Phytobiomes Alliance Newsletter – October 2020


Genome-based circumscription and phenotyping of regulated microbes

The Alliance-coordinated project funded by the USDA Animal Plant Health Inspection Service (APHIS) began in August 2019 and focuses on the select agent Ralstonia solanacearum (Rs), a select agent. Through this project, a classification system based on whole genome sequences developed by Boris Vinatzer and Linwood Heath of Virginia Tech, is used to precisely identify microbes and conclusively distinguish pathogenic and non-pathogenic Rs strains. Over the long-term and once expanded beyond Rs, this method will be beneficial for accelerating the regulatory pathway for international and interstate shipments as well as commercialization of microbial products. Due to delays related to Covid-19, the project is now expected to be completed in August 2021. Other project partners include: University of Wisconsin-Madison, Iowa State University, USDA-APHIS, and University of Hawaii. Project page

Microbiome Studies

Under the leadership of Kirsty Bayliss, Murdoch University (Australia), the Alliance participated in the submission of a microbiome proposal to Hort Innovation, Australia. The objective of this project is to develop and deploy new microbial products that increase the yield of annual and perennial horticultural crops. The products will be developed by analyzing the microbiomes associated with the life cycle of the crop, from seed to harvest. By assessing how microbiomes change when exposed to biotic or abiotic stresses, the aim is to select combinations of microorganisms that are associated with crops that exhibit higher tolerance to these stresses, and develop these into new microbial products that increase crop yield. The Alliance will be involved directly in research related to microbiomes of seeds, roots, and foliage. The proposal has passed the first stage of consideration and ultimate success will depend on securing matching funds for the project and ensuring that a microbial product can be commercialized during the life of the project. Other project partners include Valent Biosciences, Karyosoft, Austrian Institute of Technology, INRAE, University of California Davis, University of California Los Angeles, and University of Dundee.

Nutrigenomics Proposal

Again, under the leadership of Kirsty Bayliss, Murdoch University (Australia), the Alliance participated in the submission of a nutrigenomics proposal to Hort Innovation, Australia. The project will have three core areas of research: breeding and deployment of new varieties, phytobiome studies, and human health validation. The Alliance will coordinate the microbiome studies and provide international linkages to the overall project. Other partners in this project proposal include African Research University Alliance in South Africa, the Agricultural Research Council of South Africa, Colorado State University, IRD, University of Waterloo, University of California Los Angeles, and INRAE. This proposal is still pending consideration.

Classification System for Risk Prediction

The Alliance has re-submitted a proposal to USDA-APHIS to develop a “risk prediction” method for beneficial plant bacteria by integrating genome-based circumscription and phenotypic data with an initial focus on Bacillus and Burkholderia for which biocontrol activity has been identified. The overall purpose of this project is to leverage genome sequencing and genome-based classification with phenotypic data thereby enabling APHIS to rapidly predict risk when assessing field-release permits for bacteria used for plant pest management. Project partners include Virginia Tech, Auburn University, Bayer Crop Science, Iowa State University, and University of California Los Angeles.

Database to Support Microbiome Studies

The Alliance is in discussions with CABI on the development of a joint microbiome data portal that could provide a common framework for accessing and analyzing microbiome data.

Standards Development

The Alliance is involved in multiple efforts related to the development of standards ranging from microbial sequencing to microbiome studies to regulatory requirements. Recently, the Alliance has been involved with the EU MicrobiomeSupport project to develop requirements for biobanking and microbiome definitions. The Alliance is also collaborating with the Microbiome Centers Consortium, UK Crop Microbiome CryoBank (UK-CMCB), US Ag Microbiome Network, and the International Metagenomics and Microbiome Standards Alliance. In the APHIS supported sequence-based classification project (above), the project partners will develop for consideration by APHIS a metadata checklist of relevant phenotypic and geographic data, SOPs, and guidelines for using genome-based classification for circumscription of regulated bacteria.


The Alliance participated in two new publications, both of which were developed through the EU MicrobiomeSupport project.

Alliance Webinar Series

All webinars are free to attend and are scheduled at 11am Eastern, US Time. Recordings are subsequently posted to the Alliance YouTube channel. Subscribe to the channel to never miss an upload.

Upcoming webinars
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Phytobiomes Conference

The International Phytobiomes Conference will take place in Denver, Colorado, USA from 14 to 17 September 2021. Registration will open in the Spring 2021. We are looking forward to seeing you all there.

Upcoming phytobiome-related events

For updates, check the event calendar on the website.

If you are aware of an event 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.
We developed a set of standards slides about phytobiomes, the Alliance, its goals and priorities. Contact us if you wish to receive those slides in PowerPoint format to add to your presentations.

5th Microbiome Movement – AgBioTech Summit 2021, 22-24 February 2021

As the global population increases and consumers pressure to move away from chemical and synthetic farming practices, the agricultural industry must harness new technologies that maximize productivity whilst limiting chemical inputs. This is where we step in to provide you with the definitive forum to connect with your peers working to tap into the plant-soil microbiome the 5th Microbiome Movement – AgBioTech Summit.
After researching directly with the field, we have put together a program that addresses your biggest challenges. Our 30+ strong speaking faculty contains some of the hottest academic researchers, leading figures from industry and the thoughts of growers and distributors. AgBioTech 3-day program is your opportunity to harness the plant-soil microbiome to discover and translate the next generation of scientifically-driven AgBiologicals that will transfer grower yield, sustainability and commercial outcomes.
Join us on February 22-24, 2021, for the data driven presentations, thought-provoking discussions and practical applicability lessons enabling you to maximize the potential of your product candidate.
Phytobiomes Alliance members can benefit from an exclusive 15% discount by quoting the code IPBA15 or by contacting

Our Sponsors

The Phytobiomes Alliance is sponsored by Bayer Crop Science, Eversole Associates, INRAE, Novozymes, Valent BioSciences, Biovante, Colorado State University, Eurofins BioDiagnostics, Indigo, IRD, Joyn Bio, the University of Nebraska-Lincoln, NewLeaf Symbiotics, the Noble Research Institute, Penn State College of Agricultural Sciences, Pivot Bio, The Fertilizer Institute, the Waterloo Centre for Microbial Research, Aphea.Bio, BioConsortia, AIT Austrian Institute of Technology and Karyosoft.