Lactobacilli and other gastrointestinal microbiota ofPeromyscus leucopus, reservoir host for agents of Lyme disease and other zoonoses in North America

The cricetine rodentPeromyscus leucopusis an important reservoir for several human zoonoses, including Lyme disease, in North America. Akin to hamsters, the white-footed deermouse has been unevenly characterized in comparison to the muridMus musculus. To further understanding ofP.leucopus' total genomic content, we investigated gut microbiomes of an outbred colony ofP.leucopus, inbredM.musculus, and a natural population ofP.leucopus. Metagenome and whole genome sequencing were combined with microbiology and microscopy approaches. A focus was the genusLactobacillus, four diverse species of which were isolated from forestomach and feces of colonyP.leucopus. Three of the species-L.animalis,L.reuteri, and provisionally-named species L. peromysci-were identified in fecal metagenomes of wildP.leucopusbut not discernibly in samples fromM.musculus.L.johnsonii, the fourth species, was common inM.musculusbut absent or sparse in wildP.leucopus. Also identified in both colony and natural populations were aHelicobactersp. in feces but not stomach, and aTritrichomonassp. protozoan in cecum or feces. The gut metagenomes of colonyP.leucopuswere similar to those of colonyM.musculusat the family or higher level and for major subsystems. But there were multiple differences between species and sexes within each species in their gut metagenomes at orthologous gene level. These findings provide a foundation for hypothesis-testing of functions of individual microbial species and for interventions, such as bait vaccines based on an autochthonous bacterium and targetingP.leucopusfor transmission-blocking.