Unravelling plasmidome distribution and interaction with its hosting microbiome

Abstract

SummaryHorizontal gene transfer via plasmids plays a pivotal role in microbial evolution. The forces that shape plasmidomes functionality and distribution in natural environments are insufficiently understood. Here, we present a comparative study of plasmidomes across adjacent microbial environments present in different individual rumen microbiomes. Our findings show that the rumen plasmidome displays enormous unknown functional potential currently unannotated in available databases. Nevertheless, this unknown functionality is conserved and shared with published rat gut plasmidome data. Moreover, the rumen plasmidome is highly diverse compared with the microbiome that hosts these plasmids, across both similar and different rumen habitats. Our analysis demonstrates that its structure is shaped more by stochasticity than selection. Nevertheless, the plasmidome is an active partner in its intricate relationship with the host microbiome with both interacting with and responding to their environment.

Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation

“…In infections, plasmids provide key virulence determinants necessary for colonisation and establishment and factors that assist in immune evasion and pathogen transmission [6,7]. Thus, in diverse habitats, plasmids are integral constituents of microbiomes, acting as potent drivers of bacterial evolutionary ecology, in large part through their role as vehicles of HGT [8][9][10][11].…”

A Peek into the Plasmidome of Global Sewage

“…These include multiple displacement amplification (MDA) with phi29 DNA polymerase prior to DNA sequencing ( 17 ), long-read sequencing technology of plasmid DNA, or the application of advanced assembly strategies ( 18 – 21 ). These studies, however, have been restricted to a single or only a few locations, and there is limited knowledge on the similarity and differences between plasmids from a range of geographical locations ( 22 – 26 ). We recently showed differences in the AMR gene profiles in urban sewage around the globe, but the locations of these AMR genes in the bacteria remain unknown ( 7 ).…”

“…To explore the plasmidome of global sewage, which is characterized by low bacterial cell numbers and challenges to isolate plasmid DNA, as previously shown ( 22 – 26 ), we employed here an optimized plasmid DNA isolation procedure, followed by both plasmid-safe DNase treatment and MDA to obtain sufficient plasmid DNA for Oxford Nanopore sequencing from global urban sewage samples. To improve plasmidome characterizations, we developed an assembly workflow, utilizing the long-read length from the Oxford Nanopore MinION sequencer and Illumina sequences.…”

Metagenomic assembled plasmids of the human microbiome vary across disease cohorts

“…A recent comparison of rat caecal and rumen plasmidomes demonstrated conserved functional traits, including mobilization and stabilization 12 , 13 . When rumen plasmidomes were compared with their associated microbiomes it was observed that (1) plasmidomes were more diverse than the microbiome, (2) the average similarity of plasmidomes between animals was lower than that of their microbiomes, (3) the compositions of plasmidomes and microbiomes were closely correlated, and (4) the microbiome and plasmidome both changed with diet 14 . These plasmidome studies clearly indicate niche-adapting functions encoded by plasmids from gut environments, suggesting that the total diversity and functional capabilities of plasmids remains underappreciated in most microbiome studies.…”