Comparison of DNA extraction methods for human gut microbial community profiling
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Lim MY, Song EJ, Kim SH, Lee J, Nam YD
Journal
Systematic and applied microbiology
Year
2018
Keywords:
16S rRNA gene sequencing, Bead beating, DNA extraction, Gut microbiota, Human fecal sample
The human gut harbors a vast range of microbes that have significant impact on health and disease. Therefore, gut microbiome profiling holds promise for use in early diagnosis and precision medicine development. Accurate profiling of the highly complex gut microbiome requires DNA extraction methods that provide sufficient coverage of the original community as well as adequate quality and quantity. We tested nine different DNA extraction methods using three commercial kits (TianLong Stool DNA/RNA Extraction Kit (TS), QIAamp DNA Stool Mini Kit (QS), and QIAamp PowerFecal DNA Kit (QP)) with or without additional bead-beating step using manual or automated methods and compared them in terms of DNA extraction ability from human fecal sample. All methods produced DNA in sufficient concentration and quality for use in sequencing, and the samples were clustered according to the DNA extraction method. Inclusion of bead-beating step especially resulted in higher degrees of microbial diversity and had the greatest effect on gut microbiome composition. Among the samples subjected to bead-beating method, TS kit samples were more similar to QP kit samples than QS kit samples. Our results emphasize the importance of mechanical disruption step for a more comprehensive profiling of the human gut microbiome.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-9
Subjects
- Location of subjects
- Republic of Korea
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Nucleic acid extraction protocol Nucleic acid extraction protocol,nucleic acid extraction protocol
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No bead-beating method for TS kit
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Bead-beating method for TS kit
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Bead beating facilitates DNA recovery by lysing both Gram-negative and Gram-positive bacteria.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 1
- Group 1 sample size Number of subjects in the case (exposed) group
- 1
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-9
Source: Supplementary Fig. S7a
Description: Differential microbial abundance between the no-bead-beating and bead-beating groups for the TS kit, as determined by LEfSe analysis.
Abundance in Group 1: increased abundance in Bead-beating method for TS kit
Revision editor(s): Ameenatoloko, Montana-D
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-9
Source: Supplementary Fig. S7a
Description: Differential microbial abundance between the no-bead-beating and bead-beating groups for the TS kit, as determined by LEfSe analysis.
Abundance in Group 1: decreased abundance in Bead-beating method for TS kit
Revision editor(s): Ameenatoloko
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-9
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No bead-beating method for QS kit
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Bead-beating method for QS kit
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-9
Source: Supplementary Fig. S7b
Description: Differential microbial abundance between the no-bead-beating and bead-beating groups for the QS kit, as determined by LEfSe analysis.
Abundance in Group 1: increased abundance in Bead-beating method for QS kit
Revision editor(s): Ameenatoloko, Montana-D
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-9
Source: Supplementary Fig. S7b
Description: Differential microbial abundance between the no-bead-beating and bead-beating groups for the QS kit, as determined by LEfSe analysis.
Abundance in Group 1: decreased abundance in Bead-beating method for QS kit
Revision editor(s): Ameenatoloko
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