The biodiversity we eat

The biodiversity we eat: a bridge between soil, plants, and gut health

When we think about human health, we rarely consider how we nourish ourselves and, even less, the origin of the food we purchase.
Moreover, we almost never consider agricultural soil as the primary actor in the human food and health system.
And yet, what we call well-being might actually begin in the ground, beneath our feet.
In the past year, a scientific perspective published in Nature Communications has begun to take shape, inviting us to look more closely at the relationship between soil, plants, and the human gut microbiome, hypothesizing a possible biological continuity among these three compartments: a hypothesis that deserves great attention (Ma et al., 2025).

Soil is not just a physical substrate
Agricultural soil is a fully living system, extremely dense with biophysical relationships and populated by immense microbial diversity.
In fact, we can consider it a sort of “microbial seed bank,” a biological reservoir from which plants recruit part of their microbiome, both at the level of the rhizosphere and the endosphere, phyllosphere, and carposphere (Ma et al., 2025).
Moreover, previous scientific studies had already considered soil as a possible contributor, at least in part, to the composition of the human gut microbiome (Blum et al., 2019).
The idea of a possible—and indeed probable—biological continuity between soil, plant, and human gut microbiome allows us to change the way we look at food, especially plant-based foods.
A fruit, a leaf, or a root is not just a source of sugars, fibers, vitamins, or secondary metabolites such as polyphenols, flavonoids, and coumarins.
The plants we consume as food carry with them the agroecological history of the territory in which they were produced.
They transport into our bodies the agroecological “signature” of the soil in which they grew.
They contain the imprint of the interactions between plant, soil, and microorganisms.
From this perspective, food is not just nutrition: it is biological history, environmental conditions, and agroecological practices.
And this is precisely where the human microbiome comes into play, because its composition is strongly influenced by diet, lifestyle, and environmental exposure; recent literature suggests that these factors can have a profound impact and, in some cases, may be more determinant than specific host traits themselves (Parizadeh & Arrieta, 2023; Ma et al., 2025).

A possible biological continuum
The concrete possibility of this biological continuity is based on the existence of specialist microorganisms, generalists, and cross-kingdom organisms.
The first are strongly tied to a single habitat.
The second show greater ecological flexibility.
The third are the most fascinating, as they appear across the entire soil–plant–gut continuum, maintaining their presence in different environments (Ma et al., 2025).
Among the most interesting groups are Bacillus subtilis, Lactobacillus, Lactococcus, and Streptomyces, described as potentially beneficial microbes at multiple levels of the system.
We do not yet have definitive proof of the soil–plant–gut continuum, but we do have solid clues, plausible connections, and an extremely robust theoretical foundation (Ma et al., 2025).
It is enough to recall mechanisms such as horizontal gene transfer, molecular mimicry, cross-feeding, colonization resistance, and host selection as processes potentially capable of linking different microbiomes (Ma et al., 2025).
Put more simply: we are not just talking about microbes moving from one place to another.
We are dealing with real biological signals—genes, secondary metabolites, and even selective environmental pressures and agroecological relationships—that can traverse the entire system.
This perspective carries an extremely important and revolutionary implication.
If the soil is biologically rich, functionally active, and well managed, it can promote a plant with greater microbiological selection capacity and create potentially more favorable conditions for the gut microbiome.
Some studies show that, in a murine model, exposure to soil can be associated with changes in gut microbiota and signals compatible with improved immune tolerance (Ottman et al., 2019).
Additionally, other studies have shown that biodiversity interventions can affect immune regulation and health-associated microbes in children (Roslund et al., 2020).

The plant as a biological mediator
Within this system, the plant acts as an extraordinary biological mediator.
It filters.
It selects.
It translates.
It does not merely transfer microorganisms but determines metabolic effects.
At this point, it is reasonable to state that proper agroecological management of cropping systems can be reflected in the overall biological quality of food, gut biota, and therefore human health.
Indeed, foods rich in fiber and secondary metabolites can modulate the gut microbiota and support the functionality of the intestinal barrier (Wan et al., 2021).
From this perspective, the biodiversity we eat is not a suggestive metaphor, but a concrete hypothesis for rethinking agriculture, nutrition, and the gut–brain axis.

A new perspective on health
Human health does not begin in pharmacies or hospitals—it begins much earlier.
It begins in the living systems that connect soil to plants and plants to our gut, ultimately affecting the entire body.
Therefore, taking care of the soil does not simply mean improving its fertility or increasing productivity.
It also means working upstream, on the microbial biodiversity of our agricultural systems—a practice that influences the biological quality of the food we eat and the health of our gut, our “second brain.”
We must remember that the intestinal system determines both immune and mental health.
We are not separate from the earth that nourishes us.
We are its continuation.

Francesco Di Lorenzo
Agronomist

Essential bibliography –
Blum, W. E. H., Zechmeister-Boltenstern, S., & Keiblinger, K. M. (2019).
Does soil contribute to the human gut microbiome?
Microorganisms, 7(9), 287.
https://doi.org/10.3390/microorganisms7090287

Ma, H., Cornadó, D., & Raaijmakers, J. M. (2025).
The soil-plant-human gut microbiome axis into perspective.
Nature Communications, 16, 7748.
https://doi.org/10.1038/s41467-025-62989-z

Ottman, N., Ruokolainen, L., Suomalainen, A., Sinkko, H., Karisola, P., Lehtimäki, J., Lehto, M., Hanski, I., Alenius, H., & Fyhrquist, N. (2019).
Soil exposure modifies the gut microbiota and supports immune tolerance in a mouse model.
Journal of Allergy and Clinical Immunology, 143(3), 1198–1206.e12.
https://doi.org/10.1016/j.jaci.2018.06.024

Parizadeh, M., & Arrieta, M.-C. (2023).
The global human gut microbiome: genes, lifestyles, and diet.
Trends in Molecular Medicine, 29(10), 789–801.
https://doi.org/10.1016/j.molmed.2023.07.002

Roslund, M. I., Puhakka, R., Grönroos, M., Nurminen, N., Oikarinen, S., Gazali, A. M., Cinek, O., Kramná, L., Siter, N., Vari, H. K., Soininen, L., Parajuli, A., Rajaniemi, J., Kinnunen, T., Laitinen, O. H., Hyöty, H., Sinkkonen, A., & ADELE Research Group. (2020).
Biodiversity intervention enhances immune regulation and health-associated commensal microbiota among daycare children.
Science Advances, 6(42), eaba2578. https://doi.org/10.1126/sciadv.aba2578

Wan, M. L. Y., Co, V. A., & El-Nezami, H. (2021).
Dietary polyphenol impact on gut health and microbiota.
Critical Reviews in Food Science and Nutrition, 61(4), 690–711.
https://doi.org/10.1080/10408398.2020.1744512

Photo source:
Ma, H., Cornadó, D., & Raaijmakers, J. M. (2025).
The soil-plant-human gut microbiome axis into perspective.
Nature Communications, 16, 7748.