Evidence map›Paper›PMID 36180850›Full record

ArticleBMC microbiology2022

Choice of DNA extraction method affects detection of bacterial taxa from retail chicken breast.

Annika Flint, Anna Laidlaw, Leo Li, Courtney Raitt, Mary Rao, Ashley Cooper, Kelly Weedmark, Catherine Carrillo, Sandeep Tamber

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed, 1 pooled it
–field-weighted citation impact
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

4 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Review
  3. Article
  4. Article
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

9 authors.

Annika FlintBureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada.
Anna LaidlawBureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada.
Leo LiBureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada.
Courtney RaittBureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada.
Mary RaoBureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada.
Ashley CooperCanadian Food Inspection Agency, 960 Carling Road, Ottawa, ON, K1A 0Z2, Canada.
Kelly WeedmarkBureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada.
Catherine CarrilloCanadian Food Inspection Agency, 960 Carling Road, Ottawa, ON, K1A 0Z2, Canada.
Sandeep TamberBureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada. sandeep.tamber@hc-sc.gc.ca.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundSequence-based methods for the detection of bacteria such as 16S rRNA amplicon sequencing and metagenomics can provide a comprehensive view of the bacterial microbiome of food. These methods rely on the detection of gene sequences to indicate the presence of viable bacteria. This indirect form of detection can be prone to experimental artefacts. Sample handling and processing are key sources of variation that require standard approaches. Extracting sufficient quantities of high quality DNA from food matrices is challenging because target bacterial species are usually minor components of the microbiota and foods contain an array of compounds that are inhibitory to downstream DNA applications. Here, three DNA extraction methods are compared for their ability to extract high quality bacterial DNA from retail chicken breast rinses, with or without enrichment. Method performance was assessed by comparing ease of use, DNA yield, DNA quality, PCR amplicon yield, and the detection of bacterial taxa by 16S rRNA amplicon sequencing.

resultsAll three DNA extraction methods yielded DNA of sufficient quantity and quality to perform quantitative PCR and 16S rRNA amplicon sequencing. The extraction methods differed in ease of use, with the two commercial kits (PowerFood, PowerSoil) offering considerable time and cost savings over a hybrid method that used laboratory reagents for lysis and commercial column based kits for further purification. Bacterial richness as determined by 16S rRNA amplicon sequencing was similar across the three DNA extraction methods. However, differences were noted in the relative abundance of bacterial taxa, with significantly higher abundance of Gram-positive genera detected in the DNA samples prepared using the PowerFood DNA extraction kit.

conclusionThe choice of DNA extraction method can affect the detection of bacterial taxa by 16S rRNA amplicon sequencing in chicken meat rinses. Investigators should be aware of this procedural bias and select methods that are fit for the purposes of their investigation.

Indexed as

BacteriaChickensAnimalsDNA, BacterialHigh-Throughput Nucleotide SequencingReal-Time Polymerase Chain ReactionRNA, Ribosomal, 16SSequence Analysis, DNADNA, BacterialRNA, Ribosomal, 16S16S rRNA amplicon sequencingBacterial cultureBiotyperCulture independent detectionDNA extractionMetagenomicsPoultry meat

Identifiers

PMID36180850
PMCPMC9524001

What OpenQuestion holds

Textmetadata
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.