Rodents are key reservoirs of zoonotic pathogens and play an important
role in disease transmission to humans. Importantly, anthropogenic
land-use change has been found to increase the abundance of synanthropic
rodents, particularly rodent reservoirs of zoonotic disease.
Anthropogenic environments also affect the microbiome of synanthropic
wildlife, influencing wildlife health and potentially introducing novel
pathogens. Our objective was to characterize the microbiome and
investigate the prevalence of zoonotic bacterial pathogens in
synanthropic rodents in native and anthropogenic environments to better
understand their role in pathogen maintenance and transmission. We
sampled wild Peromyscus mice in agricultural and undeveloped landscapes
and forest and synanthropic habitat in Minnesota, USA and conducted 16S
amplicon sequencing using long-read Nanopore sequencing technology on
fecal samples to characterize the rodent microbiome. We compared
community composition and diversity between habitats and screened for
the presence of putative pathogenic bacteria species. Microbiome
community composition differed significantly between agricultural and
undeveloped landscapes and forest and synanthropic habitat while
microbiome richness, diversity, and evenness were lower in
undeveloped-forest habitat compared to all other habitats. We detected
overall low abundance and diversity of putative pathogenic bacteria,
though the greatest number of pathogenic bacteria were detected in the
agricultural-forest habitat. Our findings show that rodent microbiome
community composition differs across landscapes and habitat types but
suggest that landscape-level anthropogenic factors may be most important
to predict zoonotic pathogen abundance. Ultimately, understanding how
anthropogenic land-use change and synanthropy affect rodent microbiomes
and pathogen prevalence is important to managing transmission of
rodent-borne zoonotic diseases to humans.