Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes
Open Access
- 16 May 2014
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 9 (5), e97876
- https://doi.org/10.1371/journal.pone.0097876
Abstract
Unbiased high-throughput sequencing of whole metagenome shotgun DNA libraries is a promising new approach to identifying microbes in clinical specimens, which, unlike other techniques, is not limited to known sequences. Unlike most sequencing applications, it is highly sensitive to laboratory contaminants as these will appear to originate from the clinical specimens. To assess the extent and diversity of sequence contaminants, we aligned 57 “1000 Genomes Project” sequencing runs from six centers against the four largest NCBI BLAST databases, detecting reads of diverse contaminant species in all runs and identifying the most common of these contaminant genera (Bradyrhizobium) in assembled genomes from the NCBI Genome database. Many of these microorganisms have been reported as contaminants of ultrapure water systems. Studies aiming to identify novel microbes in clinical specimens will greatly benefit from not only preventive measures such as extensive UV irradiation of water and cross-validation using independent techniques, but also a concerted effort to sequence the complete genomes of common contaminants so that they may be subtracted computationally.This publication has 18 references indexed in Scilit:
- MSMB variation and prostate cancer risk: Clues towards a possible fungal etiologyThe Prostate, 2014
- MSMBgene variant alters the association between prostate cancer and number of sexual partnersThe Prostate, 2013
- Sequence-Based Discovery ofBradyrhizobium entericain Cord Colitis SyndromeNew England Journal of Medicine, 2013
- Topographic diversity of fungal and bacterial communities in human skinNature, 2013
- Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype DataAmerican Journal of Human Genetics, 2012
- Microbe HuntingMicrobiology and Molecular Biology Reviews, 2010
- A New Arenavirus in a Cluster of Fatal Transplant-Associated DiseasesNew England Journal of Medicine, 2008
- Clonal Integration of a Polyomavirus in Human Merkel Cell CarcinomaScience, 2008
- WindowMasker: window-based masker for sequenced genomesBioinformatics, 2005
- Analysis of Bacteria Contaminating Ultrapure Water in Industrial SystemsApplied and Environmental Microbiology, 2002