Metagenomics and Microbial Sequencing for Diagnostics

When: Monday 12 September

Time: 13:30-16:30

Fee: $50 when purchased independently, $40 when purchased in conjunction with the Conference registration



  • Veronica Roman-Reyna, Ohio State University, US
  • Jonathan Jacobs, Ohio State University, US
  • Caitilyn Allen, University of Wisconsin-Madison, US
  • Boris Vinatzer, Virginia Tech, US
  • Gwyn Beattie, Iowa State University, US
  • Kellye Eversole, Phytobiomes Alliance


Next-generation sequencing technologies for genomics and metagenomics has expanded our ability to precisely identify and document plant pathogens from complex environmental samples. These genomic tools allow us to digitally document causal agents of plant disease and potentially reveal new emerging threats to agriculture. Metagenomics also provides a novel way to provide context to the target sample by additionally capturing the host genome and microbiome. This rapidly advancing field however poses challenges for pathogen classification and defining acceptable thresholds for plant disease identification.

We will discuss how genomics and metagenomics improve and accelerate plant disease diagnostics in this workshop. We will cover the current short- and long-read sequencing technologies and then explain available tools for performing sequencing for diagnostics. Finally, we will show applied examples of how we use genomics, including whole genome sequence- based methods, to strengthen pathogen classification and thus accurate identification.


13:30 – 13:35Introduction to the workshop
13:35 – 14:50How to use the LINbase Web server for genome-based identification of bacterial pathogens with strain resolution
Boris Vinatzer (presenter), Reza Mazloom, Lenwood Heath  
How to use the ONT MinION sequencer for metagenome-based detection and identification of bacterial plant pathogens.
Parul Sharma (presenter), Marcela Johnson, Sahar Abdelrazek, Haijie Liu, Boris Vinatzer
14:50 – 15:50Hands-on on how to plot and interpret Illumina metagenomic data from infected samples.
Veronica Roman-Reyna (presenter), Hannah Toth, Taylor Klass, Jonathan Jacobs
15:50 – 16:30RoundTable: Limitations and Future perspectives of using genomics for diagnostics.
Parul Sharma, Boris Vinatzer, Gwyn Beattie, Kellye Eversole, Veronica Roman-Reyna, Jonathan Jacobs

The roundtable will be an open discussion on unanswered questions related to genomics for diagnostics. Participants will be able to send questions about genomics and metagenomics they will like panel to address.

Some question will be:

  • What are the limits of detection in metagenomics for diagnostics?
  • Does this differ between quarantine organisms vs. endemic problems?
  • Are our thresholds the same for metagenomics for microbial ecology compared to disease diagnostics?
  • What is the minimum amount of detection to consider it will cause the disease?
  • How can we use metagenomics to look for pathogen reservoirs?