Periodic Reporting for period 2 - MICROBE (MICRObiome Biobanking (RI) Enabler)
Berichtszeitraum: 2024-02-01 bis 2025-07-31
Microbiomes comprise communities of microorganisms (i.e. microbiota that includes bacteria, archaea, protists, fungi and microalgae) and their "theatre of activity" (i.e. structural elements, metabolites, signal molecules, mobile genetic elements, as well as surrounding environmental conditions). Microbiomes play a key role in maintaining life on Earth by providing a range of essential ecosystem services and are indispensable for the health of plants, animals and humans. Thus, there is a wide consensus that by harnessing microbiome functions, society would be better placed to tackle global challenges such as food security, health and wellbeing, food waste management, and climate change mitigation. To facilitate the science necessary to achieve key advances in microbiome research, methodologies and technologies to capture or create, ensure stable long-term maintenance, and experimentally perturb microbiomes are required. Research infrastructures currently lack optimized methodologies and technologies to preserve and provide access to microbiome samples and massive amounts of associated data MICROBE is designed to address these issues by building upon and connecting: (1) technical solutions for microbiome preservation, propagation and functionality assessment, (2) novel ecological concepts (i.e. “core microbiome” and “microbial keystone taxa”), and (3) data infrastructures. In addition, MICROBE will address essential framework issues such as standardisation, ethical and legal requirements and new business opportunities. Participation of relevant European research infrastructures, i.e. BBMRI-ERIC, MIRRI, ELIXIR, and EMBRC-ERIC, to ensure that community needs are adequately addressed and that developed solutions are efficiently adopted by the infrastructures themselves and their user communities. The long-term ambition is to ensure widespread adoption in microbiome research communities and thereby support the development of novel microbiome-based applications.
During the second reporting period, the project focused on advancing methodologies for the preservation and functional assessment of microbiomes. Comprehensive cryopreservation trials were designed and initiated for soil, seed, and marine microbiomes, with careful selection of representative samples to support inter-laboratory validation and leverage existing datasets. Concepts for both in silico and in vivo approaches for optimized functional assessment of microbiomes were further developed and partially applied to monitor cryopreservation performance. In parallel, independent trials evaluated stabilization reagents that do not require cooling chains, facilitating nucleic acid-based analyses.
Significant progress was made in standardising data-analysis methods for the identification of keystone taxa and bioinformatic workflows for metagenome analysis allowing establishment of and strain selection procedures. Harmonization of sample metadata across partners was achieved, establishing the foundation for the MICROBE Data Hub and the public-facing MICROBE data catalogue, which support discoverability, interoperability, and long-term usability of microbiome datasets in line with FAIR principles.
Guidelines for sample pre-analytics were developed and the project also established liaison relationships with ISO technical committees to contribute to emerging microbiome biobanking standards.
Regulatory work addressed ELSI and Nagoya/ABS-related requirements for access and use of microbiome samples and related data. Guidance documents were developed in collaboration with external experts.
Significant progress was made in standardising data-analysis methods for the identification of keystone taxa and bioinformatic workflows for metagenome analysis allowing establishment of and strain selection procedures. Harmonization of sample metadata across partners was achieved, establishing the foundation for the MICROBE Data Hub and the public-facing MICROBE data catalogue, which support discoverability, interoperability, and long-term usability of microbiome datasets in line with FAIR principles.
Guidelines for sample pre-analytics were developed and the project also established liaison relationships with ISO technical committees to contribute to emerging microbiome biobanking standards.
Regulatory work addressed ELSI and Nagoya/ABS-related requirements for access and use of microbiome samples and related data. Guidance documents were developed in collaboration with external experts.
MICROBE has defined eight project results that will be demonstrated within a specific deliverable. These project results are:
o PR1: Validated protocols for preservation and propagation of complex microbiome samples (D1.3)
o PR2: Novel isolates of members of key microbiomes from different domains (D2.2)
o PR3: Novel synthetic consortia reproducing the key functionalities of selected ecosystems (D2.3)
o PR4: Customised data infrastructure tools for microbiome biobanking (D3.4)
o PR5: Guidelines for implementation of standardised microbiome biobanking workflows in selected fields (D4.2)
o PR6: Guidelines for establishment of ethical and legal framework conditions that enable microbiome biobanking (D5.1)
o PR7: Business models for the implementation and exploitation of novel microbiome-based technologies and resources (D5.3)
o PR8: Portfolio of training and educational resources (D6.2)
MICROBE will provide a comprehensive operational blueprint for the establishment of microbiome biobanking infrastructure, including validated protocols for the preservation and propagation of complex microbiome samples, customised data infrastructure tools for microbiome biobanking, as well as guidance documents for the implementation of standardised microbiome biobanking workflows in selected fields and for the establishment of ethical and legal framework conditions that enable microbiome biobanking. MICROBE will provide access to new microbiome-derived resources (i.e. isolates and synthetic consortia) that can be further exploited to develop novel microbiome-based applications and products.
MICROBE will also develop a portfolio of training and educational resources and deliver training to research infrastructure staff members and industry representatives. Moreover, MICROBE will train young researchers and enable open access to new knowledge and data. MICROBE will open new business potentials and address companies willing to explore these while providing novel business models for the implementation and exploitation of novel microbiome-based technologies and resources. To support that, MICROBE will also provide guidance on compliance with respective standards, legal and ethical requirements.
Policy relevant evidence of your project
o PR1: Validated protocols for preservation and propagation of complex microbiome samples (D1.3)
o PR2: Novel isolates of members of key microbiomes from different domains (D2.2)
o PR3: Novel synthetic consortia reproducing the key functionalities of selected ecosystems (D2.3)
o PR4: Customised data infrastructure tools for microbiome biobanking (D3.4)
o PR5: Guidelines for implementation of standardised microbiome biobanking workflows in selected fields (D4.2)
o PR6: Guidelines for establishment of ethical and legal framework conditions that enable microbiome biobanking (D5.1)
o PR7: Business models for the implementation and exploitation of novel microbiome-based technologies and resources (D5.3)
o PR8: Portfolio of training and educational resources (D6.2)
MICROBE will provide a comprehensive operational blueprint for the establishment of microbiome biobanking infrastructure, including validated protocols for the preservation and propagation of complex microbiome samples, customised data infrastructure tools for microbiome biobanking, as well as guidance documents for the implementation of standardised microbiome biobanking workflows in selected fields and for the establishment of ethical and legal framework conditions that enable microbiome biobanking. MICROBE will provide access to new microbiome-derived resources (i.e. isolates and synthetic consortia) that can be further exploited to develop novel microbiome-based applications and products.
MICROBE will also develop a portfolio of training and educational resources and deliver training to research infrastructure staff members and industry representatives. Moreover, MICROBE will train young researchers and enable open access to new knowledge and data. MICROBE will open new business potentials and address companies willing to explore these while providing novel business models for the implementation and exploitation of novel microbiome-based technologies and resources. To support that, MICROBE will also provide guidance on compliance with respective standards, legal and ethical requirements.
Policy relevant evidence of your project