A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event
The Vibrio genus is notable for including several pathogens of marine animals and humans, yet characterization of Vibrio diversity using routine 16S rRNA sequencing methods is often constrained by poor resolution beyond the genus level. Here, a new high throughput sequencing approach targeting the h...
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ftdoajarticles:oai:doaj.org/article:a61fd49b55aa44fdb8fa79194fbe1f08 2023-05-15T15:58:56+02:00 A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event William L. King Nachshon Siboni Tim Kahlke Timothy J. Green Maurizio Labbate Justin R. Seymour 2019-12-01T00:00:00Z https://doi.org/10.3389/fmicb.2019.02907 https://doaj.org/article/a61fd49b55aa44fdb8fa79194fbe1f08 EN eng Frontiers Media S.A. https://www.frontiersin.org/article/10.3389/fmicb.2019.02907/full https://doaj.org/toc/1664-302X 1664-302X doi:10.3389/fmicb.2019.02907 https://doaj.org/article/a61fd49b55aa44fdb8fa79194fbe1f08 Frontiers in Microbiology, Vol 10 (2019) Vibrio Vibrio communities seawater oyster (Crassostrea gigas) DNA sequencing marine microbiology Microbiology QR1-502 article 2019 ftdoajarticles https://doi.org/10.3389/fmicb.2019.02907 2022-12-31T00:23:31Z The Vibrio genus is notable for including several pathogens of marine animals and humans, yet characterization of Vibrio diversity using routine 16S rRNA sequencing methods is often constrained by poor resolution beyond the genus level. Here, a new high throughput sequencing approach targeting the heat shock protein (hsp60) as a phylogenetic marker was developed to more precisely discriminate members of the Vibrio genus in environmental samples. The utility of this new assay was tested using mock communities constructed from known dilutions of Vibrio isolates. Relative to standard and Vibrio-specific 16S rRNA sequencing assays, the hsp60 assay delivered high levels of fidelity with the mock community composition at the species level, including discrimination of species within the Vibrio harveyi clade. This assay was subsequently applied to characterize Vibrio community composition in seawater and delivered substantially improved taxonomic resolution of Vibrio species compared to 16S rRNA analysis. Finally, this assay was applied to examine patterns in the Vibrio community within oysters during a Pacific oyster mortality event. In these oysters, the hsp60 assay identified species-level Vibrio community shifts prior to disease onset, pinpointing V. harveyi as a putative pathogen. Given that shifts in the Vibrio community can precede, cause, and follow disease onset in numerous marine organisms, there is a need for an accurate high throughput assay for defining Vibrio community composition in natural samples. This Vibrio-centric hsp60 sequencing assay offers the potential for precise high throughput characterization of Vibrio diversity, providing an enhanced platform for dissecting Vibrio dynamics in the environment. Article in Journal/Newspaper Crassostrea gigas Pacific oyster Directory of Open Access Journals: DOAJ Articles Pacific Frontiers in Microbiology 10 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Vibrio Vibrio communities seawater oyster (Crassostrea gigas) DNA sequencing marine microbiology Microbiology QR1-502 |
spellingShingle |
Vibrio Vibrio communities seawater oyster (Crassostrea gigas) DNA sequencing marine microbiology Microbiology QR1-502 William L. King Nachshon Siboni Tim Kahlke Timothy J. Green Maurizio Labbate Justin R. Seymour A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event |
topic_facet |
Vibrio Vibrio communities seawater oyster (Crassostrea gigas) DNA sequencing marine microbiology Microbiology QR1-502 |
description |
The Vibrio genus is notable for including several pathogens of marine animals and humans, yet characterization of Vibrio diversity using routine 16S rRNA sequencing methods is often constrained by poor resolution beyond the genus level. Here, a new high throughput sequencing approach targeting the heat shock protein (hsp60) as a phylogenetic marker was developed to more precisely discriminate members of the Vibrio genus in environmental samples. The utility of this new assay was tested using mock communities constructed from known dilutions of Vibrio isolates. Relative to standard and Vibrio-specific 16S rRNA sequencing assays, the hsp60 assay delivered high levels of fidelity with the mock community composition at the species level, including discrimination of species within the Vibrio harveyi clade. This assay was subsequently applied to characterize Vibrio community composition in seawater and delivered substantially improved taxonomic resolution of Vibrio species compared to 16S rRNA analysis. Finally, this assay was applied to examine patterns in the Vibrio community within oysters during a Pacific oyster mortality event. In these oysters, the hsp60 assay identified species-level Vibrio community shifts prior to disease onset, pinpointing V. harveyi as a putative pathogen. Given that shifts in the Vibrio community can precede, cause, and follow disease onset in numerous marine organisms, there is a need for an accurate high throughput assay for defining Vibrio community composition in natural samples. This Vibrio-centric hsp60 sequencing assay offers the potential for precise high throughput characterization of Vibrio diversity, providing an enhanced platform for dissecting Vibrio dynamics in the environment. |
format |
Article in Journal/Newspaper |
author |
William L. King Nachshon Siboni Tim Kahlke Timothy J. Green Maurizio Labbate Justin R. Seymour |
author_facet |
William L. King Nachshon Siboni Tim Kahlke Timothy J. Green Maurizio Labbate Justin R. Seymour |
author_sort |
William L. King |
title |
A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event |
title_short |
A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event |
title_full |
A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event |
title_fullStr |
A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event |
title_full_unstemmed |
A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event |
title_sort |
new high throughput sequencing assay for characterizing the diversity of natural vibrio communities and its application to a pacific oyster mortality event |
publisher |
Frontiers Media S.A. |
publishDate |
2019 |
url |
https://doi.org/10.3389/fmicb.2019.02907 https://doaj.org/article/a61fd49b55aa44fdb8fa79194fbe1f08 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
Frontiers in Microbiology, Vol 10 (2019) |
op_relation |
https://www.frontiersin.org/article/10.3389/fmicb.2019.02907/full https://doaj.org/toc/1664-302X 1664-302X doi:10.3389/fmicb.2019.02907 https://doaj.org/article/a61fd49b55aa44fdb8fa79194fbe1f08 |
op_doi |
https://doi.org/10.3389/fmicb.2019.02907 |
container_title |
Frontiers in Microbiology |
container_volume |
10 |
_version_ |
1766394703081635840 |