Short Communication
Subject Category: Integrated genomics and post-genomics approaches in microbial ecology
The ISME Journal (2009) 3, 1314–1317; doi:10.1038/ismej.2009.72; published online 9 July 2009
Systematic artifacts in metagenomes from complex microbial communities
Vicente Gomez-Alvarez1,3, Tracy K Teal1,3 and Thomas M Schmidt1,2
- 1Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- 2Kellogg Biological Station, Michigan State University, East Lansing, MI, USA
Correspondence: TM Schmidt, Department of Microbiology and Molecular Genetics, Michigan State University, 6180 Biomedical and Physical Sciences Building, East Lansing, MI 48824-1101, USA. E-mail: tschmidt@msu.edu
3These authors contributed equally to this work.
Received 13 February 2009; Revised 28 May 2009; Accepted 2 June 2009; Published online 9 July 2009.
Abstract
Metagenomics is providing an unprecedented view of the taxonomic diversity, metabolic potential and ecological role of microbial communities in biomes as diverse as the mammalian gastrointestinal tract, the marine water column and soils. However, we have found a systematic error in metagenomes generated by 454-based pyrosequencing that leads to an overestimation of gene and taxon abundance; between 11% and 35% of sequences in a typical metagenome are artificial replicates. Here we document the error in several published and original datasets and offer a web-based solution (http://microbiomes.msu.edu/replicates) for identifying and removing these artifacts.
Keywords:
metagenomics, microbial communities, molecular census, pyrosequencing
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