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...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-12-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2019.02907/full |
| _version_ | 1818047091315834880 |
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| author | William L. King William L. King Nachshon Siboni Tim Kahlke Timothy J. Green Maurizio Labbate Justin R. Seymour |
| author_facet | William L. King William L. King Nachshon Siboni Tim Kahlke Timothy J. Green Maurizio Labbate Justin R. Seymour |
| author_sort | William L. King |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-10T10:00:16Z |
| format | Article |
| id | doaj.art-a61fd49b55aa44fdb8fa79194fbe1f08 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-10T10:00:16Z |
| publishDate | 2019-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-a61fd49b55aa44fdb8fa79194fbe1f082022-12-22T01:53:23ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-12-011010.3389/fmicb.2019.02907498862A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality EventWilliam L. King0William L. King1Nachshon Siboni2Tim Kahlke3Timothy J. Green4Maurizio Labbate5Justin R. Seymour6School of Life Sciences, University of Technology Sydney, Ultimo, NSW, AustraliaClimate Change Cluster, University of Technology Sydney, Ultimo, NSW, AustraliaClimate Change Cluster, University of Technology Sydney, Ultimo, NSW, AustraliaClimate Change Cluster, University of Technology Sydney, Ultimo, NSW, AustraliaCentre for Shellfish Research, Vancouver Island University, Nanaimo, BC, CanadaSchool of Life Sciences, University of Technology Sydney, Ultimo, NSW, AustraliaClimate Change Cluster, University of Technology Sydney, Ultimo, NSW, AustraliaThe 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.https://www.frontiersin.org/article/10.3389/fmicb.2019.02907/fullVibrioVibrio communitiesseawateroyster (Crassostrea gigas)DNA sequencingmarine microbiology |
| spellingShingle | William L. King 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 Frontiers in Microbiology Vibrio Vibrio communities seawater oyster (Crassostrea gigas) DNA sequencing marine microbiology |
| 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_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_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_sort | new high throughput sequencing assay for characterizing the diversity of natural vibrio communities and its application to a pacific oyster mortality event |
| topic | Vibrio Vibrio communities seawater oyster (Crassostrea gigas) DNA sequencing marine microbiology |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2019.02907/full |
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