WATERSHED METAGENOMICS STAKEHOLDER WORKSHOP
The Applied Metagenomics of the Watershed Microbiome Project hosted a workshop for our stakeholders and members of the scientific and watershed management community interested in the learning about our watershed metagenomics project and the progress we have made towards designing new ways to detect fecal pollution in water. We brought together researchers and stakeholders from a wide range of fields to discuss the current and future states of watershed management and how genomic technologies can play a larger role.
The workshop featured Canadian and international speakers including:
Dr. Thomas Edge, McMaster University
Dr. Joan Rose, Michigan State University
Dr. Eric Wommack, University of Delaware
Dr. Erik Fisher, Arizona State University
Dr. Kristi Miller-Saunders, Pacific Biological Station
The Watershed Metagenomics Project gratefully acknowledges Genome BC and Genome Canada for supporting this event.
Please find links to presentations from the symposium below:
1. Temporal variability of bacterial communities in two British Columbia watersheds
Matthew Croxen, University of British Columbia
2. Metagenomic differences associated with water quality and land use in multiple watersheds over space and time
Thea Van Rossum, Simon Fraser University
3. Discovery of new biomarkers as indicators of watershed health and water quality
Anamaria Crisan, University of British Columbia and Mike Peabody, Simon Fraser University
4. The benefits and challenges of new water quality tests: what do stakeholders think?
Natalie Henrich, University of British Columbia
5. Of water, science and law: some considerations for bridging the legal divide
Ida Ngueng Feze, McGill University
6. Microbial risk governance: challenges and opportunities in freshwater management in Canada
Leila Harris, University of British Columbia
7. Metagenomics, nucleotide metabolism genes, and chaperonins reveal key biological features of unknown marine viruses.
K. Eric Wommack, University of Delaware
8. High throughput qPCR: simultaneous monitoring of pathogens and host biomarkers
Kristi Miller-Saunders, Pacific Biological Station
9. Socio-technical collaborations: building micro-foundations for responsible innovation
Erik Fisher, Arizona State University
GENOMIC TOOLS IN THE NEWS
Drs. Judy Isaac-Renton, Patrick Tang and Natalie Prystajecky were recently interviewed for a Vancouver Sun article about the use of microbes in the mining industry, highlighting the research done by the Watershed Metagenomics project as “creating detection and analysis tools that can be used to assess water quality and detect and trace pollution by building a database of metagenomic fingerprints from healthy and polluted watersheds”.
Check out our new infographic on this project
Check out the following reports that were generated based on the GE3LS work:
1. Report based on Health Authorities Water Communicators
2. Report on farming interviews
Bakker K. 2012. Water security: research challenges and opportunities. Science 337: 914-915.
Cook C., Prystajecky N., Ngueng-Feze I., Joly Y., Dunn G., Kirby E., Ozdemir V., & Isaac-Renton J.I.R. 2013. A comparison of the regulatory frameworks governing microbial testing of drinking water in three Canadian provinces. Canadian Water Resources Journal 38: 185-95.
Dunn G., Henrich N., Holmes B., Harris L., & Prystajecky N. 2014. Microbial water quality communication: public and practitioner insights from British Columbia, Canada. Journal of Water and Health 12(3):584-95.
Dunn G., Harris L., Cook C., & Prystajecky N. 2014. A comparative analysis of current microbial water quality risk assessment and management practices in British Columbia and Ontario, Canada. Science of the Total Environment. 468–469: 544-52.
Ngueng Feze I., Prystajecky N., Cook C., Kirby E., Knoppers B.M., Özdemir V., Dunn G., Isaac-Renton J., Joly Y. 2014. The regulation of water quality assessment biotechnologies: Is Canada ready to surf the next wave? Journal of Environmental Law and Practice 26 (3), 201-279.
Dunn G., Harris L., & Bakker K. 2015. Microbial risk governance: challenges and opportunities in fresh water management in Canada. Canadian Water Resources Journal / Revue canadienne des ressources hydriques DOI: 10.1080/07011784.2015.1043648
Birko, S., Dove, E.S., and Özdemir. V. 2015. A Delphi Technology Foresight Study: Mapping Social Construction of Scientific Evidence on Metagenomics Tests for Water Safety. PLoS ONE 10(6): e0129706. doi:10.1371/journal.pone.0129706.
Birko S, Dove ES, Özdemir V. 2015. Evaluation of Nine Consensus Indices in Delphi Foresight Research and Their Dependency on Delphi Survey Characteristics: A Simulation Study and Debate on Delphi Design and Interpretation. PLoS ONE 10(8): e0135162. doi:10.1371/journal.pone.0135162.
