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MICRObiome Biobanking (RI) Enabler

Periodic Reporting for period 1 - MICROBE (MICRObiome Biobanking (RI) Enabler)

Periodo di rendicontazione: 2023-02-01 al 2024-01-31

Microbiomes are communities of microorganisms that include bacteria, archaea, protists, fungi and microalgae, their structural elements, metabolites, signal molecules, mobile genetic elements and surrounding environmental conditions. They are essential for maintaining ecosystems and the health of plants, animals and humans. The EU-funded MICROBE project will cooperate with research infrastructures for the creation and development of methodologies and technologies to enable access to microbiome samples and associated data. The project objectives include technical solutions for microbiome preservation, propagation and functionality assessment, as well as data infrastructures. In addition, MICROBE will address issues associated with standardisation, ethical and legal requirements, and business opportunities.
"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 standardization, 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 properly addressed and that developed solutions are efficiently taken up by the infrastructures themselves and by their user communities. Long term ambition is to ensure widespread uptake in microbiome research communities and thus support the development of novel microbiome-based applications."
Preservation of complex microbiomes: Comprehensive preservation trials on all selected use cases were initiated. Considering that these trials are established as long-term trials, only preliminary results were obtained. Furthermore, procedures for in silico and in vivo functional assessment of three use cases were proposed (Ms3).
Use of novel ecological concepts: The work focused on establishing a consensual definition of "core microbiomes" and "keystone taxa". Therefore, an expert workshop was organised. Follow-up activities planned for the second reporting period include experimental confirmation of the definitions and preparation of a scientific publication to disseminate these results.
Data infrastructure: Guidance on microbiome sample accessioning was developed (D3.1) and applied to the samples used in the preservation trials. Key public data sets pertinent to the investigated use cases were identified.
Standardisation & QC: An inventory of standards, guidelines and best practices for microbiome sample pre-analytics was established (D4.1) and used to identify gaps that will be addressed in the guidance document that will be elaborated together with external experts in the second reporting period.
Legal and ethical framework: The microbiome R&D community was supported through the organisation of the "Nagoya Protocol for Beginners - A crash course in access and benefit-sharing" workshop. Furthermore, a clarification on the French Access and Benefit Sharing (ABS) scheme was obtained. A review on ethical, legal (including regulatory) and societal issues (ELSI) associated with the use of microbiome samples in research and biobanking was completed and will be used to elaborate guidelines for the future use of microbiomes.
Stakeholder engagement: The MICROBE consortium established collaboration with numerous key stakeholders. With some, e.g. EPSO Working Group Plants and Microbiomes, #Microbes4SustainableFoods cluster and TREC expedition, joined activities are planned in the second reporting period.
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.
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