Microbes play a vital role in how we grow and produce food, preserve nutrients, and reduce waste. These microorganisms—bacteria, fungi, and others—form microbiomes, which are natural communities found in soil, plants, animals, and even the human body. In soils and the gut, for example, they help make nutrients more available and stable—supporting plant growth and enhancing the nutritional value of food.
The European Union is increasingly recognizing the potential of microbiomes to support more sustainable farming, improve food processing, and contribute to the circular economy. However, the EU microbiome policy is still evolving, and clear, harmonized regulations remain limited—especially when it comes to new food and feed products based on microbial processes.
Why Microbiomes Matter in Agriculture and Food
Microbiomes are essential across several stages of the food system:
- In crop production, maintaining healthy microbial populations in the soil supports nutrient cycling and reduces the need for chemical inputs like fertilizers and pesticides.
- In food processing, microbes are used in fermentation to produce familiar products such as yoghurt, sourdough, and pickles.
- In animal nutrition, fermented feed products enhance digestibility, improve nutrient availability, and allow for better preservation.
The Horizon Europe-funded WHEATBIOME project is exploring how microbiomes associated with wheat can be harnessed to create microbiome-based innovations, including fermented wheat products. It also investigates how wheat by-products can be reused—contributing to a sustainable agricultural circular economy and reducing food waste.
These objectives align with the European Union’s strategic priorities for 2024-2029, particularly the commitment to sustaining our quality of life by building a competitive and resilient agriculture and food system. Additionally, initiatives such as the European Green Deal, the Farm to Fork Strategy, and the Circular Economy Action Plan remain integral to the EU’s agenda.
Regulatory Gaps in the EU
As scientific interest in microbiome applications continues to grow, aligning regulations with innovation is key to supporting sustainable food and farming across Europe.
WHEATBIOME’s legal assessment identified several areas where clearer regulatory guidance could support the development and adoption of microbiome-based products. During a 2024 consultation with Hungary’s National Food Chain Safety Office (NÉBIH), stakeholders highlighted that:
- Many microbial food and feed products fall under existing “novel” classifications, which may involve complex and comprehensive approval processes.
In addition, broader analysis across the project identified further regulatory considerations:
- Harmonized EU standards are still limited for newer applications, such as the fermentation of upcycled wheat by-products or microbiomes in plant-based feed systems.
- Existing frameworks—such as Regulation (EC) No 1831/2003 on feed additives and Regulation (EU) 2022/1438 on plant protection micro-organisms—do not yet fully reflect emerging uses, such as multifunctional microbial blends or fermented by-products.
These findings point to an opportunity to build on current legislation and develop targeted, microbiome-specific policies aligned with the EU Green Deal, Farm to Fork Strategy, and sustainable agriculture regulation goals.
Insights from Stakeholders
Preliminary findings from WHEATBIOME’s stakeholder survey revealed that regulatory and policy-related obstacles are among the most frequently cited limitations in adopting fermented wheat-based products and microbiome-related practices. The stakeholder survey combined semi-structured interviews and an online questionnaire to gather insights from a diverse group of actors, including farmers, researchers, food producers, feed manufacturers, policy advisors, consumer representatives, and other decision-makers across the food and feed value chain.
Additional feedback gathered from stakeholders highlighted:
- The need for more adaptive and flexible regulations that can accommodate emerging microbial technologies.
- A demand for clearer guidance on food safety and approval procedures.
- Interest in cross-sectoral collaboration and interdisciplinary research to support innovation in a safe and informed manner.
A Call for Harmonized Policy
There is a clear opportunity for the EU to strengthen its regulatory approach to microbiome-based innovations. Future policy development could include:
- Developing microbiome-specific guidance and regulatory frameworks under European Food Safety Authority (EFSA) or the European Commission.
- Formally recognizing microbial innovations within major EU strategies, such as the CEAP and Farm to Fork.
- Offering incentives for safe experimentation and responsible innovation, especially in using microbiomes for wheat by-products and fermentation.
- Raising public awareness and trust by highlighting the environmental, health, and economic benefits of microbiome applications in agriculture and food.
As the EU works toward a more sustainable, resilient, and circular food system, microbiomes offer a powerful—but underutilized—resource. Unlocking their potential will require clearer rules, targeted support, and continued collaboration between science, policy, and practice.
The WHEATBIOME project contributes to this effort by generating knowledge, gathering stakeholder insights, and informing policy at the EU level. With the right policy frameworks, microbiome innovation in food and agriculture can help meet Europe’s goals for climate resilience, food security, and sustainability.
Author: University of Veterinary Medicine Budapest – Aira Joy Aquino
