Sea star wasting disease: Comparing bacterial communities using metagenomics
Research Mentor(s)
Kodner, Robin
Description
Sea Star Wasting Disease (SSWD) is prevalent along the West coast of North America and was first noticed in June 2013. It is characterized by the formation of white lesions, followed by tissue decay, collapse of internal organs, and death. The wide range of SSWD, both in terms of species and geography, and its high mortality rate raise concern. High throughput metagenomic data from multiple sick and healthy sea stars, across a range of geographic regions, was obtained from Ian Hewson. This data was ran through pplacer against 56,000 known bacterial COGs (clusters of orthologous groups), in order to provide phylogenetic placement for the organisms within each sequenced sample. After obtaining phylogenetic information on sample composition, guppy was used to create squash clustering trees for selected COGs. These trees create hierarchical clusterings of the samples based on relatedness of that particular COG found within the samples. Throughout this process, a clear pattern between symptomatic and asymptomatic sea stars arose. Squash clusterings grouped symptomatic and asymptomatic samples together. Investigating the genes each of the clusterings was created from consistently showed similar bacterial community composition within sick sea stars, which was very different than the community composition of healthy sea stars. Infected individuals across the board showed roughly a 6 fold increase in Pseudomonas community size compared to healthy individuals. Surprisingly, the percent composition of different types of pseudomonas for each sample was relatively constant across sick and healthy individuals, indicating that while community size changed, composition did not. The consistent pattern of greater numbers of pseudomonas in symptomatic individuals in comparison to asymptomatic individuals is indicative of pseudomonas playing a causative role in SSWD, and hypothesized to be related to biofilm formation.
Document Type
Event
Start Date
14-5-2015 10:00 AM
End Date
14-5-2015 2:00 PM
Department
Biology
Genre/Form
student projects; posters
Subjects – Topical (LCSH)
Pisaster ochraceus--Diseases and pests--Pacific Coast (America); Chronic wasting disease--Pacific Coast (America); Pisaster ochraceus--Pathogens--Pacific Coast (America)
Type
Image
Rights
Copying of this document in whole or in part is allowable only for scholarly purposes. It is understood, however, that any copying or publication of this documentation for commercial purposes, or for financial gain, shall not be allowed without the author's written permission.
Language
English
Format
application/pdf
Sea star wasting disease: Comparing bacterial communities using metagenomics
Sea Star Wasting Disease (SSWD) is prevalent along the West coast of North America and was first noticed in June 2013. It is characterized by the formation of white lesions, followed by tissue decay, collapse of internal organs, and death. The wide range of SSWD, both in terms of species and geography, and its high mortality rate raise concern. High throughput metagenomic data from multiple sick and healthy sea stars, across a range of geographic regions, was obtained from Ian Hewson. This data was ran through pplacer against 56,000 known bacterial COGs (clusters of orthologous groups), in order to provide phylogenetic placement for the organisms within each sequenced sample. After obtaining phylogenetic information on sample composition, guppy was used to create squash clustering trees for selected COGs. These trees create hierarchical clusterings of the samples based on relatedness of that particular COG found within the samples. Throughout this process, a clear pattern between symptomatic and asymptomatic sea stars arose. Squash clusterings grouped symptomatic and asymptomatic samples together. Investigating the genes each of the clusterings was created from consistently showed similar bacterial community composition within sick sea stars, which was very different than the community composition of healthy sea stars. Infected individuals across the board showed roughly a 6 fold increase in Pseudomonas community size compared to healthy individuals. Surprisingly, the percent composition of different types of pseudomonas for each sample was relatively constant across sick and healthy individuals, indicating that while community size changed, composition did not. The consistent pattern of greater numbers of pseudomonas in symptomatic individuals in comparison to asymptomatic individuals is indicative of pseudomonas playing a causative role in SSWD, and hypothesized to be related to biofilm formation.