No organism on Earth is sterile. All living systems, from soil and plants to water and humans, are filled with bacteria, fungi, microalgae, and other microscopic life forms. Together, they form complex ecosystems called microbiomes.
Thanks to advances in DNA sequencing and computing, scientists have a growing catalogue of microbial species across these environments. Their importance to life is already evident. What is less understood is how they interact with one another and what occurs when the microbiome composition changes—such as when a species is removed or a new one is introduced.
This gap in knowledge matters because understanding and managing microbiomes could support more sustainable agriculture, healthier ecosystems, and improved human health.
For Dr. Tanja Kostic, a microbiologist at the AIT Austrian Institute of Technology, understanding these hidden communities is a frontier in biology.
“The microbiome provides essential functions in every ecosystem,” she said. “Most of the oxygen we breathe is produced by ocean microbiomes. Soil microbes help plants obtain nutrients. In our bodies, gut microbes produce vitamins we cannot make ourselves.”
Kostic is leading an EU-funded research effort called MICROBE, running from 2023 to 2027. Partners from Austria, France, Germany, and the UK are developing methods to preserve, compare, and study entire microbiomes.
Preserving living communities
Over the past decade, scientists have catalogued thousands of previously unknown microorganisms. But that is only part of the challenge.
DNA sequencing can reveal which organisms are present, but it cannot fully capture how they interact or how entire microbial communities function. To answer those questions, researchers need to preserve living microbiomes intact.
This is important because microbiomes are changing rapidly. Intensive farming, pollution, climate change, and changing diets can alter these delicate microbial ecosystems, potentially affecting everything from soil fertility to human health.
Preserving microbial diversity supports the EU Biodiversity Strategy for 2030, aiming to halt biodiversity loss and restore degraded ecosystems.
“If we can preserve these communities exactly as they exist in nature, we will be in a much stronger position to understand how they work and how we might use them responsibly,” said Kostic.
The researchers aim to preserve microbiomes, identify organisms responsible for key functions, and eventually recreate simplified microbial communities that maintain essential properties while being easier to study.
Beyond the single microbe
For decades, microbiologists mainly collected and stored individual microbial species.
Dr. Matthew Ryan, global lead for microbiology at CABI, a non-profit organisation specialising in agricultural and environmental research, believes that approach no longer reflects biological reality.
Microorganisms don’t live in isolation, he explained. They exist as complex communities whose members interact with one another.
“The idea is to move beyond the single organism model and develop methods to preserve entire microbial communities,” he said.
Preserving an entire soil microbiome, for example, could retain more biological potential than preserving isolated species. But these communities are harder to collect, store, and study.
To address this, researchers are standardising methods for collecting, preserving, and analysing microbiomes, alongside common approaches for sharing the data they generate. The aim is to ensure that microbiome samples collected in different laboratories or countries can be compared reliably.
Kostic and Ryan were involved in an earlier EU-funded research initiative (MicrobiomeSupport), which helped identify many scientific and regulatory challenges now being addressed.
“Our vision is to harmonise how microbiomes are collected and preserved so researchers everywhere are working with comparable samples,” Kostic said. “At the moment, samples are often stored under different conditions, which can change the microbial community over time and make results difficult to reproduce.”
Rather than creating a completely new network of microbiome banks, researchers are developing methods that existing European biobanks and culture collections can adopt, allowing microbiome collections to be part of Europe’s broader biological research infrastructure.
“We don’t want to establish a completely new biobank infrastructure. We want to establish new methods and technologies, and then tap into the existing infrastructure,” said Kostic.
Healthier soils, healthier people
The MICROBE research could also support wider European efforts to restore soil health under the EU Soil Strategy for 2030, which recognises healthy soils as essential for food security, biodiversity, and climate resilience.
Healthy soils contain remarkably rich microbiomes that influence crop growth, nutrient cycling, and resistance to pests and disease. Although microbial fertilisers and biopesticides already exist, their effectiveness often varies because every soil microbiome is different.
Instead of applying the same product everywhere, future farmers may be able to analyse the microbial community around a crop’s roots before receiving tailored recommendations for restoring soil health.
A similar shift is beginning in medicine.
Rather than one-size-fits-all treatments, researchers are exploring approaches targeted at groups of people with similar microbiome characteristics. It is hoped that a better understanding of how gut microbes influence nutrition, immunity, and disease will shape more personalised interventions, from diet to medication.
By preserving microbiomes consistently and linking them to
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