Phytobiomes Alliance Newsletter – April 2019


Genome-based circumscription and phenotyping of regulated microbes

The Phytobiomes Alliance project to begin developing a sequence-based classification for regulated microbes has received funding from the USDA Animal Plant Health Inspection Service (APHIS). The project will focus initially on the select agent Ralstonia solanacearum (Rs). The project is coordinated by Kellye Eversole and is under the scientific leadership of Coordinating Committee member Boris Vinatzer (Virginia Tech). Objectives include, among others:

  • sequencing and assembling the genomes of approximately 300 Rs strains;
  • constructing a whole genome-based phylogeny of all strains sequenced and all Rs strains in public databases, assigning LINs, and validating results; phenotypically characterizing representative strains to determine which cause disease on Solanaceae at low temperatures (cool virulence);
  • precisely describing and validating the LIN group that includes only strains that should be regulated as select agents; and
  • developing recommendations/guidelines in regard to the use of genome-based classification in the circumscription of regulated bacterial plant pathogens and biocontrol agents.
MicrobiomeSupport project

The 4-year (2018-2022) European-funded Coordination and Support Action held a ‘Common Ground Workshop’ in Vienna, Austria, on 4 and 5 March 2019, followed by a ‘Microbiome definition workshop’ and a ‘Biobanks & Data Storage workshop’ on 6 and 7 March 2019 in Tulln, Austria.
The MicrobiomeSupport project is a coordinated by Angela Sessitsch (AIT Austrian Institute of Technology) with members from 13 European countries, Canada, US, Australia, New Zealand, China, India, Argentina and Brazil. The project aims to:

  • Harmonize the methods, approaches and standards used in microbiome research in different types of environment (soil, aquatic environments, animals, humans, etc.) and assess their economic and public health importance;
  • Support international efforts to align research funding to avoid unnecessary duplication of research by engaging microbiome researchers, funding agencies, policy makers and industry, specifically through coordinating the working group ‘Food Microbiomes’ of the International Bioeconomy Forum (IBF);
  • Raise public awareness on the potential of microbiome applications.
Beta-Testing of Loci 1.0 software

The Alliance and Karyosoft Augmented Innovations have signed a memorandum of understanding whereby Alliance Coordinating Committee members and sponsors will participate in beta-testing Loci 1.0, a Karyosoft developed software platform that enables the efficient management, analyses, and visualizations of microbial genome sequence data and Karyosoft will allow for future purchases of Loci 1.0 to be discounted significantly for Coordinating Committee members and sponsors. For additional information about Karyosoft, please contact Rajesh Perianayagam or Kellye Eversole.

Regulatory Working Group

Natalie Breakfield (NewLeaf Symbiotics), Bharath Prithiviraj (Prime Discoveries), and Gus Anstrom (Bayer CropScience) have agreed to be part of the Alliance regulatory working group led by Kellye Eversole. The Working Group is tasked with developing a regulatory science roadmap that will facilitate the commercialization of agricultural biologicals and microbial products. Planning of a workshop with regulatory officials in Washington, DC, in the fall of 2019 will commence this summer.


Press releases and announcements
  • We developed a set of standards slides about phytobiomes, the Alliance, its goals and priorities. Contact us if you wish to receive those slides to add to your presentations.

Alliance Events

  • 12-16 January 2019: the Alliance organized the workshop ‘Exploring Phytobiomes’ during the Plant and Animal Genome Conference in San Diego, CA, USA. Slides of the presentations are available on the Alliance website.
  • 7 December 2018: the Alliance Scientific Coordinating Committee met in Montpellier, France (closed meeting, open only to members of the committee)
  • 4-6 December 2018: the Alliance organized (with INRA and IRD) the International Phytobiomes Conference 2018 in Montpellier, France. The successful event was attended by 157 researchers and scientists from the public and private sector, coming from 18 countries. The abstract book and slides of most presentations are available on the website.

Upcoming events

list of events is available on the website.
If you are going to or are aware of a conference, workshop, or seminar on phytobiome-related topics and if that event is not listed on the website, please let us know.
In case you could not join us at an event, PDFs of the latest presentations made by the Alliance Leadership team are available on the website.

New Coordinating Committee Members

We are pleased to welcome:

  • Gary Felton, as topical leader in insect-microbe-host interactions
  • Sally Flis, as representative of The Fertilizer Institute, a financial sponsor
  • Rajesh Perianayagam, as representative of Karyosoft, a financial sponsor
  • Bharath Prithiviraj, as representative of Prime Discoveries, a financial sponsor
  • Brajesh Singh, as project leader for the Global Crop Agri-Microbiomes Initiative

Our Sponsors

Welcome to our new sponsors: Prime Discoveries, Karyosoft and The Fertilizer Institute.

The Phytobiomes Alliance is sponsored by Bayer CropScience, Eversole Associates, The Climate Corporation, the French National Institute for Agricultural Research (INRA), Novozymes, Colorado State University, Evogene, Indigo Ag, the French National Research Institute for Sustainable Development (IRD), the University of Maryland, the University of Nebraska-Lincoln, NewLeaf Symbiotics, the Noble Research Institute, Penn State College of Agricultural Sciences, The Fertilizer Institute, The Waterloo Centre for Microbial Research, the American Phytopathological Society, BioConsortia, Prime Discoveries, AIT Austrian Institute of Technology, and Karyosoft.