“Microbiomes play a decisive role in the transition to sustainable and circular food systems. With innovative applications of microbiomes, we can create sustainable and high-quality alternatives to conventional approaches to health and food management. At the same time, we can reduce soil and water pollution and reduce greenhouse gas emissions,” says Angela Sessitsch, head of the Bioresources Competency Unit in the Center for Health & Bioresources at the Austrian Institute of Technology AIT.
And there is more. Increased use of microbiomes can support the development of a mature bioeconomy – and move closer to climate protection goals.
Sustainable value chain
Sessitsch coordinates the consortium of the EU-funded research project MicrobiomeSupport, which runs until October. The goal is to ensure a sustainable food and feed value chain in the long term. The researchers identified and explored the major barriers to research and commercialization of microbiome applications. Themes that emerged were insufficient funding for microbiome research, lack of adaptation of research methods and regulatory barriers.
Last but not least, consumers’ knowledge of the microbiome must be increased. Only when they understand the benefits these products can provide will they be willing to use them.
Potential of microbiomes
As part of the project, Sessitsch, together with Tanja Kostic, also from the Competence Unit Bioresources and eight international research partners, published a recommendation in Nature Microbiology entitled “Microbiome innovations for a sustainable future”. In it, the researchers explain how the potential of microbiomes can be used for a sustainable future.
Microbiomes have not yet been adequately explored. Nevertheless, complex interactions and chains of effects can be hypothesized. The researchers cite the dairy industry as an example. Feed and animal genetics affect the animals’ microbiome. Therefore also on the quality of raw milk, the milk products and the climate.
For dairy products, production waste, such as whey from cheese making, can be used for the production of biofuels and in animal feed. This promotes a sustainable bioeconomy.
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Plant protection products and fertilizers
To ensure a sustainable food and feed value chain, plant protection products and fertilizers should form the basis. Microorganisms interact with plants and soil in complex ways and can make important contributions to plant health. Nitrogen-fixing microbes – Bradyrhizobium and Azospirillum – can replace artificial fertilizers. In Brazil, they are already increasingly being used on soy plantations. This has led to a significant reduction in greenhouse gas emissions. In addition, there was a positive side effect. Production costs also fell.
In recent years, knowledge of and interest in microbiomes has increased rapidly. But they are hardly used in everyday life, says Kostic. This is primarily due to a lack of coordination of research methods. The reason for this is that research methods have recently undergone rapid development. So there are no standards.
Microbiome research mainly uses sequencing methods (genomics), but also other -omics technologies, such as proteomics or metabolomics. A common feature is experimental approaches where large amounts of data are generated.
Furthermore, no agreement has ever been reached on which accompanying data (the so-called metadata) must be collected and stored. This made it extremely difficult and in some cases impossible to compare different data sets and the reusability of older data sets. Together with external experts, the MicrobiomeSupport consortium has developed recommendations to prevent this type of problem in the future.
Sessitsch emphasizes the importance of taking into account the functions of the microbiome in policy decision-making. If microbiomes are really going to make a significant contribution to achieving various goals, the prerequisites must also be right. To this end, it is important that policy makers understand the potential of microbiome research as well as the gaps and needs.
“As the dairy farm example shows, research projects require a holistic systems approach,” adds Kostic. “In order to advance microbiome research, it is necessary to investigate interactions and interconnections between different systems. Systems such as soil – plants – animals – food – humans. Ideally, experts from different research disciplines should work together and industrial partners should also be involved. Such projects already exist, but unfortunately they are still in the minority,” says Kostic. On the other hand, the majority of research projects have to make do with a budget of less than 250,000 euros. This hardly gives the opportunity to employ a PhD student.
As the dairy farm example shows, research projects require a holistic systems approach. To advance microbiome research, it is necessary to investigate interactions and interconnections between different systems. Systems such as soil – plants – animals – food – people.
Ideally, experts from different research disciplines should work together and industrial partners should also be involved. Such projects already exist, but unfortunately they are still in the minority,” says Kostic. On the other hand, the majority of the research projects have to make do with a budget of less than 250,000 euros. It hardly gives the opportunity to employ a PhD student.
Currently, it can take up to ten years before a new biological control agent comes to market. The reason lies in legal obstacles. Manufacturers of biological pesticides currently have to go through the same regulatory process as manufacturers of chemical protection products.
“This process is already very complex for products that only contain one microorganism. But it is even more complicated for products that contain more microorganisms,” explains Kostic. Furthermore, these regulatory hurdles require significant time and financial resources that smaller companies can hardly afford. The lack of specific regulation prevents the full potential of biological control from being realized, the researchers said.
Another aspect of the regulatory hurdles is the different rules in each country.
Speed up the approval process
The problem has already been recognized at EU level. Now a new version of the existing rules should speed up the approval procedure. The new rules are based on current scientific developments and the specific properties of the individual microorganisms. If the European Parliament and the EU Council do not object, the legislative acts will enter into force in November 2022.
Jennifer Lewis, CEO of the International Biocontrol Manufacturers Association (IBMA), welcomed the change in regulation to Euraktiv. She also pointed out that it would change “a little material” on the existing requirements for microbial data. Therefore, this is “a disappointment and a missed opportunity” to align EU Commission policies with the goals of “Farm to Fork”.
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