Harris L. and Prystajecky N. (co-chairs), Henrich N., Holmes B., Bakker K., Dunn G., Ngueng-Feze I., Joly Y., Knoppers B.M., Birko, S., Dove, E.S., Özdemir V., Tang, P. & Isaac-Renton J.I.R. 2017. Improving water quality with novel diagnostics: policy brief on the potential use of metagenomics for improved water quality testing.
Langille M.G., Laird M.R., Hsiao W.W., Chiu T.A., Eisen J.A., & Brinkman F.S. 2012. MicrobeDB: a locally maintainable database of microbial genomic sequences. Bioinformatics 28:1947-1948.
Whiteside M.D., Winsor G.L., Laird M.R., & Brinkman F.S. 2013. OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. Nucleic Acid Research 41:D336-376.
Peabody, M.A., Van Rossum, T., Uyaguari-Diaz, M.I., Tian, X., Vlok, M., Cronin, K.I., Croxen, M., Crisan, A., Laird, M.R., Lo, R., Hsaio, W., Suttle, C.A., Prystajecky, N.A., Isaac-Renton, J.L., Tang, P. and F.L. Brinkman. 2014. Towards improved watershed monitoring through novel genetic tests. Genome 57(7):393.
Van Rossum, T., Peabody, M.A., Uyaguari-Diaz, M.I., Cronin, K.I., Chan, M., Slobodan, J.R., Nesbitt, M.J., Suttle, C.A., Hsaio, W., Tang, P., Prystajecky, N.A., and F.L. Brinkman. 2015. Year-long metagenomic study of river microbiomes affected by differential land use and water quality. Frontiers in Microbiology, 6:1405. doi:10.3389/fmicb.2015.01405.
Peabody, M.A., Van Rossum, T., Lo, R., and F.S. Brinkman. Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities. 2015. BMC Bioinformatics. 4;16:363; doi: 10.1186/s12859-015-0788-5.
Uyaguari-Diaz M.I., Slobodan, J.R., Nesbitt, M.J., Croxen, M.A., Isaac-Renton, J., Prystajecky, N.A., & Tang, P. 2015. Automated gel size selection to improve the quality of next-generation sequencing libraries prepared from environmental water samples. Journal of Visualized Experiments (98), e52685, doi:10.3791/52685.
Uyaguari-Diaz, M., Chan, M., Chaban, B., Croxen, M., Finke, J., Hill, J., Peabody, M., Van Rossum, T., Suttle, C., Brinkman, , Prystajecky, N., Isaac-Renton, J., and P. Tang. 2016. A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria and eukaryotes in freshwater samples. Microbiome, 4:20. doi: 10.1186/s40168-016-0166-1.
Michael Peabody. April 15, 2012. “Bioinformatics Analysis of Watershed Metagenomics Data: Towards Improved Water Quality Monitoring”. Systems Biology & the Microbiome. Seattle, Washington, USA.
Michael Peabody. June 21, 2012. “Evaluation of Bioinformatics Methods and Bioinformatics Analysis of Watershed Metagenomics Data: Towards Improved Water Quality Monitoring”. Canadian Society of Microbiologists. Vancouver, BC, Canada.
Michael Peabody. January 22, 2013. “Watershed Metagenomics to Identify Markers of Water Quality: Assessing and Using Metagenomics Analysis Methods”. 11th Annual Asia Pacific Bioinformatics Conference. Vancouver, BC, Canada.
Michael Peabody. September 15, 2014. “Identifying Markers of Water Quality Through Watershed Metagenomics”. 20th Annual International Meeting on Microbial Genomics. Lake Arrowhead, California, USA.
Michael Peabody. November 25, 2014. “Towards Improved Watershed Monitoring Through Novel Genetic Tests”. American Society for Microbiology Annual General Meeting. Ottawa, Ontario, Canada.
Michael Peabody. June 2nd, 2015. “Improving Water Quality and Watershed Monitoring Through Novel Genetic Tests Identified Using Metagenomics”. American Society for Microbiology Annual General Meeting. New Orleans, Louisiana, USA.
Anamaria Crisan. Jun 2nd, 2015. “Exploring the Impact Human Activity on Watershed Bacterial and Protozoa Microbial Communities”.American Soceity for Microbiology Annual General Meeting. New Orleans, Louisiana, USA.
Anamaria Crisan. May 6th, 2015. “An improved and generalizable framewrok for microbial biomarker discovery”. Applied Bioinformatics and Public Health Microbiology. Hinxton, Cambridge, UK.
Gemma Dunn, Leila Harris, & Karen Bakker. November 4, 2013. “Factors That Facilitate And Constrain Microbial Risk Governance In BC And Ontario, Canada”. Water Quality Technology Conference, American Water Works Association. Long Beach, CA, USA.
Natalie Prystajecky. November 5, 2013. “Waves of change: Using metagenomics to discover novel markers of water quality”. BC Food Association. Vancouver, BC, Canada.
