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Related Concept Videos

Methods to Assess Microbial Communities01:19

Methods to Assess Microbial Communities

Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
11:23

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

Systematic artifacts in metagenomes from complex microbial communities.

Vicente Gomez-Alvarez1, Tracy K Teal, Thomas M Schmidt

  • 1Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.

The ISME Journal
|July 10, 2009
PubMed
Summary
This summary is machine-generated.

Metagenomics sequencing using 454 pyrosequencing contains a systematic error. This error causes overestimation of gene and taxon abundance due to artificial replicates, impacting microbiome research.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Metagenomics offers insights into microbial communities across diverse environments.
  • Accurate assessment of microbial diversity and function is crucial for ecological studies.

Purpose of the Study:

  • To identify and quantify a systematic error in 454-based pyrosequencing metagenomes.
  • To address the overestimation of gene and taxon abundance caused by artificial replicates.

Main Methods:

  • Analysis of published and original metagenomic datasets.
  • Identification of artificial replicate sequences within datasets.
  • Development of a web-based tool for artifact removal.

Main Results:

  • A systematic error was identified in 454 pyrosequencing metagenomes.
  • Artificial replicates accounted for 11% to 35% of sequences in typical metagenomes.
  • A web-based solution was developed to detect and remove these artifacts.

Conclusions:

  • The identified error significantly impacts the accuracy of metagenomic analyses.
  • Removing artificial replicates is essential for reliable microbiome studies.
  • The provided web tool aids researchers in correcting metagenomic data.