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Microbial map reveals countless hidden connections between our food, health, and planet

31 Jul 2025

Researchers have mapped how microbes underpin healthy food systems - and how we can stop their decline.

Published in , the map of ‘agri-food system microbiomes’ reveals how players at every stage of the food system can restore and protect dwindling microbiomes to help boost human and planetary health.

When microbiomes are diverse and balanced, they keep our food safe, nutritious, and sustainable, and our planet healthy—but the quality of these networks is declining across the whole system. This can be seen in the uptick of antimicrobial resistance (AMR), crop failures, loss of microbial diversity in soil, water, and the human gut, and increased food spoilage.    

The authors say this is due in part to a combination of highly processed diets that disrupt natural microbiomes, the climate crisis, intensive farming, antibiotic and fertilizer overuse, and pollution.

“Microbes explain everything from why strawberries rot and how farmed salmon get sick, to why locally produced, minimally processed and probiotic-rich foods are good for our health,” says first author Dr Paula Fernández-Gómez from Teagasc Food Research Centre and APC Microbiome Ireland, a world-leading Research Ireland centre based at ��ҹ���޸����þ� College Cork. “Declining microbial health is mirrored in the health of people and planet—showing up in dwindling food quality and availability, and in rising chronic disease for animals and plants.”

To tackle this, researchers are increasingly looking to the hidden communities of microbes that underpin these systems, such as those found in plants, animals, soil, agriculture, aquaculture, and food processing. This review draws them together into a single map and identifies where microbial networks are breaking down. This has illuminated where targeted interventions such as probiotics, microbial consortia, or biofertilizers may have the biggest impact.

“Just as microbes work together, so must we—at every point in the food system—to make microbe-friendly choices, from grower to consumer,” says senior author Prof Paul Cotter, also from Teagasc Food Research Centre and APC Microbiome Ireland.

Redressing the balance

The map demonstrates how a joined-up approach from consumers, agricultural innovators, regulators, educators, and scientists, can help to protect and restore these hidden networks. The authors say this will help to boost the sustainability and resilience of global food systems, as well as restoring the health of food sources and therefore of animals, people, and the planet.

It reveals how each player in the food system can help to redress the balance:

• everyday consumers: choose fresh, minimally processed, and locally produced food, and support microbe-friendly policies
• industry: scale up microbe-based innovations in farming, food processing, and aquaculture
• regulators: build evidence-based frameworks for safe, effective use of microbiome-based interventions
• educators and communicators: raise awareness and build trust in microbiome science
• scientists: deepen understanding of microbiome functions through experimental and omics-based approaches.

“Our paper details how microbial communities are interconnected along the food chain—revealed with the help of advanced omics that have deepened our understanding of microbiome dynamics and interactions like never before,” says Prof Cotter.

Mapping the system

The map of microbiomes—webs of trillions of bacteria, fungi, viruses, and the connections between them—captures the hidden links between food, our bodies, and the planet.

To capture the whole system, the authors combined findings from more than 250 omics studies on microbial interactions in horticulture, silviculture, livestock farming, and aquatic environments. They also looked at the microbes found spanning food processing, food distribution and transport, storage, markets and shops, to consumers and their interactions with the human body.

The authors identify several areas where microbiome-based solutions can help improve components of the food production system, including:

• applying microbes to crops to protect against salt, drought, and pathogens
• planting clover to lock nitrogen into the soil for plants to use
• using bacteria to produce higher quality animal feed
• supplementing animal diets with probiotics to improve health
• reducing food waste by applying cultures that prolong shelf life.

Some of these approaches are already in use. For example, yeast can reduce post-harvest decay in strawberries. Similarly, bacteria can help desert crops become more resilient to environmental stress. Strengthening microbiomes may also help to reduce antibiotic use in livestock, limiting the spread of AMR.

“Healthy microbial networks underpin our existence,” says co-author Dr Tanja Kostic from AIT Austrian Institute of Technology and MicrobiomeSupport Association. “They drive nutrient cycling, food production, disease resistance, environmental resilience, as well as human and environmental health.”

Human impact

Climate breakdown, as well as human activity such as antibiotic and pesticide overuse, can disrupt microbiome dynamics and interactions. This contributes to crop failure, food spoilage, spread of AMR, and chronic disease in humans, animals, and plants.

For example, heavy fertilizer use can alter nutrient levels in rivers and lakes, which severely disrupt aquatic microbiomes. This alteration of microbial levels in aquatic environments can lead to algal blooms that deplete oxygen in the water and kill fish.

Similarly, antibiotic use in fish farms to prevent infections can increase AMR in the environment. Other pollutants, too, such as medicines, pesticides, and fertilizers can increase AMR genes.

Specifically deciphering the functional roles of microbiome constituents also remains a challenge. Culture-based approaches are crucial for translating this research into innovations and for understanding the causal links within the system. Similarly, the authors say that omics data should be combined with synthetic biology, high-throughput screening, and targeted experimental approaches to validate the functions of these microbiomes.