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Sustainable innovation of microbiome applications in food system

Periodic Reporting for period 3 - SIMBA (Sustainable innovation of microbiome applications in food system)

Reporting period: 2021-11-01 to 2022-10-31

The threat of food insecurity is a critical global challenge, compounded by climate change, biodiversity loss and population growth. Currently the food system are challenges new threats, such as COVID-19 pandemic and the Ukraine war. Therefore, solutions are needed to meet this challenge and one potential area for exploration is microbiomes, which are communities of microbes (bacteria, viruses, fungi, etc.) in a certain environment. Microbiomes are known to regulate the productivity and health of major food sources across land and sea. Therefore, they can positively impact food production, food and nutrition security and ultimately influence human health. However, we lack a deep understanding of the microbiomes associated with our food systems.

The main aim of SIMBA is to tackle the growing challenge of supplying food to meet the global population demands within a changing climate, through innovative solutions utilising microorganisms in our food system. Now more than ever, amidst the global uncertainty of the COVID-19 pandemic, we need to utilise innovative ideas to promote sustainable food production, and the microbiome can offer a possible alternative to intensive and unsustainable agriculture practices.
The SIMBA project brings together 21 partners from across the European continent. SIMBA is comprised of leading research groups from the terrestrial, marine, food and human gut microbiomes fields. The consortium forms a well-balanced mix between fundamental scientists with expertise in ecology and microbiome evolution, and applied scientists who bridge fundamental science to applications in the food industry. A number of small to medium enterprises (SME) within the consortium are key to testing novel techniques and provide “near to market” solutions for field testing and economical evaluation. This cross-sectoral collaboration ensures that the results of fundamental research will be exploited by the consortium and transferred to the market.
In the third reporting, there has been a lot of progress made in the project. Microbiome data analysis has been made available to the European research community by hosting a user friendly and easily accessible annotated user database. In this phase of the project the database was tested on microbiome data provided from within the consortium and field tested with partners. We haveexplered the full potential of Plant Growth Promoting Microorganisms (PGPMs) by optimising the efficacy and reproducibility of field applications. This involved identifying and selecting the most promising PGPMs for the target crops (wheat, maize, potatoes and tomatoes), and carrying out field trials with the chosen consortia on the four target crops in Italy and Germany to monitor and improve performance and resilience.
Marine macro-and microalgae were extensively studied with respect to the natural associated microbiomes and several potential modulating bacterial strains were isolates and are being tested to serve as growth promoting microbiomes. Microalgae were selected and tested for their nutritional value and use in fish feed. Saline agriculture of potatoes was performed inhouse and amendments with bacterial isolates and whole microbiome transplants were performed. Increased potato yield was observed for some microbiomes, that are now subject to molecular analysis to identify plant growth promoting genes and gene products.
Studies on side streams in circular economy has focused on tomato, potato and maize. Selected pulses, soy and rapeseed meal were fermented to develop new products and ingredients. In pulse-based raw-materials, fermentations of pea were continued in a bioreactor. A set of analyses, including oligosaccharides, protein degradation, peptides, vitamin B12 and K, were performed. For studying gastrointestinal digestion of fermented foods, static in vitro simulation was used for fermented pulses and samples were collected for analyses. During the current reporting period the work on human health consisted: i) The trial studying the effects of a fermented canola-seaweed product in human subjects suffering from metabolic syndrome has been completed ii) Cell culture studies testing the major polyphenol and bile acid metabolites on immune cell differentiation and gut epithelial barrier function were carried out to obtain insights into the mechanisms whereby diet-derived and microbiota-modified compounds affect metabolic health. To address the readiness to produce of selected micro-organisms in a bioreactor was established and technical procedure for pilot scale starter production and pea fermentation was drafted. Of the soil microbes, complex PGPM were designed and a pilot-scale fermentations was carried out to test various cultivation conditions. For typing of relevant micro-organisms to be used in specific applications, collection of protocols to be used for rapid identification of microbes was carried out. The environmental and social evaluation of sustainability focused on using microbial application during fish production; the economic evaluation focus on using these innovations during potato (starch and seed) and wheat production. The overall sustainability evaluation used a quantitative assessment for potato production and a qualitative evaluation for tomato production.
• Open access central database containing microbiome data that facilitate the identification of potentially useful microbes or groups of interacting microbes that have useful function in the food production process.
• Enhanced consistency of microbiomes in field applications through the identification of best mixtures of plant growth-promoting microorganisms and bio-active compounds.
• Improved understanding of the role of salt-tolerant microbiomes and their role in the cultivation of salt resistant crops, contributing to the reclaiming of land lost to desertification and increasing arable land.
• Starter cultures to be applied in food products with beneficial compounds, contributing to health human benefits.
• Improved understanding of the functions of individual and sustainable diet-induced variations in gut microbiota, and their interaction with diet and foods, which is expected to contribute to the prevention of certain chronic diseases, such as Type 2 diabetes.
• Near to market ready development of new and cost-effective applications, products and services of new microbes, food, crop and algae products through upscaling from laboratory to pilot scale processes.
• Proven increase in sustainability of European food systems by implementing the microbial interventions.
Potential impacts
• Knowledge and applications of terrestrial, marine, and food driven microbiomes to increase productivity, quality, safety, sustainability and nutrition security in the food chain
• Nutrition security can be better ensured adopting a food system approach based on sustainability, linking land and sea and encompassing the entire food value chain
• Public and private food system stakeholders can increase their innovation capacities and facilitate their access to contemporary scientific knowledge