2.50
Hdl Handle:
http://hdl.handle.net/10033/620853
Title:
Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River.
Authors:
Vezzulli, L ( 0000-0002-4368-1454 ) ; Grande, C; Tassistro, G; Brettar, I; Höfle, M G; Pereira, R P A; Mushi, D; Pallavicini, A; Vassallo, P; Pruzzo, C
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.
Affiliation:
Helmholtz Centre for infection research, Ihoffenstr. 7, 38124 Braunschweig, Germany.
Citation:
Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River. 2016: Microb. Ecol.
Journal:
Microbial ecology
Issue Date:
25-Nov-2016
URI:
http://hdl.handle.net/10033/620853
DOI:
10.1007/s00248-016-0902-x
PubMed ID:
27888291
Type:
Article
Language:
en
ISSN:
1432-184X
Appears in Collections:
publications of the research group vaccinology and applied microbiology (VAC)

Full metadata record

DC FieldValue Language
dc.contributor.authorVezzulli, Len
dc.contributor.authorGrande, Cen
dc.contributor.authorTassistro, Gen
dc.contributor.authorBrettar, Ien
dc.contributor.authorHöfle, M Gen
dc.contributor.authorPereira, R P Aen
dc.contributor.authorMushi, Den
dc.contributor.authorPallavicini, Aen
dc.contributor.authorVassallo, Pen
dc.contributor.authorPruzzo, Cen
dc.date.accessioned2017-03-08T14:36:40Z-
dc.date.available2017-03-08T14:36:40Z-
dc.date.issued2016-11-25-
dc.identifier.citationWhole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River. 2016: Microb. Ecol.en
dc.identifier.issn1432-184X-
dc.identifier.pmid27888291-
dc.identifier.doi10.1007/s00248-016-0902-x-
dc.identifier.urihttp://hdl.handle.net/10033/620853-
dc.description.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.en
dc.language.isoenen
dc.relationinfo:eu-repo/grantAgreement/EC/FP7/311846en
dc.rightsopenAccessen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/*
dc.titleWhole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River.en
dc.typeArticleen
dc.contributor.departmentHelmholtz Centre for infection research, Ihoffenstr. 7, 38124 Braunschweig, Germany.en
dc.identifier.journalMicrobial ecologyen
This item is licensed under a Creative Commons License
Creative Commons
All Items in HZI are protected by copyright, with all rights reserved, unless otherwise indicated.