| Title |
Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River
|
|---|---|
| Published in |
Microbial Ecology, November 2016
|
| DOI | 10.1007/s00248-016-0902-x |
| Pubmed ID | |
| Authors |
L. Vezzulli, C. Grande, G. Tassistro, I. Brettar, M. G. Höfle, R. P. A. Pereira, D. Mushi, A. Pallavicini, P. Vassallo, C. Pruzzo |
| Abstract |
The detection and typing of Vibrio cholerae in natural aquatic environments encounter major methodological challenges related to the fact that the bacterium is often present in environmental matrices at very low abundance in nonculturable state. This study applied, for the first time to our knowledge, a whole-genome enrichment (WGE) and next-generation sequencing (NGS) approach for direct genotyping and metagenomic analysis of low abundant V. cholerae DNA (<50 genome unit/L) from natural water collected in the Morogoro river (Tanzania). The protocol is based on the use of biotinylated RNA baits for target enrichment of V. cholerae metagenomic DNA via hybridization. An enriched V. cholerae metagenome library was generated and sequenced on an Illumina MiSeq platform. Up to 1.8 × 10(7) bp (4.5× mean read depth) were found to map against V. cholerae reference genome sequences representing an increase of about 2500 times in target DNA coverage compared to theoretical calculations of performance for shotgun metagenomics. Analysis of metagenomic data revealed the presence of several V. cholerae virulence and virulence associated genes in river water including major virulence regions (e.g. CTX prophage and Vibrio pathogenicity island-1) and genetic markers of epidemic strains (e.g. O1-antigen biosynthesis gene cluster) that were not detectable by standard culture and molecular techniques. Overall, besides providing a powerful tool for direct genotyping of V. cholerae in complex environmental matrices, this study provides a 'proof of concept' on the methodological gap that might currently preclude a more comprehensive understanding of toxigenic V. cholerae emergence from natural aquatic environments. |
X Demographics
The data shown below were collected from the profiles of 3 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 2 | 67% |
| Austria | 1 | 33% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 2 | 67% |
| Scientists | 1 | 33% |
Mendeley readers
The data shown below were compiled from readership statistics for 66 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Brazil | 2 | 3% |
| New Zealand | 1 | 2% |
| Unknown | 63 | 95% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 13 | 20% |
| Student > Ph. D. Student | 10 | 15% |
| Student > Doctoral Student | 8 | 12% |
| Student > Master | 8 | 12% |
| Student > Postgraduate | 4 | 6% |
| Other | 9 | 14% |
| Unknown | 14 | 21% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 22 | 33% |
| Biochemistry, Genetics and Molecular Biology | 7 | 11% |
| Immunology and Microbiology | 6 | 9% |
| Environmental Science | 4 | 6% |
| Medicine and Dentistry | 2 | 3% |
| Other | 5 | 8% |
| Unknown | 20 | 30% |
Attention Score in Context
This research output has an Altmetric Attention Score of 9. 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 05 December 2016.
All research outputs
#3,976,413
of 24,885,505 outputs
Outputs from Microbial Ecology
#327
of 2,166 outputs
Outputs of similar age
#71,911
of 426,983 outputs
Outputs of similar age from Microbial Ecology
#15
of 46 outputs
Altmetric has tracked 24,885,505 research outputs across all sources so far. Compared to these this one has done well and is in the 84th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 2,166 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.3. This one has done well, scoring higher than 84% of its peers.
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We're also able to compare this research output to 46 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 69% of its contemporaries.