Understanding microbial communities can restore sustainable and healthy food systems

Over the last few decades, we’ve become increasingly aware of the importance of health-promoting bacteria and other microorganisms. This has prompted wider availability and consumption of probiotics and fermented foods in the hope of health benefits.

However, we rarely consider the wider web of interconnected microbes—trillions of bacteria, fungi and viruses—that work together to fuel the entire food production system, our bodies, and the planet.

In their Frontiers in Science lead article, Fernández-Gómez et al. map our current understanding of the microbes in food systems, known as agri-food system microbiomes, based on biochemistry techniques called omics. They produce a comprehensive snapshot of the whole system, and call on scientists, food producers, educators, regulators, and consumers to protect our microbial connections.

This explainer summarizes the article’s main points.

What is an agri-food system microbiome?

A microbiome is a community of bacteria, viruses, fungi, and other microbes in a specific habitat that live in connected environments and influence one another. Interactions between microbiomes form an ever-changing yet delicately balanced ecosystem.

Each step in the food system, from growth and production to preparation and consumption, features a distinct microbiome. This includes soil where crops are grown, water and farms where fish and animals are raised, factories where food is processed, transport networks where food is distributed, and the human gut where food is digested.

Healthy microbial networks drive nutrient cycling, disease resistance, environmental resilience, and human and environmental health. Yet if the balance is disrupted, it can allow harmful microbes—called pathogens—to gain a foothold in the microbiome, alter the environment, and thrive. This can lead to disease and even to the spread of antimicrobial resistance (AMR) across food systems.

How do microbes affect the food system?

Microbes influence, and are influenced by, the food system in various ways. Agri-food system microbiomes form an interconnected network that can be traced across soil and marine environments to primary agriculture, farming, and food processing.

Bacteria, for example, play a vital role in making nutrients like nitrogen, phosphorus, and minerals available in the soil for plants to use for growth. They can also help plants adapt to harsh environments, such as soil with high salt levels or low moisture.

Heavy fertilizer use can alter nutrient levels in rivers and lakes, which severely disrupt aquatic microbes. Altering microbial levels in aquatic environments can tip the balance and lead to algal blooms that deplete oxygen in the water and kill fish.

Certain microbes are essential for some processes while devastating in others. Viruses called bacteriophages can help reduce the risk of food spoilage and infections in humans or animals by killing pathogenic bacteria. On the other hand, bacteriophages can ruin fermentation processes by infecting the ‘good’ microbes in bacterial culture.

The complexity of studying the true impact of different microbes across the food system has limited our understanding of their overall influence. However, new technologies are providing much more insight.

How are new technologies helping us understand these microbiomes?

Advances in genetic sequencing have allowed scientists to capture the total genetic makeup of a wide range of organisms—including microbes. Known as genomics and transcriptomics, these approaches can reveal the activity of cells and how they change over time and in different environments. Other techniques, known as proteomics and metabolomics, let us know which proteins are produced and how nutrients are metabolized within specific systems.

These omics technologies are now so sensitive that scientists can move beyond studying one type of microbe to analyzing an entire microbiome instead. This is known as meta-omics, and it helps us understand how these microbial communities interact with each other and their environment. This zoomed-out approach has already discovered a much greater diversity of microbes in the food system than previously thought—particularly for viruses.

What has meta-omics revealed about the impact of changing agri-food system microbiomes?

Meta-omics studies have shown that microbiomes across food systems are strongly interconnected. For example, microbes from soil or silt move up the food chain to grass or water, then to cows or fish. Similarly, microbes on crops are transported to processing plants and can eventually reach the human gut.

This is particularly relevant to concerns about the spread of AMR. Research has shown that AMR genes can pass from livestock manure into the soil microbiome and then again into other grazing animals. 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 also contribute to the spread of AMR genes.

Studies have also revealed a loss of diversity in the human gut microbiome, which may contribute to health problems. Ultra-processed foods, which are stripped of most naturally occurring microbes and often lack the complex nutrients, prebiotics, and fiber that promote microbial diversity, are increasingly common in Western diets. Similarly, more and more food is produced far from the consumer, causing distributors to reduce microbes for extended shelf life. This marks a change from historic diets of fresh, locally produced, unprocessed food, which introduce natural microbes to the gut.

How can we alter agri-food system microbiomes to improve global animal, human and environmental health?

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 resistance.

Using omics to better understand agri-food system microbiomes can help everyone involved in food systems to strengthen and restore them. However, implementing these practices will require:

• food producers and distributors to implement microbiome-friendly solutions for farming, fishing, and food production and distribution

• consumers to make healthy, minimally processed food choices

• scientists to continue advancing microbiome research

• educators and communicators to build awareness and trust

• regulators to build frameworks for safe use.