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Microbial Communities in Nature and Laboratory - Interview
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Genome-reconstruction for eukaryotes from complex natural microbial communities.

Patrick T West1, Alexander J Probst2, Igor V Grigoriev1,3

  • 1Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.

Genome Research
|March 3, 2018
PubMed
Summary
This summary is machine-generated.

A new method, EukRep, enables recovery of eukaryotic genomes from environmental DNA. This approach reveals significant shifts in microbial community metabolism, particularly the enrichment of eukaryotes, following organic carbon addition.

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Area of Science:

  • Microbiology
  • Genomics
  • Ecology

Background:

  • Microbial eukaryotes are vital to ecosystem function but often excluded from metagenomic studies.
  • Current metagenomic analyses predominantly focus on prokaryotes, neglecting eukaryotic contributions.
  • Accurate analysis of microbial communities requires the inclusion of both prokaryotic and eukaryotic organisms.

Purpose of the Study:

  • To develop a method for recovering eukaryotic genomes from complex metagenomic samples.
  • To enable the inclusion of eukaryotes in environmental and ecosystem studies.
  • To analyze the impact of organic carbon on a geyser microbial community's eukaryotic component.

Main Methods:

  • Developed EukRep, a k-mer-based strategy for eukaryotic sequence identification.
  • Applied EukRep to separate eukaryotic and prokaryotic DNA fragments in metagenomic data.
  • Reconstructed and evaluated eukaryotic genomes for completeness and metabolic potential.

Main Results:

  • EukRep successfully enabled eukaryotic genome recovery and metabolic potential prediction.
  • Organic carbon addition to a geyser community led to a significant shift in metabolism, favoring eukaryotes.
  • Near-complete genomes of fungi and an arthropod were reconstructed, revealing functional changes like increased protease and lipase activity.

Conclusions:

  • EukRep is a valuable tool for including eukaryotes in metagenomic analyses.
  • The study demonstrates significant eukaryotic metabolic shifts in response to environmental changes.
  • This method facilitates cultivation-independent analysis of entire microbial communities, including eukaryotes.