From the soil that grows our crops to the bacteria in our gut, microbes are the hidden engines of the food system. But those microbial networks are under threat and that could have far-reaching effects on our health and the planet.
A new review published in Frontiers in Science maps these “agri-food system microbiomes,” showing how microbes connect farming, food processing and human health. It also pinpoints where these networks are breaking down and offers strategies for restoring them.
“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,” said first author Dr. Paula Fernández-Gómez from Teagasc Food Research Centre and APC Microbiome Ireland.
The review draws on more than 250 studies to illustrate how microbial communities, which span soil, water, crops, livestock, aquaculture, food processing and the human gut, are being disrupted by intensive farming, heavy fertilizer and antibiotic use, climate change and highly processed diets. The authors warn these disruptions can lead to antimicrobial resistance, worsening food spoilage, crop failures and chronic disease in humans, animals, and plants.
But the review also highlights solutions. These include using biofertilizers and microbial “consortia” to support soil health, applying food cultures that extend shelf life and reduce waste, supplementing animal feed with probiotics and adopting microbe-friendly farming practices.
“Just as microbes work together, so must we — at every point in the food system — to make microbe-friendly choices, from grower to consumer,” said senior author Prof. Paul Cotter of Teagasc Food Research Centre.
The authors suggest steps for each stakeholder: consumers can choose fresh, minimally processed and locally produced foods; farmers and producers can scale up microbial innovations in agriculture and aquaculture; and regulators can create frameworks for safe, evidence-based microbiome interventions.
By strengthening these microbial networks, the researchers say we can build more sustainable, resilient food systems while protecting human, animal and planetary health.
This work was supported by Science Foundation Ireland (APC Microbiome Ireland and VistaMilk), the Irish Department of Agriculture, Food and the Marine, the European Union’s Horizon 2020 program, Friesland Campina, PrecisionBiotics Group, PepsiCo and Danone.