Host DNA Depletion in Saliva Samples for Improved Shotgun Metagenomics

Clarisse Marotz; Cristal Zuniga; Livia Zaramela; Rob Knight; Karsten Zengler

doi:10.1007/978-1-0716-1518-8_6

Host DNA Depletion in Saliva Samples for Improved Shotgun Metagenomics

Methods Mol Biol. 2021:2327:87-92. doi: 10.1007/978-1-0716-1518-8_6.

Authors

Clarisse Marotz¹, Cristal Zuniga², Livia Zaramela², Rob Knight^{2

3

4}, Karsten Zengler^{2

3}

Affiliations

¹ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. [email protected].
² Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
³ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
⁴ Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.

PMID: 34410641
DOI: 10.1007/978-1-0716-1518-8_6

Abstract

Host DNA makes up the majority of DNA in a saliva sample. Therefore, shotgun metagenomics can be an inefficient way to evaluate the microbial populations of saliva since often <10% of the sequencing reads are microbial. In this chapter, we describe a method to deplete human DNA from fresh or frozen saliva samples, allowing for more efficient shotgun metagenomic sequencing of the salivary microbial community.

Keywords: Bacteria; Metagenomics; Microbial DNA enrichment; Oral; Propidium monoazide (PMA).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA / genetics
Humans
Metagenome
Metagenomics*
Microbiota* / genetics
Saliva
Sequence Analysis, DNA

Substances

DNA