Roadmap for the integration of environmental microbiomes in risk assessments under EFSA's remit
- Debode, F. , Caulier, S. , Demeter, S. , Dubois, B. , Gelhay, V. , Hulin, J. , Muhovski, Y. , Ninane, V. , Rousseau, G. & Bragard, C. (2024). Roadmap for the integration of environmental microbiomes in risk assessments under EFSA's remit.CRA-W, UCLouvain, 1-93.
| Type | Report |
| Year | 2024 |
| Title | Roadmap for the integration of environmental microbiomes in risk assessments under EFSA's remit |
| Institution | CRA-W, UCLouvain |
| Label | U12-0124-Debode-2024 |
| Pages | 1-93 |
| Date | 30 January 2024 |
| Endnote Keywords | bioinformatics, environmental microbiome, harmonisation, metabarcoding, omics, risk assessment, standardisation |
| Abstract | Scientific interest in the use of environmental microbiomes for risk assessment is rapidly growing, as exemplified by various EFSA opinions. In the absence of official regulatory guidelines on how to integrate environmental microbiomes in risk assessment, the aims of this report are therefore to determine whether microbiome studies can be used for such purposes, and to propose a roadmap for the integration of environmental microbiomes in risk assessments under EFSA’s remit. The report identifies the current gaps (in terms of knowledge and from a technical point of view) and barriers that might delay the implementation of the methods, and offers recommendations for standardised (multi-)omics techniques for risk assessment purposes. Our main findings identified five priorities: (i) defining the core microbiome (what it encompasses and what it is made of, including the identification of bioindicators) to assess the impact of any type of disturbance; (ii) standardising methodologies and protocols, from sampling to interpretation, to guarantee comparability of analyses; (iii) developing tools to facilitate interpretation; (iv) collecting microbiome-based data in shared, curated and maintained databases; and (v) setting up a European Network of Microbiome Laboratories to reach an agreement on how to standardise microbiome studies, to facilitate interactions between researchers and access to data or samples, and to actively include multiple stakeholders in discussions involving environmental microbiomes and risk assessment. There are both short- and longer-term priorities, all of which highlight the need to mobilise concurrently different agencies or institutions, as well as environmental microbiome research. The roadmap also points out the need for capacity building and training, for acceptance of this emerging technology, and communication issues. These recommendations will hopefully contribute to the elaboration of widely accepted guidelines in the regulatory framework EFSA is dealing with. |
| Fichier | |
| Lien | doi: 10.2903/sp.efsa.2024.EN–8602 |
| Authors | Debode, F., Caulier, S., Demeter, S., Dubois, B., Gelhay, V., Hulin, J., Muhovski, Y., Ninane, V., Rousseau, G., Bragard, C. |
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