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Discovery of new biomarkers as indicators of watershed health and water quality Anamaria Crisan & Mike Peabody
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What are biomarkers and how do we find them? bi·o·mark·er /ˈbīōˌmärkər/ Functional biomarkers Taxonomic biomarkers Biological functions that may be specific to a single organism or shared among multiple organisms Can be a specific species, but most often is a category of organisms – also called Operational Taxonomic Unit (OTU). Measureable biological property that can be indicative of some phenomena, such as an infection, disease, or environmental disturbance
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123456 Digitize DNA Identify Potential Biomarkers ( OTUs or Functional Genes ) Quantify Biomarker Abundance Select Useful Biomarkers Obtain Biological Samples Extract DNA What are biomarkers and how do we find them?
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DISCOVERY VALIDATION o Bioinformatics Software - Takes the raw digitized genet data and performs QC and biomarker quantification o Use math – applied statistical methods can help us find useful biomarkers o Design Primers – biological “hooks” that pick out our biomarker of interest from a sample o qPCR – measures how many times primers (hooks) manage to snag our biomarker of interest What are biomarkers and how do we find them?
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What makes a good biomarker?
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How can biomarkers add value to current testing procedures? How can we make biomarkers easily accessible to those that routinely test water quality? 1 2 What makes a good biomarker?
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We found bacterial and protist biomarkers We analysed bacteria using two methods : - 16S rRNA amplicon sequencing - Shotgun metagenomics sequencing Protists are analysed using 18S rRNA amplicon sequencing We’ll discuss the amplicon data together, and afterwards we’ll discuss the shotgun metagenomics data
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Looked at community ecology & biomarkers We found bacterial and protist biomarkers
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Accomplishments This is a landmark study providing key baseline knowledge for understanding the variability of watershed microbiomes, and developing new, more accurate water quality tests We have developed a method to sequence large numbers of water samples across size fractions Collaborated with industry to improve sequencing pipeline (insert length) We have provided a proof of concept that we can find markers for affected sites
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Next Steps Next steps include examining –Are markers robust to watershed location? Should custom markers should be made for particularly problematic locations? –Expand water metagenomics methodology to other applications (e.g. mining project, microbiome changes under other pollution conditions, microbiome changes impacting aquatic- based food production)
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