Plasmids are the main drivers in development and spread of antibiotic resistance, virulence factors or xenobiotic degradation capabilities between bacterial genera. Contrary to popular belief, this does not mean that the majority of plasmids in natural environments carries accessory genes, but rather reflects the methods of investigation. Recently, several metagenomic approaches have evolved to investigate the naturally non-selected gene pool of environmental microbes. We have earlier demonstrated that one rat gut mobilome contains hundreds of hitherto unknown circular plasmids and DNA elements with few accessory genes. In this study we analyse the mobile gene pool in rat gut microbiota from environments of contrasting anthropogenic pressures to investigate the environmental effect on the plasmid presence and diversity. Brown rats from Danish hospital sewers and urban settings, and brown rats from remote and pristine islands in the Falkland Islands archipelago were sampled and chromosomal-DNA-free mobilomes were produced from cecal content and subsequently sequenced on HiSeq and MiSeq Illumina platforms using two approaches. Identification of complete, circular plasmids within the assembled sequences was performed with a bespoke pipeline verifying circularity independently twice. Using this methodology, we compare hundreds of newly discovered, completely assembled, circular and novel plasmids between the geographically separated and contrasting environments. Intriguingly, circular elements first identified in samples from the sewers of Danish hospitals are can also be found in highly conserved versions in samples from the Falkland Islands. Further metagenomic analysis on antibiotic resistance genes and virulence genes and 16S rRNA genes from the rat bacteria is compared to describe the environmental influence on gut microbiota DNA.