ena-STUDY-NATIONAL FOOD INSTITUTE - DTU-06-11-2020-21:02:48:625-229
A Peak into the Plasmidome of Global Sewage
Plasmids are self-replicating extra chromosomal entities predominantly found in bacterial cells. Supplying the cell with a wide range of beneficial traits, for example antimicrobial, heavy metal resistances, virulence factors, or metabolic functions. Making them an important research topic especially in public health research for their key role in the spread of antimicrobial resistances and plasmid mediated outbreaks. However, identification and reconstruction of plasmid remain a hard task from isolates as well as metagenomic samples.We present a proof-of-concept study to extract plasmids from complex metagenomic samples as well as assembly from single Nanopore reads. For this, we combine amplification using F29 DNA polymerase with Nanopore sequencing to create reads of tandem-repeats that are then reduced to represent the complete plasmid sequence.Using our method on 24 sewage samples from 5 different continents, we recovered 181,219 circular elements of which 74,100 harbor plasmid and 15,735 viral related genes. Furthermore, we investigated their functional properties as well as their identity to known plasmids.
Plasmids are self-replicating extra chromosomal entities predominantly found in bacterial cells. Supplying the cell with a wide range of beneficial traits, for example antimicrobial, heavy metal resistances, virulence factors, or metabolic functions. Making them an important research topic especially in public health research for their key role in the spread of antimicrobial resistances and plasmid mediated outbreaks. However, identification and reconstruction of plasmid remain a hard task from isolates as well as metagenomic samples.We present a proof-of-concept study to extract plasmids from complex metagenomic samples as well as assembly from single Nanopore reads. For this, we combine amplification using F29 DNA polymerase with Nanopore sequencing to create reads of tandem-repeats that are then reduced to represent the complete plasmid sequence.Using our method on 24 sewage samples from 5 different continents, we recovered 181,219 circular elements of which 74,100 harbor plasmid and 15,735 viral related genes. Furthermore, we investigated their functional properties as well as their identity to known plasmids.