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While the term microbiome is most often used in reference to the microorganisms living on our skin or within our gut, microbiomes can also be found in nature, including in soils, plants and our oceans. These tiny communities have a huge impact on people and the planet, and could play an important role in delivering Europe’s strategy for a resilient food system that is fit for the future.
“Microbiomes are very important and have a huge innovation potential that could benefit the global food system,” explains MicrobiomeSupport project coordinator, Angela Sessitsch. “But leveraging this potential requires coordinated research, which traditionally hasn’t been the case.”
According to Sessitsch, although microbiome research is popular and happens around the world, it remains highly fragmented. “Most research is very siloed, with very little cooperation between researchers,” she adds. “The result is that often researchers are reinventing the wheel, having to develop their own tools and methods which may already exist.”
This fragmented, insular approach is a barrier to effective, groundbreaking research, which is why the MicrobiomeSupport Coordination Support Action set out to shatter these research silos.
A map towards coordinated research
Bringing together scientists from different disciplines, industrial stakeholders and policymakers, the project started by looking at the existing landscape. “Our goal was to catalogue all the programmes, activities, facilities, methods, tools and work that was currently happening within the microbiome field,” explains Sessitsch.
With this database in hand, the project team mapped out where they thought research should be by 2030. This allowed MicrobiomeSupport to identify the gaps and define the strategic research and innovation agendas needed to bridge these gaps to benefit our health, climate, environment and communities.
For a complete understanding of these systems, it’s necessary to look at the host and all of its symbiotic microorganisms as a whole, something that is known as a holobiont. Yet the mapping confirmed that while microbiome research is being performed in many ecosystems, it remains fragmented, with few connections between disciplines. The work highlighted how this landscape is evolving, albeit slowly, as more and more research and innovation strategies focus their attention on microbiomes.
“This evolution needs to be quickly translated into multidisciplinary research activities in food systems, connecting different areas of microbiome research with other disciplines,” says Sessitsch. “Such research is particularly urgent as a means of securing sustainable food systems.”
Turning data into results
The project also provided support to the technical side of coordinated research, with a particular focus on data.
“With the increased attention to microbiome research in the last decade, we are seeing an explosion in the availability of microbiome data – with thousands of relevant data sets stored in public and private repositories,” notes Sessitsch.
However, this huge library of microbial knowledge has generated little benefit. The reason: inconsistent recording that makes it difficult to use data across research projects. “Scientists are not speaking the same language, which complicates collaboration across research teams and disciplines,” adds Sessitsch.
To help overcome this obstacle, the MicrobiomeSupport project drafted a paper calling attention to the pressing need to harmonise metadata standards. Based on conversations between over 70 researchers and industry partners, the paper recommends an easy-to-use, well-structured, flexible and compatible system that would standardise how data is stored and accessed, thus vastly improving the ability to retrieve and reuse it to advance microbiome analysis.
From soil to gut
According to Sessitsch, safe, healthy and sustainable food starts with the soil or water and ends in the human gut – all of which involve microbiomes. “Food system microbiomes are highly connected in different environments and represent key players for planetary and human health,” she says.
The project’s work to streamline microbiome research and data will help facilitate the microbiome analysis needed to make food systems more sustainable and to deliver food that is safe and healthy and, ultimately, improves gut health.
“By raising awareness about the role of food system microbiomes, emphasising the need for coordinated research, and highlighting the importance of suitable education and training, our work contributes to achieving a sustainable global food system and thus helps ensure healthy and safe food for future generations,” concludes Sessitsch.