↓ Skip to main content

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

Overview of attention for article published in BMC Genomics, January 2015
Altmetric Badge

About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (78th percentile)

Mentioned by

twitter
15 tweeters

Citations

dimensions_citation
75 Dimensions

Readers on

mendeley
276 Mendeley
citeulike
2 CiteULike
You are seeing a free-to-access but limited selection of the activity Altmetric has collected about this research output. Click here to find out more.
Title
Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes
Published in
BMC Genomics, January 2015
DOI 10.1186/s12864-014-1207-4
Pubmed ID
Authors

Manuel Kleiner, Lora V Hooper, Breck A Duerkop

Abstract

BackgroundViruses are a significant component of the intestinal microbiota in mammals. In recent years, advances in sequencing technologies and data analysis techniques have enabled detailed metagenomic studies investigating intestinal viromes (collections of bacteriophage and eukaryotic viral nucleic acids) and their potential contributions to the ecology of the microbiota. An important component of virome studies is the isolation and purification of virus-like particles (VLPs) from intestinal contents or feces. Several methods have been applied to isolate VLPs from intestinal samples, yet to our knowledge, the efficiency and reproducibility between methods have not been explored. A rigorous evaluation of methods for VLP purification is critical as many studies begin to move from descriptive analyses of virus diversity to studies striving to quantitatively compare viral abundances across many samples. Therefore, reproducible VLP purification methods which allow for high sample throughput are needed. Here we compared and evaluated four methods for VLP purification using artificial intestinal microbiota samples of known bacterial and viral composition.ResultsWe compared the following four methods of VLP purification from fecal samples: (i) filtration¿+¿DNase, (ii) dithiothreitol treatment¿+¿filtration¿+¿DNase, (iii) filtration¿+¿DNase¿+¿PEG precipitation and (iv) filtration¿+¿DNase¿+¿CsCl density gradient centrifugation. Three of the four tested methods worked well for VLP purification. We observed several differences between methods related to the removal efficiency of bacterial and host DNAs and biases against specific phages. In particular the CsCl density gradient centrifugation method, which is frequently used for VLP purification, was most efficient in removing host derived DNA, but also showed strong discrimination against specific phages and showed a lower reproducibility of quantitative results.ConclusionsBased on our data we recommend the use of methods (i) or (ii) for large scale studies when quantitative comparison of viral abundances across samples is required. The CsCl density gradient centrifugation method, while being excellently suited to achieve highly purified samples, in our opinion, should be used with caution when performing quantitative studies.

Twitter Demographics

The data shown below were collected from the profiles of 15 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 276 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Brazil 4 1%
South Africa 2 <1%
Switzerland 2 <1%
United Kingdom 2 <1%
Canada 2 <1%
United States 2 <1%
Unknown 262 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 68 25%
Researcher 67 24%
Student > Master 50 18%
Student > Bachelor 19 7%
Professor > Associate Professor 13 5%
Other 37 13%
Unknown 22 8%
Readers by discipline Count As %
Agricultural and Biological Sciences 108 39%
Biochemistry, Genetics and Molecular Biology 52 19%
Immunology and Microbiology 34 12%
Medicine and Dentistry 12 4%
Engineering 10 4%
Other 29 11%
Unknown 31 11%

Attention Score in Context

This research output has an Altmetric Attention Score of 7. 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 24 May 2019.
All research outputs
#2,875,171
of 15,096,298 outputs
Outputs from BMC Genomics
#1,473
of 8,627 outputs
Outputs of similar age
#46,391
of 217,513 outputs
Outputs of similar age from BMC Genomics
#1
of 1 outputs
Altmetric has tracked 15,096,298 research outputs across all sources so far. Compared to these this one has done well and is in the 80th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 8,627 research outputs from this source. They receive a mean Attention Score of 4.3. This one has done well, scoring higher than 82% 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 217,513 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 78% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them