Evidence map›Paper›PMID 25261520›Full record

ArticleApplied and environmental microbiology2014

Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling.

Stephen J Salipante, Toana Kawashima, Christopher Rosenthal, Daniel R Hoogestraat, Lisa A Cummings, Dhruba J Sengupta, Timothy T Harkins, Brad T Cookson, Noah G Hoffman

Erratum issuedAbstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Applied and environmental microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 139 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
139citing papers in PubMed, 2 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

139 citing papers in PubMed, 2 syntheses or guidelines pooled it.

  1. Diagnostic accuracy of the metagenomic next-generation sequencing (mNGS) for detection of bacterial meningoencephalitis: a systematic review and meta-analysis.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2022
    Pooled it
  2. Pooled it
  3. Trial
  4. Article
  5. Article
  6. Article
  7. Review
  8. Review
  9. Article
  10. Review
  11. Review
  12. Article
  13. Article
  14. Article
  15. Review
  16. Article
  17. Review
  18. Article
  19. Review
  20. Article

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

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Stephen J SalipanteDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA stevesal@uw.edu ngh2@uw.edu.
Toana KawashimaDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
Christopher RosenthalDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
Daniel R HoogestraatDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
Lisa A CummingsDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
Dhruba J SenguptaDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
Timothy T HarkinsLife Technologies, South San Francisco, California, USA.
Brad T CooksonDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA Department of Microbiology, University of Washington, Seattle, Washington, USA.
Noah G HoffmanDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA stevesal@uw.edu ngh2@uw.edu.

Funding

Institute of Translational Health SciencesUL1TR000423 · NCATS · UNIVERSITY OF WASHINGTON · PI DISIS, MARY L. · 2012 to 2016
$49.4M
NCATS NIH HHS UL1 TR000423NCATS NIH HHS UL1TR000423
6 · The paper itself

Abstract

High-throughput sequencing of the taxonomically informative 16S rRNA gene provides a powerful approach for exploring microbial diversity. Here we compare the performances of two common "benchtop" sequencing platforms, Illumina MiSeq and Ion Torrent Personal Genome Machine (PGM), for bacterial community profiling by 16S rRNA (V1-V2) amplicon sequencing. We benchmarked performance by using a 20-organism mock bacterial community and a collection of primary human specimens. We observed comparatively higher error rates with the Ion Torrent platform and report a pattern of premature sequence truncation specific to semiconductor sequencing. Read truncation was dependent on both the directionality of sequencing and the target species, resulting in organism-specific biases in community profiles. We found that these sequencing artifacts could be minimized by using bidirectional amplicon sequencing and an optimized flow order on the Ion Torrent platform. Results of bacterial community profiling performed on the mock community and a collection of 18 human-derived microbiological specimens were generally in good agreement for both platforms; however, in some cases, results differed significantly. Disparities could be attributed to the failure to generate full-length reads for particular organisms on the Ion Torrent platform, organism-dependent differences in sequence error rates affecting classification of certain species, or some combination of these factors. This study demonstrates the potential for differential bias in bacterial community profiles resulting from the choice of sequencing platform alone.

Indexed as

BacteriaBacterial InfectionsDNA, BacterialHigh-Throughput Nucleotide SequencingHumansRNA, Ribosomal, 16SDNA, BacterialRNA, Ribosomal, 16S

Identifiers

PMID25261520
PMCPMC4249215

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.