Under the Microscope: MICROBE Project Paves the Way for Effective Microbiota Biobanking

How can we preserve an entire microbial community without changing what makes it unique? This question lies at the heart of the MICROBE (MICRObiome Biobanking Enabler) project, a Horizon Europe initiative working to develop innovative methods and infrastructures for microbiome biobanking. 

By bringing together experts from across Europe, the project aims to establish reliable approaches for preserving microbiotas while maintaining their biodiversity and functional capacities, ultimately providing biological resource centres with the knowledge and tools needed to support future microbiome research. 

Among the partners of this project is the French Collection for Plant-associated Bacteria (CIRM-CFBP), a partner of the French National Node of MIRRI-ERIC, which holds more than 7.000 bacterial strains that represent strategic resources for plant health. Every year, the collection distributes approximately 500 bacterial strains to researchers and educators worldwide, supporting scientific research, innovation, and teaching.

 

Interest in the microbiome area is rising

CIRM-CFBP noticed that, increasingly, researchers have been asking not only to preserve individual microbial strains, but also entire microbiotas. Unlike single strains, microbiotas are complex and heterogeneous communities that include both cultivable and non-cultivable microorganisms. Preserving them without altering their taxonomic composition or functional diversity is a significant scientific challenge. 

Given this, participation in an initiative such as this project was crucial. Within MICROBE, CIRM-CFBP focused on the seed microbiota use case. The team designed and conducted experiments to evaluate different storage conditions for seed-associated microbiotas, systematically analysing their taxonomic composition and functional diversity before preservation and after one week, three months, and one year of storage. 

Researchers also investigated the preservation of defined microbial communities. These simplified microbial communities are attracting growing interest because they are easier to study and could provide practical solutions for applications in agriculture and other sectors. 

 

Last project's sprint 

As the project approaches its conclusion, with the end of the project set for January 2027, CIRM-CFBP has gained valuable insights into how seed microbiotas can be handled, how effectively they can be preserved, and how microbiotas may be integrated into the routine activities of biological resource centres.

The outcomes of the MICROBE project will benefit the wider scientific community by providing biological resource centres with data, guidelines and operational blueprints for microbiota preservation. In doing so, the project is helping lay the foundations for effective microbiota biobanking and enabling broader access to these valuable biological resources for future research and innovation.

 

MICROBE results to be discussed in upcoming events

As the MICROBE project approaches its conclusion, its results and lessons learned will be shared with the wider scientific community through upcoming events. The project will be highlighted during the ECCO XLIV Meeting, taking place in Ponta Delgada, Portugal, where Tanja Kostic will deliver the keynote lecture "Microbiome Biobanking: Navigating Complexity – Insights from the MICROBE Journey". The lecture will offer an opportunity to reflect on the challenges addressed throughout the project and the insights gained from its work on microbiome biobanking.

MICROBE will also be featured during the upcoming online "Microbiome biobanking: Bridging technical challenges, data management and regulation", taking place on 9 December, 2026. Organised by the International Phytobiomes Alliance in collaboration with the U.S. Culture Collection Network, the event will bring together experts to discuss the technical solutions developed by MICROBE, as well as challenges related to microbiome data management, regulation and ethical frameworks. The webinar will provide an opportunity to explore how the project’s outputs can support the broader uptake of microbiome-based solutions across research and industry.

 

Under the Microscope: the best way to keep on track of MIRRI-ERIC 

Every first Friday of each month, MIRRI-ERIC releases a news article from the series "Under the Microscope", showcasing key developments, from funded research projects to collaboration opportunities and milestones across our network. Stay tuned!

 

This text was prepared in collaboration with Perrine Portier (CIRM).