2014 Genome Biology Meeting

September 24, 2014
September 24, 2014 - September 25, 2014


UC Davis, Davis, CA


Over 50 scientists came together at UC Davis in a meeting hosted by the Phaff Yeast Culture Collection and the UC Davis Viticulture and​ Enology yeast collection to interact with the general topic of genome programs and genome data for culture collections.


Boundy-Mills, Kyria et al. “The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections.” Applied and environmental microbiology vol. 81,17 (2015): 5671-4. doi:10.1128/AEM.01176-15


“Exploring Synergy between Microbial Genome/Metagenome Research and US Living Microbe Culture Collections”

Wednesday, September 24, 2014. UC Davis Putah Creek Lodge
8:30-9:00 AM      Poster Hanging with Coffee
9:00- 9:15 AM    Welcome and Remarks | Campus and departmental representatives, Kyria Boundy-Mills and Lucy Joseph
9:15 -9:30 AM      Overview of USCCN RCN | Kevin McCluskey

  • Peter Countway, Bigelow Labs, National Center for Marine Algae
  • David Nobles, UTEX The Culture Collection of Algae at the University of Texas at Austin
  • Richard Castenholz, University of Oregon and Sherry Cady, PNNL. “The Importance of Cultures of Micro-phototrophs”
  • Matthias Hess, PNNL, “Systems Biology of Phototrophic Consortia: Towards a Multi-scalar Understanding of Carbon and Nitrogen Cycling”

10:30-10:45 AM      Coffee

  • Daniel Brown, University of Florida, “The Mollicutes Collection of Cultures and Antisera” (TMC)
  • Soraya Foutouhi, Weimer lab, UC Davis, 100K Bacterial Genomes Project
  • George Garrity, Michigan State University
  • Jonathan Eisen, UC Davis
  • Supratim Mukherjee, DOE JGI, Genomic Encyclopedia of Bacteria and Archaea ,“Genomic Exploration of 1000 Microbial Type Strains”

12:00-1:30 PM      Lunch
12:45 – 1:30     Walk to the Robert Mondavi Institute for tours of the UC Davis Teaching and Research Winery; Jess S. Jackson Sustainable Winery Building | Tour guide: Karen Block

  • Lucy Joseph, UC Davis, Wine Yeast and Bacteria Collection, “Intentionally of Interest to Industry”
  • Kyria Boundy-Mills, UC Davis, Phaff Yeast Culture Collection, “Yeasts of Yesterday and Today, for Discoveries of Tomorrow”
  • Kevin McCluskey, University of Missouri at Kansas City, Fungal Genetic Stock Center, “Relocating the Fungal Genetics Stock Center”
  • Barbara Dunn, Stanford
  • Kevin Dietzel, Amyris, “Engineering Microbes to Produce Renewable Hydrocarbons”

3:00-3:15 PM    Break

  • Jason Stajich, UC Riverside, 1000 Fungal Genomes Project
  • Igor Grigoriev, JGI, Fungal genome sequencing

4:00 – 5:00 PM    3- minute Lightning Presentations of posters; Reception; Poster Sessions by Culture Collection Curators, Users and Potential Users of Culture Collections.
6:00-8:00 PM    Dinner for Participants at the Good Life Garden, at the Robert Mondavi Institute, University of California, Davis.

  1. Meghan May, University of New England, College of Osteopathic Medicine, “The Class Mollicutes Genomics Initiative”
  2. Daniel Brown, University of Florida, Mollicutes Collection, “The Mollicutes Collection of Cultures and Antisera”
  3. Kyria Boundy-Mills, UC Davis, Phaff Yeast Culture Collection, “New Discoveries from an Old Collection”
  4. Kevin McCluskey, Kansas State University, “Fungal Genetic Stock Center”
  5. Kevin McCluskey, Kansas State University, “US Culture Collection Network”
  6. Carolee Bull, USDA, Salinas, CA, “Type and pathotype strains are essential components of culture collections and taxonomy of plant pathogenic bacteria”

+ ad hoc posters

Thursday September 25, 2014. UC Davis Robert Mondavi Institute (RMI), Winery Classroom

8:30-9:00 AM    Coffee
9:00-12:00PM    Presentations and discussions:
    Introductions of participants
    Set the agenda for discussions
    Kevin McCluskey: Presentation of USCCN activities, website, etc.
    Matt Ryan, CABI (UK): Culture collection support in Europe and UK including MIRRI, ECCO, UKNCC
    Resources and guidelines for Culture Collection Management, e.g. WFCC Guidelines, OECD Best Practice Guidelines for BRCs
    Opportunities available to culture collections for genome work
    Kyria Boundy-Mills, Recap of “Sustaining Biological Infrastructure” workshop
    Kevin McCluskey, Report on TRUST Workshop Participation
    Round Table Discussion: Convention on Biological Diversity and Nagoya Protocol
    Other issues
12:00-1:00 PM    Lunch
1:00-1:30 PM    Tours of RMI Complex: Phaff Yeast Culture Collection, Wine Yeast and Bacteria Collection, Sensory Building, teaching and research facilities
1:30 – 2:30     Tour nearby UC Davis Collections: Entomology, Wildlife collections.
2:30 – 3:30    Compare funding models and other strategies with natural history collections and other UC Davis programs such as enlisting volunteers, outreach/broader impacts, endowments, “Friends of the Collection”.

  • Lynn Kimsey, Professor and curator of the Bohart Museum of Entomology
  • Deborah Golino, Director, Foundation Plant Sciences

3:30-5:00 PM    Working groups:
    Planning the USCCN workshop for Spring 2015
    Updating the USCCN website
    Prospects for a US Society for Culture Collections
    Other business
    Wrap up: Acknowledgments, Travel reimbursement issues, etc.