Metagenomic analysis of wild urban Rats (Rattus spp.) highlights the sympatric nature of rat and human microbial ecology. Metagenomic analysis of wild urban Rats

Norway and black rats (Rattus norvegicus and Rattus rattus) are the source of a number of zoonotic bacteria responsible for human morbidity and mortality in cities worldwide. Past research has been narrowly focused on pathogens traditionally associated with rats (e.g., Leptospira interrogans, Yersinia pestis, etc.) therefore the true range of rat-associated zoonotic risk remains unknown. Additionally, given that past studies have relied on traditional diagnostic approaches (e.g., serology, culture, and PCR), there is very little known about the microbial ecology of wild rats. This study used metagenomics to characterize bacterial and viral populations in the lungs and feces of wild, urban Norway and black rats, and to identify bacteria with the potential to cause disease in people. A number of potentially pathogenic bacteria were detected, including genera that had not been detected in rats before, such as Haemophilus and Neisseria, and were likely acquired from sympatric human populations. Genes associated with bacterial resistance and mobile pathogenicity islands were also identified. Microbiome composition varied markedly among rats collected from a relatively small geographic area and the majority of this variation was likely the result of a complex interaction of factors unique to individual rats. These results suggest that the potential public health risks associated with wild rats are more broad and complex than previously appreciated.