MANY WAYS

Vision

Microbiomes in the food and feed system can have beneficial and adverse effects on human, animal and environmental health. They can impact on food and feed quality, safety and sustainability, either directly or indirectly. Microbiomes are therefore an integral part of the “One Health” framework. More consideration should be placed however on the role of microbiomes to ensure further progress is made in chemical risk assessment. We must also explore how this can best be achieved in a regulatory context for food and feed safety and sustainability. As the Joint Research Centre (JRC) and the Food and Agriculture Organisation (FAO) have several ongoing projects on microbiomes, in particular regarding soil/plant health and the food system, this session will be co-developed with them.

Background – Challenges and opportunities

Communities of microorganisms and their genomes that exist in a defined environment are collectively referred to as microbiomes. They are found in most environments such as soils, aquatic habitats, surfaces and specific lumen of plants, animals and humans.

Research has shown associations between microbiomes and a wide range of human diseases. The gut microbiome is currently viewed as an additional modulator of both potentially beneficial and adverse effects of environmental exposure (namely diet, chemicals, pathogens, etc.). There is compelling evidence of gut microbiome involvement in the metabolic transformation of chemicals in broad chemical classes, including metals, polycyclic aromatic hydrocarbons (PAHs), pesticides and persistent organochlorines, nitrosamines and aromatic amines, and other toxicant classes. The optimal balance within soil microorganisms is directly attributed to improved plant health and soil fertility. However, the actual balance may be impaired by several anthropogenic factors, such as antimicrobials, heavy metals and plant protection products (PPP).

There is currently no internationally agreed guidance nor methodology in place to systematically account for possible effects on microbiomes or effects by microbiomes on host health or environment. Knowledge of how the human microbiome modulates the pharmacokinetics and metabolism of chemicals is lacking. Translating a decrease in microbiome diversity into a functional consequence is challenging as there are as yet no standards to define a healthy microbiome. Therefore, more data are required for a better understanding of covariates driving the human and animal gut microbiome variation within ranges not leading to adverse effects. This knowledge is needed to further assess when a change either in structure and/or function of the microbiome profile goes beyond those variations and translates into an adverse biological effect on the host. Furthermore, there are no standardised approaches to characterise healthy soil from a microbiome perspective. We need to define specific microbial groups to serve as a proxy for the microbiome as a whole. This would provide us with an agreed starting point for a protocol to study the links with microbial biodiversity, metabolic functions and interaction with anthropogenic factors. Although multi-omics approaches hold enormous potential to unravel links between a compromised microbiome and disease status, more experimental work is needed to confirm causality.

Research on the microbiome is proceeding at a very fast pace and it is critical that we evaluate how our greater understanding of the role of microbiomes in host and environmental health may need to be integrated into regulatory scientific assessment processes. Clarity is needed on which data are required to include microbiome considerations into risk assessment. Currently, several Horizon 2020 EU initiatives are investigating systems-level microbiome effects on the whole food chain from a wider perspective. The European Food Safety Authority (EFSA) awarded two grants in early 2021 to build capacity for the evaluation of the impact of various modulators under EFSA assessment on microbiomes and of microbiomes on host health. In parallel, the JRC LUCAS Soil Programme is currently undertaking the largest systematic assessment of the soil microbiome so far, with a view to develop policy indicators that capture the impact of land management and emissions on soil health. While there is a lot of research on the links between the soil microbiome, soil fertility and plant health, many open questions remain to be explored, both from a purely research point of view and regulatory science point of view. The ongoing FAO literature review on the soil microbiome will provide a list of key research gaps.

As microbiome assessment lies at the very heart of the intersection between chemical and biological risk assessment, there will be ample opportunities in the future for these two disciplines to collaborate and foster mutual understanding on their respective risk assessments.

Scope and objectives

The thematic session aims to clarify our current understanding of the relevance of microbiome structural changes to the risk assessment of chemicals and to identify goals for developing risk assessment. An important avenue is to enhance the evidence base that demonstrates the causality between a structurally altered microbiome and subsequent change(s) in metabolic pathways leading to adverse effects in the host

The focus will be on chemicals to which humans and animals are exposed via dietary intake (preferably within EFSA’s remit for risk assessment) and via the environment, but new evidence on other chemicals is also relevant. The thematic session will present proof of concepts from a wider human, animal and environmental perspective. This could be complemented by an overview of current models and what is needed to validate them to meet accepted standards for use in risk assessment.

This session is connected to goal 2 and 3 of the EFSA 2022 conference by advancing food/feed regulatory science and showcasing & sharing relevant developments on how microbiome considerations can be integrated into chemical risk assessment. A collaborative approach is followed by co-creating the event with JRC and FAO.

The main objectives of the thematic sessions are to:

• Improve understanding of the relevancy of microbiome for regulatory chemical risk assessment;
• Identify development goals for chemical and environmental risk assessment;
• Enhance the evidence base that demonstrates the causality.

Part I - Microbiome and host health interplay

Part II - Panel discussion & wrap up