Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles

Maria T. Nelson, Christopher E. Pope, Robyn L. Marsh, Daniel J. Wolter, Eli J. Weiss, Kyle R. Hager, Anh T. Vo, Mitchell J. Brittnacher, Matthew C. Radey, Hillary S. Hayden, Alexander Eng, Samuel I. Miller, Elhanan Borenstein, Lucas R. Hoffman

Research output: Contribution to journalArticlepeer-review

Abstract

Nelson et al. describe a method for reducing both human cellular DNA and extracellular DNA (human and bacterial) in a complex respiratory sample using hypotonic lysis and endonuclease digestion. This method increases effective microbial sequencing depth and minimizes bias introduced into subsequent phylogenetic analysis by bacterial extracellular DNA.

Original languageEnglish
Pages (from-to)2227-2240.e5
JournalCell Reports
Volume26
Issue number8
DOIs
StatePublished - 19 Feb 2019

Keywords

  • clinical samples
  • cystic fibrosis
  • extracellular DNA
  • human DNA
  • infection samples
  • metagenome
  • microbiome
  • microbiota
  • polymicrobial infections
  • sputum

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