A Consensus Statement on establishing causality, therapeutic applications and the use of preclinical models in microbiome research

In a significant collaborative effort, an international team of researchers supported by the Human Microbiome Action Consortium, a global initiative funded by the European Union’s Horizon 2020 program, has published a comprehensive consensus statement in Nature that establishes clear guidelines for determining causality within gut microbiome studies and explores novel therapeutic opportunities. The article provides a comprehensive framework for determining causality in gut microbiome studies and identifies new therapeutic opportunities, addressing one of the most pressing challenges in microbiome science: distinguishing correlation from causation in the relationship between gut microbes and human health.

The IHMAC, a collaborative network of over 30 leading research institutions, industry partners, and stakeholders across Europe and beyond, is dedicated to advancing microbiome research and its applications for human health. By fostering interdisciplinary collaboration, the consortium aims to standardize methodologies, improve data sharing, and translate scientific discoveries into actionable solutions. This consensus statement reflects the IHMAC’s commitment to unifying the field and driving progress in microbiome research.

Key highlights of the publication include:

– Establishing Clear Causality: The consensus emphasizes robust experimental designs and analytical frameworks to differentiate between associations and direct causal effects, ensuring more reliable and actionable insights.

– Therapeutic Implications: By providing clear guidelines, the HMAC paves the way for targeted microbiome interventions, offering potential for treating conditions such as inflammatory bowel disease, metabolic disorders, and neurological conditions.

– Collaborative Approach: Reflecting the HMAC’s collaborative ethos, the statement fosters improved reproducibility, translatability, and innovation in microbiome research.

“This consensus statement represents a significant step forward in our understanding of the gut microbiome.  By establishing clear criteria for causality, we can design more effective clinical trials and develop therapies that have the potential to improve patient care.

The publication is expected to serve as a key reference for future research and has already generated interest among clinicians, researchers, and industry leaders working to translate microbiome science into real-world therapeutic solutions.

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Metwaly, A., Kriaa, A., Hassani, Z. et al. A Consensus Statement on establishing causality, therapeutic applications and the use of preclinical models in microbiome research. Nat Rev Gastroenterol Hepatol (2025). https://doi.org/10.1038/s41575-025-01041-3