MICROBIOMES4SOY co-develops regional transition pathways with stakeholders to advance sustainable, plant-based protein diets by integrating microbiome applications into food and feed systems, aligned with EU FOOD 2030 priorities. 

Hence, the project is dedicated to co-developing regional transition pathways with food system stakeholders to enable a shift toward sustainable, plant-based protein diets. The focus is on integrating microbiome applications into plant-based food and feed systems, in line with the EU’s FOOD 2030 priorities. This is achieved by engaging diverse stakeholders—including farmers, advisors, industry, and policymakers—to identify leverage points for transforming food systems. 

This task applies a participatory, co-creation approach to identify leverage points and develop solutions with practitioners, industry, and policymakers. 

Key achievements include:

• Structured workshops with stakeholders to map out transition pathways that account for impacts on education, innovation, and regulation. These sessions identify concrete actions that can lead to systemic change in food systems.
• Development of educational materials—factsheets, webinars, and tutorials—targeting stakeholders across the soya bean value chain to increase understanding of the role and benefits of microbiomes in plant protein systems.
• Identification of innovation opportunities that support sustainable plant protein production, including microbiome-based approaches in crop cultivation, feed systems, and product development. The task also explores viable business models and value chain improvements.
• Co-development of policy and regulatory recommendations to address barriers to the adoption of microbiome applications in agriculture and food production.
• A comprehensive meta-analysis of data from across the project to reveal key microbiome patterns and their potential benefits along the food and feed value chain, supporting decision-making for stakeholders.

Objective: 

Aquaculture is one of the fastest growing food industries and offers a way forward to supply a growing population with sustainably produced animal protein. However, the required aquaculture feed currently contains fish meal as a protein source that derives from wild caught fish, leading to dangers of overfishing and overexploiting natural resources. To achieve sustainability, other alternatives for fish meal need to be found and fermented soyabeans are a potential source for such a replacement. We aim to improve the fermentation process by searching for novel microorganisms and enzymes that are capable of fermenting soyabeans at higher temperature to reduce the occurrence of Anti-Nutritional Factors (ANFs), compounds that reduce the availability of nutrients in the soybeans, and therefore produce a healthier fish feed.  

Results: 

Novel strains of bacteria have been isolated from Icelandic hot springs, capable of growing and fermenting soyabeans at higher temperatures. Together with additional bacterial strains from various other sources, more than 40 strains of bacteria are tested to find the best one's capable of fermenting soyabeans and reducing ANFs. Fermentation of soyabeans, using the best bacteria strains, will be optimized and upscaled for the production of protein to be included into an aquaculture fish feed formula. Fish feeding trials will be performed to observe the effect of the fermented soybean replacement on the fish performance, health and gut microbiome and compare it to a traditional feed formula. 

Practical implications/recommendations: 

The novel fish feed formula based on fermented soyabeans will offer the aquaculture industry a sustainable alternative to fishmeal-based feeds with tested health and performance benefits.

Objective: European soyabean farmers face challenges with crop performance due to soil health, climate conditions, and high chemical costs. This project aims to boost soyabean yields using natural soil microbes that improve plant health and resilience.

Expected results:

• We will identify beneficial soil microbes from 100 European soyabean fields, which potentially help soyabean plants absorb nutrients, grow stronger, and resist diseases.
• We will develop AI-based models to match the right consortia of microbes with specific field conditions, ensuring effective use.
• We will test these beneficial microbes in both lab and field conditions, to identify consortia of microbes that can provide significant improvements in soyabean growth and resilience.

Practical implications:

• Yield improvement: Farmers can achieve better harvests using recommended beneficial microbes, while reducing input of agrochemicals.
• Healthier crops: With the help of the helper microbes, soybeans may become more resilient to environmental stresses with less use of agrochemicals.
• Reduced costs: Less need for chemical inputs means lower expenses.
• Easy adoption: Farmers will receive guides and online resources for learning more about how beneficial microbes can help in their crop system.

Main  benefits:

• Healthier crops and reduced chemical use lead to better profits and more sustainable farming.

This project is a collaboration between European universities, research institutes, and agricultural companies to help farmers grow better soyabeans using nature’s own solutions.

Objective: A switch from consuming animal protein to plant protein instead offers considerable benefits for sustainability, and potentially also for consumer health. Excessive animal protein consumption in red meat affects the host directly, but there also indirect effects mediated by the gut microbiome. Here we first confirm the safety of microbiome-improved soil while meanwhile we test the effect on the gut microbiome of replacing red meat with tofu instead, using DNA sequencing technologies to investigate microbiome function.

Expected results:

• We will confirm the absence of toxins in soy beans grown and harvested using natural soil microbes that improve plant health and resilience.
• We will determine the effect of replacing animal protein in a typical Western diet with plant-derived protein delivered in a (soya-based) tofu, by measuring the composition, function and transcription of the microbiome. These cutting-edge omics methods will provide detailed insight into the microbiome.
• We will determine the effect of the meat-tofu swap on chemicals in human blood produced by gut microbes, and the human body response, by measuring the metabolome in serum

Practical Implications:

• Evidence basis for dietary protein replacement recommendations with special reference to long-term effects wrought by the activity of the gut microbiome
• Data on how the composition of the microbiome changes when the protein source changes can inform consumer choices
• Progress in distinguishing direct and indirect microbiome-host interaction

Main benefits:

• Direct high-quality evidence from human studies, as distinct from laboratory in vitro trials, on diet-microbiome interaction

Agricultural management affects plant performance, yield and also soil and plant-associated microbial communities, also termed microbiota or microbiomes. Plants host very specific microbiota, which are important for plant growth and health as they contribute to nutrient provision and plant stress resilience. It can be expected that agricultural management and plant-associated microbiota also influence plant quality traits such as agronomic seed quality or the nutritional content of plants or seeds specifically. 

In MICROBIOMES4SOY we assess if and how agricultural management including the application of newly developed microbial inoculants affect plant performance and seed quality. Greenhouse, lysimeter and field experiments are performed to provide information on:
-    which agronomic practises favour soya bean yields and influence agronomic quality and nutritional content of soya bean seeds
-    whether microbial inoculation practises, either by applying individual microbial strains or a combination of selected strains, can improve stress (e.g., drought) resilience of soya bean plants
-    whether microbial inoculation practises, either by applying individual microbial strains or a combination of selected strains, can improve seed quality aiming to achieve “microbiome-improved seeds”. Apart from agronomic traits, we will specifically address nutritional quality of seeds targeting e.g., protein content or contents of antinutritional factors.