Microbiome diversity and zoonotic bacterial pathogen prevalence in Peromyscus mice from agricultural landscapes and synanthropic habitat

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 rodents that
thrive in human-built environments (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
examine the effect of agricultural development and synanthropic habitat on
microbiome diversity and the prevalence of zoonotic bacterial pathogens in
wild Peromyscus mice to better understand the role of these rodents in
pathogen maintenance and transmission. We conducted 16S amplicon
sequencing on fecal samples using long-read Nanopore sequencing technology
to characterize the rodent microbiome. We compared microbiome diversity
and composition between forest and synanthropic habitats in agricultural
and undeveloped landscapes and screened for putative pathogenic bacteria.
Microbiome richness, diversity, and evenness were higher in the
agricultural landscape and synanthropic habitat compared to
undeveloped-forest habitat. Microbiome composition also differed
significantly between agricultural and undeveloped landscapes and forest
and synanthropic habitat. We detected overall low diversity and abundance
of putative pathogenic bacteria, though putative pathogens were more
likely to be found in mice from the agricultural landscape. Our findings
show that landscape- and habitat-level anthropogenic factors affect
Peromyscus microbiomes and suggest that landscape-level agricultural
development may be important to predict zoonotic pathogen prevalence.
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.