Natalie Prystajecky. October 2, 2013. “Navigating water microbiology: Guidelines and regulations”. Res’eau Impact – Joint conference of BC First Nations, water operators and Res’eau. Vancouver, BC, Canada.
Fiona Brinkman. June 26, 2013. “Improved genome-scale analysis of host and pathogen responses”. EMBO Workshop: Integrating omic Approaches to Host-pathogen Interactions. Liverpool, UK.
Natalie Prystajecky. June 2, 2013. “Introduction to microbiology – why we treat our water”. Tl’azt’en Nation. Fort St. James, BC, Canada.
Gemma Dunn, Leila Harris, Natalie Prystajecky & Christina Cook. May 28, 2013. “A comparative analysis of microbial water quality risk assessment and management practices in British Columbia and Ontario, Canada”. Canadian Meteorological & Oceanographic Society (CMOS) & Canadian Water Resources Association (CWRA). Saskatoon, SK, Canada.
Fiona Brinkman. May 11, 2013. “Ripples of Change: Transforming water quality testing using genomics”. SFU, Burnaby, BC, Canada.
Fiona Brinkman. (Keynote Speaker) April 9, 2013. “From genes, to genomes to networks, with community aided curation”. Biocuration Conference. Cambridge, UK.
Judith Isaac-Renton. January 22, 2013. ”Applied metagenomics of the watershed microbiome”. Genome BC Winter Symposium, Vancouver, BC, Canada.
Fiona Brinkman. January 15, 2013. “Improvements in ‘omic analysis of host, pathogen and the environment – toward more holistic, sustainable infectious disease control”. Dept. of Microbiology & Immunology (The University of British Columbia) Seminar Series, Vancouver, BC, Canada.
Patrick Tang. (Keynote Speaker) November 29, 2012. “The new age of microbiology: Holistic microbiology”. 5th Annual BC Centre for Disease Control Forum, Vancouver, BC, Canada.
Gemma Dunn. November 21, 2012. “Water security indicators: The Canadian experience”. Global Water Partnership Expert Consultation on Water Security Indicators, Stockholm, SE.
Fiona Brinkman. (Distinguished Speaker) May 25, 2012. “Using microbial evolution to aid infectious disease control”. National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Fiona Brinkman. April 13, 2012. “Ripples of change: Using metagenomics to transform water quality monitoring”. IRMACS, SFU, Burnaby, BC, Canada.
Fiona Brinkman. April 12, 2012. “Bioinformatics for combating infectious diseases (and more)”. SFU Health Research Day, Burnaby, BC, Canada.
Fiona Brinkman. January 24, 2012. “Evaluating and improving bioinformatics analysis of metagenomics and pathway data”. Genome BC Winter Symposium. Vancouver, BC, Canada.
Fiona Brinkman. March 30, 2012. “Metagenomics analysis of watershed microbiomes”. TCS. Pune, India.
Karen Bakker. February 17, 2012. “Water security: Competing perspectives, multi-disciplinary challenges”. American Association for the Advancement of Science, Vancouver, BC, Canada.
Natalie Prystajecky. February 17, 2012. “Of friends, family, and food: Tales of Norovirus transmission”. Public event on Water Security in Canada sponsored by the American Association for the Advancement of Science, the Canadian Water Network, the Royal Society of Canada and the University of British Columbia. Held in conjunction with the AAAS in Vancouver, BC, Canada.
Judith Isaac-Renton. February 17, 2012. “Ripples of change: Need for vigilance”. Public event on Water Security in Canada sponsored by the American Association for the Advancement of Science, the Canadian Water Network, the Royal Society of Canada and the University of British Columbia. Held in conjunction with the AAAS in Vancouver, BC, Canada.
Fiona Brinkman. November 16, 2011. “Metagenomics analysis of watershed microbiomes – toward improved water quality monitoring”. Harvard School of Public Health. Boston, MA, USA.
Natalie Prystajecky, Jennifer Gardy, Patrick Tang & Judith Isaac-Renton. September 30, 2011. “A changing tide for public health: Application of genomics for water quality testing in protected, urban, agricultural and multi-use watersheds across BC”. Soil Seminar, Faculty of Land and Food Science, University of British Columbia, Vancouver, BC, Canada.
Judith Isaac-Renton, Natalie Prystajecky, Jennifer Gardy & Patrick Tang. September 23, 2011. “Ripples of change: Using metagenomics to explore new frontiers in water quality testing”. BC Centre for Disease Control Grand Rounds, Vancouver, BC, Canada.
Patrick Tang. May 6, 2011. “Metagenomics of the watershed microbiome.” 9th Annual Genomics Forum. Genome British Columbia, Vancouver, BC, Canada.