BBMRI.at representative active in MICROBE led workshop on pre-analytical requirements plant microbiome samples

6th EPSO Workshop on Plants and Microbiomes

At the 6th Workshop on Plants and Microbiomes, organized by the European Plant Science Organisation (EPSO), experts from across Europe came together to discuss the latest advances in plant microbiome research and infrastructure development. The event held in Antequera, Spain, on 3 November 2025, featured three thematic sessions:

1. Microbiome crops – new projects, initiatives and highlights
2. MICROBE/EPSO workshop on minimal metadata requirements and critical pre-analytical parameters for plant microbiome samples
3. New microbiome technologies and discoveries

The second session was led by Cornelia Stumptner (Med Uni Graz, BBMRI.at and MICROBE), who also serves as Work Package Leader in the EU Project MICROBE. The interactive workshop brought together around one hundred participants to discuss how to ensure quality and reproducibility in plant microbiome research through well-defined pre-analytical workflows and metadata standards. Angela Sessitsch (Austrian Institute of Technology), Mette Haubjerg Nicolaisen (University of Copenhagen), and Soledad Sacristán (Universidad Politécnica de Madrid) (all EPSO) supported as group instructors.

Focus on the often-overlooked pre-analytical phase

In her introduction, Stumptner emphasized that the pre-analytical phase—covering all phases before the analysis including the ‘donor’, sample collection, preservation, processing and storage—is a crucial yet often underestimated and neglected part of microbiome studies. “In human healthcare, most diagnostic testing errors occur during this phase. In research, poor pre-analytics can lead to irreproducible results, wasted resources, and wrong conclusions,” she noted, adding that the same challenges apply to plant microbiome research.

Drawing parallels to the human microbiome field, she presented how European CEN and international ISO standards for human microbiome specimens—developed with contributions from BBMRI.at and the SPIDIA4P project—are now serving as a model for developing plant-specific standards within the MICROBE/EPSO collaboration.

Developing pre-analytical requirements for plant microbiome samples

Building on outcomes from previous MICROBE/EPSO meetings, the workshop introduced a draft workflow for plant microbiome sample handling, covering all steps from the field or greenhouse location, through collection, preservation, intermediate storage and transport, processing, analyte isolation, and storage of samples and analytes.

Participants were divided into working groups to review and prioritise metadata and process requirements for different workflow stages. Each group assessed which requirements are “minimum and must-have” versus “optional or study-specific” across different study types and growth conditions—natural, field, greenhouse, or artificial without soil.

Evidence from literature shows how multiple variables—such as plant type, plant compartment, sampling time and site, sample processing (e.g. homogenization before or after subsampling), intermediate storage duration and condition until preservation and DNA extraction protocols—can significantly affect microbial community profiles.

The lively group discussions confirmed several of these aspects for the different study types and growth conditions and pointed out current hurdles concerning implementation and manageability are.

Towards reproducible and FAIR microbiome research

The workshop underscored that high-quality, FAIR (Findable, Accessible, Interoperable, and Reusable) microbiome data depends on well-characterized and quality-controlled samples. Documenting pre-analytical metadata and data about the handling of the sample during the preanalytical process, enables reproducibility, comparability between studies, and the secondary use of data. Data are becoming increasing important in computational models or AI applications.

“The better this phase is standardized, the less we suffer from the ‘garbage in – garbage out’ problem,” Stumptner concluded.

A joint effort between MICROBE and EPSO

The MICROBE/EPSO collaboration is an important step toward harmonizing plant microbiome research practices across Europe. Together, the two initiatives aim to support the microbiome research community infrastructures through best practices.

The high level of engagement at this EPSO workshop reflects the growing interest in ensuring quality and reproducibility as well as reuse of samples and data in plant microbiome science.

About BBMRI.at and MICROBE

BBMRI.at, the Austrian node of the Biobanking and BioMolecular resources Research Infrastructure – European Research Infrastructure Consortium (BBMRI-ERIC), plays a leading role in the EU Project MICROBE, which aims to establish the first European blueprint for microbiome biobanking and research. BBMRI.at contributes its long-standing expertise in biobanking, standardization, and pre-analytical quality assurance to this initiative, ensuring that microbiome research in non-human species and environments is conducted on a robust and harmonized foundation.