“Genome Sequencing and Microbial Resources” workshop

February 19, 2024
June 10, 2024 - June 11, 2024


UC Davis, CA, USA


The increasing power of DNA sequencing technologies presents new opportunities to utilize microbial specimens and associated data in exciting ways to broaden scientific discovery. This workshop will explore the challenges and opportunities related to microbial genome sequencing, with focus on living microbes, whether sourced from a researcher’s freezer or a large formal repository. Discussions will explore opportunities to integrate phenotypic and genotypic information, specimen and data storage, preservation procedures, licensing of both intellectual and tangible property and emerging requirements of the Nagoya Protocol.


Monday, June 10

8:00 am – Registration and badge pick-up

8:30 am – Welcome and Introductions – Dusti Gallagher, USCCN Project Manager

U.S. Culture Collection Network Overview – Slides

Session 1: Challenges and Opportunities with Microbial Collections

8:45 am – Panel Discussion – Moderator: Dusti Gallagher

    • Kyria Boundy-Mills, Phaff Yeast Culture Collection – Slides
    • Sayeh Homayounpour, Ginkgo Bioworks
    • Michael Lomas, Bigelow Laboratory for Ocean Sciences – Slides
    • Catalina Salgado-Salazar, USDA-ARS

09:45 am – Michael Lomas, Bigelow Laboratory for Ocean Sciences

Implementation of a Specimen Management Plan for federally funded research Slides

10:15 am – Networking Break

Session 2: The Power of Data – Leveraging Collections to Answer Scientific Questions

10:30 am – Edward Dudley, Pennsylvania State University

Leveraging the E. coli Reference Center to identify new serotypes and predict bacteriophage susceptibility

11:00 am – Caitilyn Allen, University of Wisconsin-Madison

Cool Virulence: Drawing on a Legacy Culture Collection to Uncover New Biology Slides

11:30 am – Tiffany Lowe-Power, UC-Davis

Integrating Undergraduate Researchers into Genome Analysis of Bacterial Culture Collections Slides

12:00 pm – Titus Brown, UC Davis

Bioinformatics approaches for making use of microbial genome sequences for taxonomy, function, and pangenomics Slides

12:30 pm – Adam Newman, Ginkgo Bioworks

Using genomic and phenotypic data to realize value from a microbial strain collection: an industrial perspective

1:00 pm – Networking Lunch

Session 3: Unique Opportunities and/or Projects Within the Collections and Scientific Communities

2:15 pm – Tanja Woyke & Rekha Seshadri, JGI

The Joint Genome Institute’s User Programs Slides
Unlocking Insights from Isolate Genome Collections

3:00 pm – Lutz Froenicke, The Genome Center, UC Davis

High-throughput Omics at the Genome Center Cores

3:30 pm – Marco Riojas, ATCC

BEI Resources: Supporting the Infectious Disease Research Community Slides

4:00 pm – Maher Al Rwahnih, NCPN-Grapes, UC-Davis

Quality Control at Foundation Plant Services

4:30 pm – Open Discussion/Q&A

4:50 pm – Special Recognition presented by Kyria Boundy-Mills

5:00 pm – Wrap-up Day 1 & Announcements

5:30 pm – 7:00 pm: Networking Reception with Hors D’oeuvres – UC-Davis Winery Classroom

Tuesday, June 11

7:55 am – Welcome & Announcements

Session 4: The Nagoya Protocol: Potential Impacts on Data, Information, Licensing & Agreements

8:00 am – Amber Hartman-Scholz, DSMZ

Who “owns” (microbial) biodiversity? From the Nagoya Protocol to the Digital Sequence Information debate – Slides

8:30 am – Matthew Ryan, CABI

CABI’s approach to the Nagoya Protocol on ABS – An international perspective – Slides

9:00 am – Q&A & Discussion

9:30 am – Dianna Francis, UC-Davis

Intellectual property and tangible property licensing – Slides

10:10 am – Q&A & Discussion

10:40 am – Workshop Wrap-up and Tour Announcements

10:45 am – Networking Break

Session 5: Collection Tours

11:15 am – Departure for Morning Tours

  • 11:30-12:00 | Tour #1: UC-Davis Teaching Brewery
  • 12:00-12:30 | Tour #2: UC-Davis Teaching Winery

12:45 pm – Box lunch, UC-Davis Alumni Center

1:30 pm – Departure for Afternoon Tours

  • 1:45-3:00pm | UC-Davis Bohart Museum of Entomology
    • Wildlife Collection
    • Insect Collection

3:30pm – End of Workshop

Practical information

The workshop will take place at the Walter A. Buehler Alumni Center
University of California, Davis
530 Alumni Ln, Davis, CA 95616, USA


The closest hotel to the venue is the Hyatt Place UC Davis, located at walking distance (5 minutes) from the workshop venue. There are several other hotels in the city of Davis, very close to the UC Davis campus.