21Rodents are major reservoirs of pathogens that can cause disease in humans and livestock. It is 22 therefore important to know what pathogens naturally circulate in rodent populations, and to 23 understand the factors that may influence their distribution in the wild. Here, we describe the 24 incidence and distribution patterns of a range of endemic and zoonotic pathogens circulating among 25 rodent communities in northern France. The community sample consisted of 713 rodents, including 26 11 host species from diverse habitats. Rodents were screened for virus exposure (hantaviruses, 27 cowpox virus, Lymphocytic choriomeningitis virus, Tick-borne encephalitis virus) using antibody 28 assays. Bacterial communities were characterized using 16S rRNA amplicon sequencing of splenic 29 samples. Multiple correspondence (MCA), regression and association screening (SCN) analyses 30 were used to determine the degree to which extrinsic factors contributed to pathogen community 31 structure, and to identify patterns of associations between pathogens within hosts. We found a rich 32 diversity of bacterial genera, with 36 known or suspected to be pathogenic. We revealed that host 33 species is the most important determinant of pathogen community composition, and that hosts that 34 share habitats can have very different pathogen communities. Pathogen diversity and co-infection 35 rates also vary among host species. Aggregation of pathogens responsible for zoonotic diseases 36 suggests that some rodent species may be more important for transmission risk than others. 37Moreover we detected positive associations between several pathogens, including Bartonella, 38Mycoplasma species, Cowpox virus (CPXV) and hantaviruses, and these patterns were generally 39 specific to particular host species. Altogether, our results suggest that host and pathogen specificity 40 is the most important driver of pathogen community structure, and that interspecific pathogen-41 pathogen associations also depend on host species. 42 43