2018 Workshop 2

Agricultural microbiome data: data platforms, standards, and analytical tools needed for advancing our science (ICPP, Boston, MA)

Workshop Program (July 29, 10:30am-12:00pm, Room 206 Hynes Convention Center)

 Welcome and Introductions

Linda Kinkel, University of Minnesota

Existing platforms:  What is the state of the art for microbiome data? (45 minutes)

- The National Microbiome Data Collaborative (Lynn Shriml, University of Maryland, and Emiley Eloe-Fadrosh, JGI)

- The Joint Genome Institute (Susannah Tringe, JGI)

- The Genetics*Environmental*Management*Socioeconomic platform (Kevin Silverstein, University of Minnesota GEMS)

- LINbase classification and database (Boris Vinatzer, Virginia Tech)

- Questions and BRIEF discussion

Discussion breakouts 

A.    Discussion One:  Metadata 

*What minimum information should be included in a standard metadata checklist for agricultural microbiome studies? 

*Are metadata standards likely to vary among sub-domains of agricultural systems (e.g. soil vs. plant vs. post-harvest vs. insect microbiomes)? 

*Are there metadata within existing microbiome databases that are not needed for agricultural microbiomes? 

B.    Discussion Two:  Standards 

*What standards are needed for:  i) plant or soil sampling; ii) sample storage pre- or post-extraction; iii) extraction; iv) data processing; v) access to raw and/or processed data? 

*Who should determine these and how should adoption or compliance with standards be encouraged (e.g.  grant submission requirements, journal requirements, other)?   

C.     Discussion Three:  Database needs 

*What will success look like for a collective agricultural microbiomes database?

*What data types are going to be part of a database now and in the future?

*What role should the agricultural microbiomes research community play in database development? 

D. Overall summary and next steps:  wrap-up

List of participants

Name, Country

Kellye Eversole, USA

Leland Pierson, USA

Boris Vinatzer, USA

Gwyn Beattie, USA

Alejandra Huerta, USA

Audrey Kalil, USA

Ewa Lojkowska, POLAND

Marta  Potrykus, POLAND

Deborah Samac, USA

Linda  Kinkel, USA

Jose Pablo Dundore-Arias, USA

Neelam Redekar, USA

Sarah Castle, USA

Kenneth Frost, USA

Joshua Herr, USA

Anjali Iyer-Pascuzzi, USA

Thais Egreja, USA

Paul Schulze-Lefert, GERMANY

Jagdeep Kaur, USA

Bharath Prithiviraj, USA

Alejandro Rojas, USA

Kevin Silverstein, USA

Tijana Glavina del Rio, USA

James Tiedje, USA

Susannah Tringe, USA

Fiona Brennan, IRELAND

Joanne Emerson, USA

Lynn Schriml, USA

Sydney Everhart, USA

Rosalie Calderon, USA

Jhonson Leonard, USA

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