Evidence map›Paper›PMID 23684993›Full record

ArticleJournal of microbiological methods2013

A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples.

Shantelle Claassen, Elloise du Toit, Mamadou Kaba, Clinton Moodley, Heather J Zar, Mark P Nicol

Open access · hybridAbstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of microbiological methods, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.

0numbers the graph read from it
0cells of the map it votes in
85citing papers in PubMed
5.6field-weighted citation impact, top 3% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

85 citing papers in PubMed, 174 citations in OpenAlex.

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25 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors at 3 institutions in 1 country.

Shantelle ClaassenDivision of Medical Microbiology, Department of Clinical Laboratory Science, University of Cape Town, Cape Town, South Africa. Electronic address: shantelle.claassen@gmail.com.
Elloise du ToitDivision of Medical Microbiology, Department of Clinical Laboratory Science, University of Cape Town, Cape Town, South Africa.
Mamadou KabaDivision of Medical Microbiology, Department of Clinical Laboratory Science, University of Cape Town, Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
Clinton MoodleyNational Health Laboratory Service, National Institute for Communicable Diseases, Groote Schuur Hospital, Cape Town, South Africa.
Heather J ZarDepartment of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa.
Mark P NicolDivision of Medical Microbiology, Department of Clinical Laboratory Science, University of Cape Town, Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
University of Cape Town · ZAGroote Schuur Hospital · ZARed Cross War Memorial Children's Hospital · ZA

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Differences in the composition of the gut microbiota have been associated with a range of diseases using culture-independent methods. Reliable extraction of nucleic acid is a key step in identifying the composition of the faecal microbiota. Five widely used commercial deoxyribonucleic acid (DNA) extraction kits (QIAsymphony® Virus/Bacteria Midi Kit (kit QS), ZR Fecal DNA MiniPrep™ (kit Z), QIAamp® DNA Stool Mini Kit (kit QA), Ultraclean® Fecal DNA Isolation Kit (kit U) and PowerSoil® DNA Isolation Kit (kit P)) were evaluated, using human faecal samples. Yield, purity and integrity of total genomic DNA were compared spectrophotometrically and using gel electrophoresis. Three bacteria, commonly found in human faeces were quantified using real time polymerase chain reaction (qPCR) and total bacterial diversity was studied using denaturing gradient gel electrophoresis (DGGE) as well as terminal restriction fragment length polymorphism (T-RFLP). The measurements of DNA yield and purity exhibited variations between the five kits tested in this study. Automated kit QS exhibited the best quality and highest quantity of DNA. All kits were shown to be reproducible with CV values≤0.46 for DNA extraction. qPCR results showed that all kits were uniformly efficient for extracting DNA from the selected target bacteria. DGGE and T-RFLP produced the highest diversity scores for DNA extracted using kit Z (H'=2.30 and 1.27) and kit QS (H'=2.16 and 0.94), which also extracted the highest DNA yields compared to the other kits assessed.

Indexed as

Genetic TechniquesBacteriaDenaturing Gradient Gel ElectrophoresisDNA, BacterialFecesHumansPolymerase Chain ReactionReagent Kits, DiagnosticDNA, BacterialReagent Kits, DiagnosticBacteriaDGGEDNA extractionFaecesReal-time PCRT-RFLP

Identifiers

PMID23684993
PMCPMC5809576
OpenAlexW1987557410

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.