The soil-plant-human gut microbiome axis into perspective

Haikun Ma; Deborah Cornadó; Jos M. Raaijmakers

doi:10.1038/s41467-025-62989-z

The soil-plant-human gut microbiome axis into perspective

Haikun Ma^* (Corresponding author)
, Deborah Cornadó
, Jos M. Raaijmakers^* (Corresponding author)

^*Corresponding author for this work

NIOO - Microbial Ecology (ME)

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

15 Citations (Scopus)

Abstract

Microbiomes of soil, plants, and the animal gut are pivotal for key life processes such as nutrient cycling, stress resilience, and immunity. While studies have hinted at a shared microbial reservoir connecting these environments, compelling evidence of a soil-plant-gut microbiome axis is scarce. This perspective explores the potential continuum and diversification of microbes along this axis, highlighting specific microorganisms capable of moving from soil to plants to the human gut. A conceptual framework is proposed to better understand the mechanisms driving interactions among these microbiomes. We also examine how soil, plant, and gut microbiomes may co-evolve and influence one another through reciprocal effects. We consider external environmental factors that could strengthen their interconnections, potentially creating beneficial feedback loops that impact ecosystem and human health.

Original language	English
Article number	7748
Journal	Nature Communications
Volume	16
Issue number	1
Early online date	20 Aug 2025
DOIs	https://doi.org/10.1038/s41467-025-62989-z
Publication status	Published - Dec 2025

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AB - Microbiomes of soil, plants, and the animal gut are pivotal for key life processes such as nutrient cycling, stress resilience, and immunity. While studies have hinted at a shared microbial reservoir connecting these environments, compelling evidence of a soil-plant-gut microbiome axis is scarce. This perspective explores the potential continuum and diversification of microbes along this axis, highlighting specific microorganisms capable of moving from soil to plants to the human gut. A conceptual framework is proposed to better understand the mechanisms driving interactions among these microbiomes. We also examine how soil, plant, and gut microbiomes may co-evolve and influence one another through reciprocal effects. We consider external environmental factors that could strengthen their interconnections, potentially creating beneficial feedback loops that impact ecosystem and human health.

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The soil-plant-human gut microbiome axis into perspective

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