Impact of soil microbiodiversity on the development of wild mammal gut biota and immune function

Project Information

SOIL2GUT

Grant agreement ID: 101110279

DOI

10.3030/101110279

Project closed

EC signature date 14 July 2023

Start date 1 November 2023

End date 31 October 2025

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 172 750,08

Coordinated by

FONDAZIONE EDMUND MACH
Italy

Periodic Reporting for period 1 - SOIL2GUT (Impact of soil microbiodiversity on the development of wild mammal gut biota and immune function)

Reporting period: 2023-11-01 to 2025-10-31

Summary of the context and overall objectives of the project

Healthy gut microbiota is essential for immune balance and overall well-being. Yet, modern urban lifestyles often limit contact with natural biodiversity, which may contribute to rising rates of immune-related conditions such as allergies and inflammatory diseases. The SOIL2GUT project set out to explore whether exposure to soil microbial communities during early development can influence gut microbiota and immune function.

Our objectives were twofold:
1. Determine if soil microbes affect not only gut bacteria but also gut fungi (mycobiota).
2. Assess whether the origin of soil—urban versus natural—leads to distinct impacts on gut microbiota and immune responses.

By addressing these gaps, the project aimed to provide evidence for nature-based strategies that promote health and resilience. The findings have implications for public health, urban planning, and biodiversity conservation, supporting EU priorities on sustainability and well-being.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We conducted a controlled biodiversity intervention using a wild-derived rodent model (bank vole). Animals were exposed for 4–5 weeks post-weaning to either sterile bedding (Control), soil from national parks (Park), or soil from urban greenspaces (Urban). Gut microbiota was analyzed using high-throughput sequencing of bacterial and fungal markers, and host immune responses were assessed through RNA sequencing of colon tissue.

Key achievements include:
-Soil exposure significantly altered gut microbiota composition and organization.
-Gut fungi showed a stronger response than bacteria, with many species acquired directly from soil.
-Urban soil exposure increased the abundance of potentially pathogenic bacterial genera (Allobaculum, Brachybacterium).
-Host gene expression revealed activation of innate immunity in animals exposed to urban soil, marked by upregulation of epithelial defense genes.
-Natural forest soils promoted immune tolerance, while urban soils triggered stronger immune activation.

All scientific objectives were met. All data and workflows have been archived in open repositories (ENA and Zenodo) to ensure transparency and reproducibility.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The project provides the first experimental evidence that soil exposure affects gut fungi as well as bacteria, highlighting fungi as a key but often overlooked component of biodiversity interventions. It also demonstrates that soil origin influences immune responses, with urban soils eliciting stronger activation of defense pathways. These findings advance the Biodiversity Hypothesis by showing that environmental microbial diversity impacts gut microbiota networks and host health in complex ways. Potential impacts include:
-Informing urban greenspace design to maximize health benefits while minimizing risks from pathogenic microbes.
-Supporting nature-based solutions in public health strategies to combat immune-mediated diseases.
-Opening new research avenues on the role of soil fungi in gut health and disease prevention.

Further uptake will require interdisciplinary studies linking soil management, microbiome science, and health policy, as well as guidelines for safe biodiversity interventions in schools, parks, and urban planning.

Outdoor activities in natural environments support gut microbiota development and immune health.