. Here, we describe the incidence and distribution patterns of a range of endemic and zoonotic pathogens circulating among rodent communities in northern France. The community sample consisted of 713 rodents, including 11 host species from diverse habitats. Rodents were screened for virus exposure (hantaviruses, cowpox virus, Lymphocytic choriomeningitis virus, Tick-borne encephalitis virus) using antibody assays. Bacterial communities were characterized using 16S rRNA amplicon sequencing of splenic samples. Multiple correspondence (MCA), regression and association screening (SCN) analyses were used to determine the degree to which extrinsic factors contributed to pathogen community structure, and to identify patterns of associations between pathogens within hosts. We found a rich diversity of bacterial genera, with 36 known or suspected to be pathogenic. We revealed that host species is the most important determinant of pathogen community composition, and that hosts that share habitats can have very different pathogen communities. Pathogen diversity and co-infection rates also vary among host species. Aggregation of pathogens responsible for zoonotic diseases suggests that some rodent species may be more important for transmission risk than others. Moreover we detected positive associations between several pathogens, including Bartonella, Mycoplasma species, Cowpox virus (CPXV) and hantaviruses, and these patterns were generally specific to particular host species. Altogether, our results suggest that host and pathogen specificity is the most important driver of pathogen community structure, and that interspecific pathogen-pathogen associations also depend on host species. FILE DESCRIPTION: MiSeq raw sequences of the 16Sv4 rRNA gene from spleen rodent samples This ZIP file contains 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 749 multiplexed PCR products were indexed using both forward and reverse indices. Information of the multiplexed samples (n=363 in replicate) and positive (n= 6) & negative controls (n= 17) is provided in the following XLSX file titled: 16S_raw_abundance_data.xlsx File name: MiSeq raw sequences of the V4 region 16S rRNA gene.zip Raw input and output files generated by the mothur program This ZIP file contains all the input and output files generated during the MiSeq sequence analysis with the mothur program. File name: Raw input and output files generated by the mothur program.zip Log file generated by the mothur program This TXT file contains is the history of all the command lines and parameters used during the MiSeq sequence analysis with the mothur program. File name: mothur.1428506786.logfile Raw abundance table of the 16v4 rRNA gene from spleen rodent samples before data filtering This XLSX file contains the number of reads for each distinct Operational Taxonomic Unit (OTU) and each of the PCR products, including the 332 spleen rodent samples analyzed in the study and the negative & positive controls, sequenced in the MiSeq run before the data filtering. This file contains also the following information: Study_site, Study_year, Sample_habitat, Host_species, Host_age, Host_sex, PCR_ID and the taxonomic classification (Kingdom to Genus) of each OTU. File name: 16S_raw_abundance_data.xlsx 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 332 spleen rodent samples analyzed in the study. File name: 16S_presence_absence_data.xlsx Statistical Analysis Scripts and Data File This ZIP file contains the R scripts for performing statistical analyses reported in the main text and supplemental materials. There is one main file (Analyses.R), as well as two source scripts required for association screening analyses (SCN.txt and FctTestScreenENV.txt). It also includes an R-legible data file containing occurrences (presence: 1 ; absence: 0) for all pathogen exposure variables on which statistical analyses were conducted (PA_DATA.csv) for each of the 332 spleen rodent samples analyzed in the study. The column names for bacterial exposures correspond to the “Pathogen Code” given in the 16S_presence_absence_data.xlsx file. File name: Statistical Analysis Scripts and Data File.zip

This study was partly funded by the INRA Metaprogram MEM Hantagulumic, and by the European programme FP7-261504 EDENext. The manuscript is registered with the EDENext Steering Committee as EDENext409.