Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River.
4. Vezzulli et al (Supplementary ...
Cast your vote
You can rate an item by clicking the amount of stars they wish to award to this item.
When enough users have cast their vote on this item, the average rating will also be shown.
Your vote was cast
Thank you for your feedback
Thank you for your feedback
Höfle, M G
Pereira, R P A
MetadataShow full item record
AbstractThe 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.
CitationWhole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River. 2016: Microb. Ecol.
AffiliationHelmholtz Centre for infection research, Ihoffenstr. 7, 38124 Braunschweig, Germany.
The following license files are associated with this item:
- The Dynamics of Genetic Interactions between Vibrio metoecus and Vibrio cholerae, Two Close Relatives Co-Occurring in the Environment.
- Authors: Orata FD, Kirchberger PC, Méheust R, Barlow EJ, Tarr CL, Boucher Y
- Issue date: 2015 Oct 9
- A glimpse into the expanded genome content of Vibrio cholerae through identification of genes present in environmental strains.
- Authors: Purdy A, Rohwer F, Edwards R, Azam F, Bartlett DH
- Issue date: 2005 May
- Evolutionary genetic analysis of the emergence of epidemic Vibrio cholerae isolates on the basis of comparative nucleotide sequence analysis and multilocus virulence gene profiles.
- Authors: O'Shea YA, Reen FJ, Quirke AM, Boyd EF
- Issue date: 2004 Oct
- DNA fingerprinting of Vibrio cholerae strains with a novel insertion sequence element: a tool to identify epidemic strains.
- Authors: Bik EM, Gouw RD, Mooi FR
- Issue date: 1996 Jun
- Application of duplex-PCR in rapid and reliable detection of toxigenic Vibrio cholerae in water samples in Thailand.
- Authors: Chomvarin C, Namwat W, Wongwajana S, Alam M, Thaew-Nonngiew K, Sinchaturus A, Engchanil C
- Issue date: 2007 Aug