来自复杂微生物群落的宏基因组中的系统假象。

Systematic artifacts in metagenomes from complex microbial communities.

作者信息

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

机构信息

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

出版信息

ISME J. 2009 Nov;3(11):1314-7. doi: 10.1038/ismej.2009.72. Epub 2009 Jul 9.

DOI:10.1038/ismej.2009.72

PMID:19587772

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.

摘要

宏基因组学为我们提供了前所未有的视角，来了解微生物群落的分类多样性、代谢潜力及其在诸如哺乳动物胃肠道、海洋水柱和土壤等多样生物群落中的生态作用。然而，我们发现基于454焦磷酸测序产生的宏基因组中存在一个系统性错误，该错误导致对基因和分类单元丰度的高估；在一个典型的宏基因组中，11%至35%的序列是人工重复序列。在此，我们记录了几个已发表数据集和原始数据集中的这一错误，并提供了一个基于网络的解决方案（http://microbiomes.msu.edu/replicates），用于识别和去除这些人为产物。