Microbiomes are vital for the health of humans, animals, plants, and the planet, providing key metabolic and ecological functions, but. it’s not easy to decide how to preserve or care for them, who should be responsible, and how to know the strategy succeeded. Microbiome scientists have increasingly been demonstrating the importance of microbial ecologies for human and environmental health. In spite of this, no protections are in place on policy levels to ensure the health of microbiomes, which in turn are the foundation of larger ecosystems.  Microbiome stewardship (MiSt) is a strategic, evidence-based approach to maintaining microbial biodiversity and functions across habitats to support health and ecosystem stability.

This paper provides guidance on setting up partnerships, assessing microbial communities, outlying goals for stewardship strategies, and thinking about the long-term benefits of maintaining microbial communities for environmental and public health. Led by Kieran O’Doherty, who leads the Microbiome Stewardship research group, the paper features authors from that core group as well as other researchers who have joined the group, and in doing so, co-developed and helped us refine our ideas. We received from the Canadian Institutes for Health Research (CIHR) for a four-year project on how our collective microbiomes (the diverse microbes we share between humans and our environments) impact health to support this research. We hope this could serve as a starting point for developing public policy around conservation of natural and built environments in ways that promote long-term health of everyone – people, plants, animals, microbes, and the planet.

The guidelines paper is published in the scientific journal Sustainable Microbiology. It will join our recently published paper, “Microbes first into the life rafts: preserving microbiomes to secure health in degrading ecosystems” in a collection curated by some of the MiSt team to highlight work on stewardship.

“Microbiome Stewardship: Definition and Guiding Principles for Implementation“

Authors: O’Doherty KC, Beijbom M, Allen-Vercoe E, Choudoir MJ, Silva DS, Bonilla C, Debelius J, Elton S, Hauptmann AL, Heyland A, Morar N, Skillings D, Sun Z, Wolf PM, Beiko RG, Ishaq SL.

Sustainable Microbiology, qvag028, https://doi.org/10.1093/sumbio/qvag028. Published: 24 June 2026

Abstract: Microbiomes are essential for ecosystem, plant, animal, and human health. There is accumulating evidence that changes to microbiomes from anthropogenic activities are associated with adverse health outcomes. Despite this evidence and calls for action, almost no oversight mechanisms exist to protect microbiomes or their key functions, in part due to uncertainty about what to protect, and how. We have previously proposed microbiome stewardship as a foundational concept that can act across policy domains to facilitate the ongoing presence of key microbial communities and their functions. The purpose of this article is to provide a working definition of microbiome stewardship and develop guiding principles to support its implementation. The concept of microbiome stewardship is relevant to a wide range of policy domains, such as public health, clinical care, environmental protection, food production, and agriculture. Nonetheless, the implementation of microbiome stewardship will be highly specific, as it needs to be guided by considerations of microbial habitat, objectives of stewardship, and available opportunities for intervention. Accordingly, aligning stewardship responsibility with specific institutions and governance mechanisms will be context dependent. We conclude with a discussion that situates microbiome stewardship relative to other initiatives.

Highlights

1. Accumulating evidence suggests that some human-induced changes to microbiomes are linked to adverse health outcomes in hosts and ecosystems.
2. We develop guiding principles of microbiome stewardship that comprise a set of premises, responsibilities, and practices aimed at maintaining microbial biodiversity and microbiome functioning across microbial habitats.
3. The premises of microbiome stewardship include knowledge that is necessary to understand the foundational roles of microbiomes for the health of organisms and ecosystems.
4. The responsibilities of microbiome stewardship include imperatives for sustaining health of humans and other organisms.
5. The actions of microbiome stewardship provide guidance for implementing microbiome stewardship goals in practice.