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Related Concept Videos

Plasmids01:28

Plasmids

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Plasmids are extrachromosomal DNA molecules found in bacteria, archaea, and some eukaryotic microbes like yeast. These small, circular DNA structures typically contain fewer than 30 genes, although some may exist linearly. Plasmids vary in their number within a cell, known as copy number. Single-copy plasmids are present in one copy per cell and multi-copy plasmids are present in multiple copies, reaching over 100 copies per cell.Plasmids usually replicate independently of the chromosomal DNA...
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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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Conjugation is a form of horizontal gene transfer that primarily occurs in bacteria and some archaea, promoting genetic diversity and adaptation. Bacteria can acquire resistance genes through conjugative plasmids, allowing them to survive antibiotic treatments that would otherwise be lethal. This process involves direct contact between cells through specialized structures such as the sex pilus and is mediated by conjugative plasmids, including the F (fertility) factor.Conjugation requires...
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Bacteriophages, or phages, are viruses that specifically infect bacteria, utilizing their genetic material to hijack host cellular machinery for replication. DNA bacteriophages employ single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) genomes. These phages exhibit diverse replication strategies and host interactions, influencing their ecological roles and applications in biotechnology and medicine.ssDNA BacteriophagesssDNA phages, with their small genomes, utilize unique strategies to...
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Updated: Oct 11, 2025

Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach
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PLSDB: advancing a comprehensive database of bacterial plasmids.

Georges P Schmartz1, Anna Hartung1, Pascal Hirsch1,2

  • 1Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.

Nucleic Acids Research
|December 1, 2021
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Summary

The Plasmid Database (PLSDB) has doubled in size, now containing over 34,000 entries. This updated resource improves plasmid identification in metagenomic data by enhancing data quality, analysis functions, and accessibility for researchers.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Microbiology

Background:

  • Plasmids carry crucial genes for virulence and antibiotic resistance, making them vital in metagenomic studies.
  • The rapid growth of metagenomics data has led to an increase in false positives from misassembled plasmids.
  • Existing plasmid databases require continuous updates and improved functionality to address these challenges.

Purpose of the Study:

  • To present an updated and enhanced version of the Plasmid Database (PLSDB).
  • To improve the reliability and usability of plasmid data for metagenomic research.
  • To provide researchers with better tools for identifying and analyzing plasmids in complex biological samples.

Main Methods:

  • Aggregation of community feedback to guide database improvements.
  • Implementation of new filtering, annotation, and preprocessing steps for enhanced data quality.
  • Development of a new web-server with improved user interaction and visualization features.
  • Creation of an application programming interface (API) and Python library for automated database queries.

Main Results:

  • The PLSDB has expanded to over 34,513 entries, more than doubling its previous size.
  • Significant improvements in data quality, analysis functionality, performance, and accessibility have been implemented.
  • New web-server features facilitate deeper understanding of custom sequences through similarity visualization.
  • API and Python library enable seamless integration into automated bioinformatics workflows.

Conclusions:

  • The updated PLSDB serves as a reliable and significantly improved resource for plasmid identification in metagenomics.
  • Enhanced features and accessibility empower researchers to more effectively analyze plasmid-borne traits.
  • The continuous development of PLSDB supports the growing needs of large-scale metagenomic data analysis.