The microbiome of P. leucopus, a notable reservoir host species for emerging infectious diseases in North America

Microbiome studies generally focus on guts, and a large proportion of the detected species therefore are commensal bacteria. Here we propose a first analysis of the liver microbiome using next generation sequencing as a tool to detect potentially pathogenic strains. We used the main reservoir host species of Lyme disease in eastern North America, Peromyscus leucopus, as a model and we sequenced the V5-V6 regions from the 16S gene from 18 populations in southern Quebec, Canada. The liver microbiome was dominated by the genus Lactobacillus. We also detected a large proportion of individuals contaminated by Bartonella vinsonii arupensis, a human pathogenic bacteria responsible for endocardiotis, as well as Borrelia burgdorferi, the pathogen responsible for Lyme disease in North America. We report for the first time, the presence of B. burgdorferi in a mammal on the north shore of the St-Lawrence river, supporting models predicting the northern spread of Lyme disease in Canada. Finally, we also compared the microbiomes among two distinct genetic clusters of mice living on either side of the St-Lawrence river, but we did not find any effect of the host genotype on the liver microbiome assemblages .