Cited by 512Microbial Community Ecology and PhysiologyGut microbiota and healthGenomics and Phylogenetic Studies

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Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

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Yuan, Sanqing, Cohen, Dora B., Ravel, Jacques, Abdo, Zaid, Forney, Larry J.·2012·PLoS ONE

DOI 10.1371/journal.pone.0033865PMC PMC3311548

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Abstract

BACKGROUND: DNA extraction is an essential step in all cultivation-independent approaches to characterize microbial diversity, including that associated with the human body. A fundamental challenge in using these approaches has been to isolate DNA that is representative of the microbial community sampled. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we statistically evaluated six commonly used DNA extraction procedures using eleven human-associated bacterial species and a mock community that contained equal numbers of those eleven species. These methods were compared on the basis of DNA yield, DNA shearing, reproducibility, and most importantly representation of microbial diversity. The analysis of 16S rRNA gene sequences from a mock community showed that the observed species abundances were significantly different from the expected species abundances for all six DNA extraction methods used. CONCLUSIONS/SIGNIFICANCE: Protocols that included bead beating and/or mutanolysin produced significantly better bacterial community structure representation than methods without both of them. The reproducibility of all six methods was similar, and results from different experimenters and different times were in good agreement. Based on the evaluations done it appears that DNA extraction procedures for bacterial community analysis of human associated samples should include bead beating and/or mutanolysin to effectively lyse cells.

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Authors: Yuan, S., Cohen, D. B., Ravel, J., Abdo, Z., & Forney, L. J.
Affiliations: University of Idaho (US)
University of Maryland, Baltimore (US)
Corresponding author: Forney, Larry J.
ORCID: Ravel, Jacques
Abdo, Zaid
Forney, Larry J.
Venue: PLoS ONE
Publisher: Public Library of Science (PLoS)
Published: 2012-03-23
Volume: 7
Issue: 3
Pages: e33865
ISSN: 1932-6203 (ISSN-L)
DOI: 10.1371/journal.pone.0033865
PMC: PMC3311548
OpenAlex: W2090110425
Cited by: 511
References: 73
Citations by year: 2026: 16 · 2025: 19 · 2024: 24 · 2023: 29 · 2022: 24 · 2021: 57 · 2020: 50 · 2019: 50 · 2018: 63 · 2017: 60 · 2016: 37 · 2015: 28 · 2014: 32 · 2013: 20 · 2012: 2
FWCI: 23.16
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (unspecified)
Locations: PLoS ONE (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Figshare (submittedVersion, cc-by)
Funders: National Institutes of Health (5u01ai070921-07)
National Institute of Allergy and Infectious Diseases (U01-AI070921)
Topics: Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: DNA extraction, human microbiome, mock communities, bead beating, mutanolysin, DNA shearing, 16S rRNA gene, microbial diversity, extraction method comparison, cell lysis
MeSH terms: Bacteria, DNA, Bacterial, Humans, Biodiversity

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Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

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