Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples

PLoS Pathog. 2014 Nov 20;10(11):e1004437. doi: 10.1371/journal.ppat.1004437. eCollection 2014 Nov.


The high level of accuracy and sensitivity of next generation sequencing for quantifying genetic material across organismal boundaries gives it tremendous potential for pathogen discovery and diagnosis in human disease. Despite this promise, substantial bacterial contamination is routinely found in existing human-derived RNA-seq datasets that likely arises from environmental sources. This raises the need for stringent sequencing and analysis protocols for studies investigating sequence-based microbial signatures in clinical samples.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Nucleic Acid*
  • Equipment Contamination*
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Infections / diagnosis*
  • Infections / genetics*

Associated data

  • GEO/GSE30611