Plasmids, Viruses, And Other Circular Elements In Rat Gut

Circular DNA such as plasmids and some viruses is the major source of genetic variation in bacteria and thus has the same important evolutionary function as sexual reproduction in eukaryotic species: It allows dissemination of advantageous traits through bacterial populations. Here, we present the largest collection of novel complete extrachromosomal genetic elements to date, and compare the diversity, distribution, and content of circular sequences from 12 rat cecum samples from the pristine Falkland Islands and Danish hospital sewers, two environments with contrasting anthropogenic impact. Using a validated pipeline, we find 1,869 complete, circular, non-redundant sequences, of which only 114 are previously described. While sequences of similar size from the two environments share general features, the size distribution of the elements between environments differs significantly, with hospital sewer samples hosting larger circular elements than Falkland Island samples, a possible consequence of the massive anthropogenic influence in the hospital sewer environment. Several antibiotic resistance genes have been identified with a notably larger diversity in hospital sewer samples than in Falkland Islands samples in concordance with expectations. Our findings suggest that even though sequences of similar length carry similar traits, the mobilome of rat gut bacteria are affected by human activities in that sewer rats have larger elements and more diverse large elements than pristine island rats. More than 1000 novel and not classified small sequences was identified and hint the existence of a biological unit not previously described on a community level. List of figures Sampling sites and Rat gut anatomy Rarefaction curves of circular elements Elements shared between environments Size distribution plots of rep, mob, stab, capsid carrying elements. Graphical representation of representative elements Replication genes content, diversity Rep_2 plasmid replication gene phylogeny Table Resfams findings List of appendices basic statistics table Phylogeny of plasmid replication genes List of known plasmids and circular sequences found in 1869 elements Automatic identification of identical circular elements with different breaking points Test of separation of plasmids and viruses based on predicted, annotated genes No false positive circular sequences from MG1655 genomic sequencing.