Plasmids, Viruses, And Other Circular Elements In Rat Gut

Abstract

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

A specific class of infectious agents isolated from bovine serum and dairy products and peritumoral colon cancer tissue

“…BLASTN comparisons to available DNA databanks, revealed similarity mainly to bacterial plasmids ( A. baumannii str). AYE plasmid p4ABAYE [34], A. baumannii strain A85 plasmid pA85-1 [35], and A. baumannii strain DS002 plasmid pTS236 [36], but also to ssDNA isolates from Rat gut (pRGRH0103 and pRGRH0636) [37] (Suppl. Table 2).…”

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

“…First, the DTR contigs were used as input to VirFinder v.1.1 with default parameters, and to CheckV to identify viral and microbial marker genes. We additionally searched for genes related to plasmids and other nonviral mobile genetic elements using a database of 141 HMMs from recent publications [57][58][59] . A contig was classified as viral if the number of viral genes exceeded that of microbial and plasmid genes (n = 99,345), or VirFinder reported a P < 0.01 with no plasmid genes and no more than one identified microbial gene (n = 36,084).…”

CheckV: assessing the quality of metagenome-assembled viral genomes

“…First, the DTR contigs were used as input to VirFinder v1.1 with default parameters and to CheckV to identify viral and microbial marker genes. We additionally searched for genes related to plasmids and other non-viral mobile genetic elements using a database of 141 HMMs from recent publications [50][51][52]. A contig was classified as viral if the number of viral genes exceeded number of microbial and plasmid genes (N=99,345), or VirFinder reported a p-value < 0.01 with no plasmid genes and <= 1 microbial gene (N=36,084).…”