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Archaeal viruses play a crucial role in the ecosystems of extremophilic archaea, particularly those belonging to the phyla Euryarchaeota and Crenarchaeota. By shaping host evolution and facilitating gene transfer, these viruses influence microbial communities and contribute to genetic diversity in extreme environments. The archaea they infect thrive in acidic hot springs and hydrothermal vents characterized by high temperatures and low pH. Archaeal viruses exhibit remarkable structural...
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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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The human body harbors a vast and diverse viral community known as the human virome. The virome includes bacteriophages that infect bacteria, and eukaryotic viruses that infect human cells. Transient dietary and environmental viruses also contribute to this dynamic ecosystem. Estimates suggest the human body may contain on the order of 10¹³ viral particles, though abundance varies widely by body site and detection method.Comprehensive characterization of the virome has become possible...
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Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
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Navigating prokaryotic viral genome analysis from metagenomic data.

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  • 1Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany.

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This minireview simplifies viral metagenomics for non-specialists, focusing on bacterial and archaeal DNA viruses. It guides users through challenges and a typical viromic workflow for analyzing microbial communities.

Keywords:
DNA virusesarchaeabacteriabioinformatics methodscomputational biologymetagenomicsviromics

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Virology

Background:

  • Viruses are vital components of microbial ecosystems.
  • Viromic analysis is complex and rapidly evolving.
  • Analyzing viral DNA from metagenomic data presents significant challenges.

Purpose of the Study:

  • To support non-specialists in understanding viromic analysis.
  • To provide a guide to bacterial and archaeal DNA virus analysis from metagenomic data.
  • To address key challenges in viromics, including diversity, biases, and tool selection.

Main Methods:

  • Review of current viromic analysis workflows.
  • Explanation of steps from data acquisition to downstream analysis.
  • Focus on analysis of bacterial and archaeal DNA viruses.

Main Results:

  • A typical viromic workflow is described.
  • Background information is provided for each analytical step.
  • Challenges such as viral diversity and methodological biases are discussed.

Conclusions:

  • This review equips non-specialists to confidently perform virome analysis.
  • It offers resources and background for navigating the viromic landscape.
  • The guide facilitates understanding of viral DNA analysis in microbial ecosystems.