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Related Experiment Videos

Divide and conquer: enriching environmental sequencing data.

Anne Bergeron1, Mahdi Belcaid, Grieg F Steward

  • 1Computer Science, Université du Québec à Montréal, Montreal, Canada. bergeron.anne@uqam.ca

Plos One
|September 6, 2007
PubMed
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Splitting microbial communities before sequencing improves genome assembly, especially in high-diversity environments. This strategy maximizes information recovery from sequencing efforts by increasing the proportion of usable sequences.

Area of Science:

  • Environmental sequencing
  • Metagenomics
  • Genomics

Background:

  • Environmental sequencing projects aim to reconstruct microbial genomes from mixed DNA samples.
  • High species diversity or uneven species distribution leads to a high proportion of non-overlapping sequences, hindering genome assembly.
  • Dominant species can be over-sequenced, reducing coverage for rare species.

Purpose of the Study:

  • To investigate if splitting microbial communities prior to sequencing enhances genome assembly.
  • To determine the effectiveness of community splitting across various diversity distributions.

Main Methods:

  • Utilized the Lander-Waterman model to assess the impact of splitting on singleton sequences.
  • Constructed simulated microbial communities with uniform and non-uniform distributions.

Related Experiment Videos

  • Evaluated the proportion of sequences that could be assembled after splitting.

    • Main Results:

    • Splitting microbial communities significantly increases the proportion of sequences that can be assembled.
    • The Lander-Waterman model indicates splitting is beneficial when singleton sequences exceed 25%.
    • Simulations confirmed that community splitting improves assembly even with highly non-uniform species distributions.

    Conclusions:

    • Splitting microbial communities before sequencing is a recommended strategy for maximizing information recovery in high-diversity environments.
    • Methods for splitting communities based on physical properties are readily available.
    • This approach enhances the yield of assembled genomes from environmental sequencing projects.