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A multi-amplicon 16S rRNA sequencing and analysis method for improved taxonomic profiling of bacterial communities

Overview of attention for article published in Journal of Microbiological Methods, September 2018
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  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (79th percentile)
  • High Attention Score compared to outputs of the same age and source (92nd percentile)

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Title
A multi-amplicon 16S rRNA sequencing and analysis method for improved taxonomic profiling of bacterial communities
Published in
Journal of Microbiological Methods, September 2018
DOI 10.1016/j.mimet.2018.09.019
Pubmed ID
Authors

Andrew E Schriefer, Paul F Cliften, Matthew C Hibberd, Christopher Sawyer, Victoria Brown-Kennerly, Lauren Burcea, Elliott Klotz, Seth D Crosby, Jeffrey I Gordon, Richard D Head

Abstract

Metagenomic sequencing of bacterial samples has become the gold standard for profiling microbial populations, but 16S rRNA profiling remains widely used due to advantages in sample throughput, cost, and sensitivity even though the approach is hampered by primer bias and lack of specificity. We hypothesized that a hybrid approach, that combined targeted PCR amplification with high-throughput sequencing of multiple regions of the genome, would capture many of the advantages of both approaches. We developed a method that identifies and quantifies members of bacterial communities through simultaneous analysis of multiple variable regions of the bacterial 16S rRNA gene. The method combines high-throughput microfluidics for PCR amplification, short read DNA sequencing, and a custom algorithm named MVRSION (Multiple 16S Variable Region Species-Level IdentificatiON) for optimizing taxonomic assignment. MVRSION performance was compared to single variable region analyses (V3 or V4) of five synthetic mixtures of human gut bacterial strains using existing software (QIIME), and the results of community profiling by shotgun sequencing (COPRO-Seq) of fecal DNA samples collected from gnotobiotic mice colonized with a defined, phylogenetically diverse consortium of human gut bacterial strains. Positive predictive values for MVSION ranged from 65%-91% versus 44%-61% for single region QIIME analyses (p < .01, p < .001), while the abundance estimate r2 for MVRSION compared to COPRO-Seq was 0.77 vs. 0.46 and 0.45 for V3-QIIME and V4-QIIME, respectively. MVRSION represents a generally applicable tool for taxonomic classification that is superior to single-region 16S rRNA methods, resource efficient, highly scalable for assessing the microbial composition of up to thousands of samples concurrently, with multiple applications ranging from whole community profiling to targeted tracking of organisms of interest in diverse habitats as a function of specified variables/perturbations.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 104 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 104 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 21 20%
Researcher 18 17%
Student > Ph. D. Student 13 13%
Student > Bachelor 7 7%
Professor 4 4%
Other 18 17%
Unknown 23 22%
Readers by discipline Count As %
Agricultural and Biological Sciences 22 21%
Biochemistry, Genetics and Molecular Biology 20 19%
Immunology and Microbiology 12 12%
Environmental Science 6 6%
Medicine and Dentistry 5 5%
Other 10 10%
Unknown 29 28%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 10. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 19 December 2019.
All research outputs
#3,713,898
of 25,394,764 outputs
Outputs from Journal of Microbiological Methods
#128
of 2,350 outputs
Outputs of similar age
#72,354
of 352,672 outputs
Outputs of similar age from Journal of Microbiological Methods
#3
of 38 outputs
Altmetric has tracked 25,394,764 research outputs across all sources so far. Compared to these this one has done well and is in the 85th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 2,350 research outputs from this source. They receive a mean Attention Score of 3.7. This one has done particularly well, scoring higher than 94% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 352,672 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 79% of its contemporaries.
We're also able to compare this research output to 38 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 92% of its contemporaries.