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New microbial map uncovers hidden concern for dwindling network

Scientists are learning more about the role microbes play in global food systems, advocating for their protection to preserve and enhance the world's food supply.

In a July 2025 study, researchers from various European universities and institutes are exploring how the globe can harness agri-food system microbiomes for sustainability and human health.

“The presence of diverse and balanced microbial communities is a strong indicator of a healthy food system,” first author Dr Paula Fernández-Gómez from Teagasc Food Research Centre and APC Microbiome Ireland, told Ingredients Network. Beneficial microorganisms play a crucial role in nutrient cycling, enhancing disease resistance, supporting environmental resilience, and promoting both human and ecosystem health.

“However, when this balance is disrupted, harmful microorganisms can proliferate, contributing to the spread of disease and antimicrobial resistance throughout the food system,” she added.

Microbial networks are on the decline

Various factors are driving the deterioration of these microbial networks across the food system, namely, agricultural methods and environmental pressures. Intensive agricultural practices, particularly the overuse of antibiotics and fertilisers, can damage soil and aquatic microbiomes, accelerating the spread of antimicrobial resistance.

The climate crisis adds further pressure. Increasing weather extremes introduce a wide range of challenges, such as prolonged droughts, extreme flooding, and biodiversity loss. These areas disrupt food system microbiomes and weaken microbial networks’ ability to self-regenerate.

An increasing body of research explores the progress of soil, plant, animal, and marine microbiome research in agriculture and aquaculture practices, including practical management strategies along with sustainable and resilient food system-related interventions.

However, the study’s researchers said that this understanding is only one element of supporting and promoting microbiome health and diversity. Developing microbiome knowledge, particularly that which expands beyond predicting microbiome functionality, along with using new technologies, has identified numerous challenges within global microbiome networks.

Uncovering hidden microbes

In the study, published in Frontiers in Science, researchers have documented numerous microbial networks together into a single map and identified where they are disintegrating. By discovering where microbes are breaking down, scientists can see where targeted interventions like probiotics, microbial consortia, or biofertilisers can have the most significant effect.

By mapping the microbiome network, the study’s researchers found that microbiome solutions can help the food production system. Microbes can be helpful to crops to protect them against salt, drought, and pathogens. Planting clover can also lock nitrogen into the soil for plants to use. Bacteria can produce higher-quality animal feed, probiotics can enhance animal diets to improve health, and cultures can reduce food waste and prolong shelf life.

Collaboration is at the centre of fostering a global food system that can readdress the microbial balance. From the research study, it becomes evident how each of the players within the environment can progress the protection and preservation of microbes.

Consumers play their part by choosing fresh, minimally processed and locally produced food, and by supporting microbe-friendly policies. The food sector can scale microbe-based developments in farming, food processing, and aquaculture. The wider landscape sees regulators produce evidence-based frameworks for the safe and effective use of microbiome-based interventions. Educators and communicators can build awareness and trust in the science around microbiomes, while scientists can broaden knowledge on microbiome functions through investigations that utilise experimental and omics-based approaches.

Using technology to use beneficial microorganisms

To bolster the planet’s food systems, action needs to focus on reducing microbial network loss. Researchers have suggested that applying advanced technologies to further investigate biological systems and the components that make them up is crucial to reverse dwindling microbial communities.

“Reducing the loss of vital microbial networks starts with a deeper understanding of agri-food system microbiomes, supported by advances in omics technologies,” Fernández-Gómez said. The omics suite of techniques is used to analyse large-scale biological molecules to examine and gain a comprehensive understanding of organisms’ structure, formation and movement.

Some promising strategies include the use of beneficial microorganisms to improve crop resilience, enhance livestock productivity and health, and extend food shelf life to lower waste.

“Successfully implementing these solutions will require coordinated efforts from scientists, farmers and policymakers,” Fernández-Gómez added. While progress and change do require cross-sector collaboration, the researchers conclude that the translation of microbiome research into innovation in food systems has the potential to improve human and planetary health.