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

The DOI matches its Crossref record; 72 of the 73 references it cites were found in a registry or an index.

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

Open access
Yuan, Sanqing, Cohen, Dora B., Ravel, Jacques, Abdo, Zaid, Forney, Larry J.·2012·PLoS ONE
DOI 10.1371/journal.pone.0033865PMC PMC3311548
Open this paper in CoChat — free accountOpen PDF

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.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1371/journal.pone.0033865

Cites

72 of 72 references verified0 citation errors · 0 not checkable

Statistics

Figures

Figure 1 Boxplot of Euclidean distances between observed and expected species proportions. Euclidean distances between observed and expected proportions were calculated for each of eight replicates of each method.
Figure 1 Boxplot of Euclidean distances between observed and expected species proportions. Euclidean distances between observed and expected proportions were calculated for each of eight replicates of each method.CC BY · PubMed Central
Figure 2 Boxplot of Euclidean distances between observed and grand proportions. To calculate grand proportions, the total counts of 16S rRNA gene reads of each species were calculated for eight replicates of each method. Then grand proportions were calculated based on total counts of 16S rRNA gene reads of each species per method. Grand proportions were used to calculate Euclidean distances between observed and grand proportions.
Figure 2 Boxplot of Euclidean distances between observed and grand proportions. To calculate grand proportions, the total counts of 16S rRNA gene reads of each species were calculated for eight replicates of each method. Then grand proportions were calculated based on total counts of 16S rRNA gene reads of each species per method. Grand proportions were used to calculate Euclidean distances between observed and grand proportions.CC BY · PubMed Central
Figure 3 DNA extractions using different enzymatic lysis modes. The mean concentrations (columns) were calculated based on nine replicated extractions per sample per mode. Pair-wise comparisons of DNA concentrations between modes per sample were performed by using Wilcoxon rank sum test. Bonferroni correction was used for multiple testing. Letters at the top of columns indicate whether there is significantly difference between columns per sample. Means with the same letter are not significantly different.
Figure 3 DNA extractions using different enzymatic lysis modes. The mean concentrations (columns) were calculated based on nine replicated extractions per sample per mode. Pair-wise comparisons of DNA concentrations between modes per sample were performed by using Wilcoxon rank sum test. Bonferroni correction was used for multiple testing. Letters at the top of columns indicate whether there is significantly difference between columns per sample. Means with the same letter are not significantly different.CC BY · PubMed Central

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 73 references

Research works printed but not linked: 1

  1. J Ravel, 2010, Microbes and Health Sackler Colloquium: Vaginal microbiome of reproductive-age women., Proc Natl Acad Sci U S A

Cited by

Sorted by citations

Related

See all

Metadata

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
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
Licence
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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review