The Global Inter-Health Microbiome Observatory, a Unique Scientific Infrastructure
50 scientific cohorts, 25 countries, 5 continents: it is on this Human Microbiome Cohorts Alliance, intended to expand, that the Global Inter-Health Microbiome Observatory will rely, a new permanent infrastructure for collecting, harmonizing, and analyzing microbiomes on a global scale, announced on April 8, 2026, and coordinated by INRAE, with VIB-KU Leuven and the support of Inserm, and led by the World Microbiome Partnership.
Over 500,000 human microbial profiles have already been collected through this alliance, with the goal of reaching 1 million human microbiomes collected by 2030 to ensure statistically representative data to date, and then expand the research scope to soil, ocean, and plant microbiomes by 2028, a more complex but necessary area for covering the entire One Health continuum.
The expected outcomes are twofold: to produce actionable knowledge for research and private innovation, and to provide public authorities and citizens with consensus health indicators and access to microbiome-based solutions.
“The microbiome is both a trigger and a solution to major societal challenges: the rise of chronic diseases, the development of antimicrobial resistance, erosion of biodiversity, climate change, and the transition of agricultural and food systems.” – Philippe Mauguin, CEO of INRAE
What One Million Profiles Make Possible
Human microbiomes vary significantly based on diet, agricultural practices, or exposure to contaminants. One strength of this alliance lies in the diversity of collected profiles, with partners from dozens of countries with contrasting health and environmental contexts – Germany, Armenia, Cambodia, Cyprus, South Korea, Egypt, Spain, USA, Italy, Japan, Mexico, Singapore, and many others. Research has faced several obstacles: lack of harmonized standards between countries, fragmented regulatory frameworks, and unequal access to innovations for teams in the Global South, with over 70% of available human metagenomic data today coming from North America and Europe. These are the challenges the observatory aims to address.
“Achieving one million harmonized profiles would unlock current barriers, with as much a methodological as scientific challenge,” explains Thierry Caquet, INRAE Vice President for International. “The strength of the approach lies in sharing the largest possible amount of standardized data.”
This statistical power could help identify global signatures, develop early diagnostic biomarkers, advance personalized therapeutic solutions, fuel large-scale predictive models, particularly through artificial intelligence, opening new prospects in personalized medicine and precision nutrition. The economic stakes are also high: the global market for microbiome-based products for human health is estimated at $1.4 billion in 2027, while the agricultural applications market is estimated at nearly $12 billion yearly.
“This ambitious international project requires engagement at all levels, government institutions, and funding bodies, to support its development and foster dialogue between science and decision-making.” – Philippe Mauguin, CEO of INRAE
Shotgun Metagenomics, French Expertise since 2010
Shotgun metagenomics emerged in France in 2010, notably through the MetaHIT project (2008-2013), a European consortium of 13 partners from 8 countries, funded by the European Commission, where INRAE led scientific coordination. A Nature publication in 2010 established a reference catalog of genes in the human gut microbiome, with 3.3 million genes, 150 times more than the human genome, serving as the basis for further work on human microbiome diversity and functions. The new global observatory builds on the national programs France 2030 PEPR SAMS and France Cohorts, with 30 million euros invested through the French Gut project.
The expansion from 2028 to soils, oceans, and agroecosystems follows a direct scientific logic. As Thierry Caquet highlights, “Our microbiota depends heavily on our environment: diet, chemical environment, contact with more or less polluted soils. We share our microbes with other living organisms and with environmental compartments – water, soil, animals, plants. This can be seen as a unifying trait of the One Health approach.” Microbiomes thus become indicators to inform public policies and measure their impact, whether it is reducing agricultural inputs, monitoring antimicrobial resistance, soil health, or pollution control.
The World Microbiome Partnership
Founded in 2023, the WMP brings together research, industry, and policy actors around microbiomes in a One Health approach. It aims to remove scientific and regulatory barriers and promote the development of applications (biomarkers, products, interventions) for human, animal, and environmental health. The initiative is chaired by Joël Doré, research director at INRAE. Emmanuelle Maguin, research director at INRAE, serves as the general secretary. The institute is involved in WMP development, particularly through its international priority program on Microbiomes and Global Health, contributing to structuring this scientific cooperation.
PREZODE: World Bank Joins Zoonotic Disease Emergence Prevention Initiative
The World Bank has officially announced its support for the PREZODE initiative, with a targeted commitment to projects in Central and West Africa. The initiative has also seen significant expansion: seven new countries have joined – Armenia, Cyprus, Ivory Coast, Indonesia, Kenya, Libya, and Mauritania – and its financial base has expanded with the entry of the Islamic Development Bank. Institutionally, framework agreements have been signed with the Economic and Monetary Community of Central Africa (CEMAC), the Pacific Community (CPS), and the Brazilian institution Fiocruz, anchoring PREZODE in the regional health architectures of 3 continents.
Launched during the 2021 One Planet Summit by CIRAD, INRAE, and IRD, PREZODE now has over 280 members and observers working towards the common goal of preventing zoonotic disease emergence. With international governance, it relies on working groups bringing together 87 experts from 36 countries, as well as shared workspaces with WHO, FAO, and OIE on emerging disease indicators, the return on investment of One Health approaches, and the state-science-society dialogue.
From the inception of PREZODE, we were convinced that only a science-based One Health approach could lead to the necessary changes to prevent future pandemics. Five years later, we are proud of the progress made: PREZODE has achieved a global scale, with international governance involving 90 countries and ministerial commitment from 30 of them, working at the science-policy interface. The initiative is internationally recognized, has developed joint activities with WHO, OIE, and FAO, and contributes to major global negotiations. We are grateful to all PREZODE members and determined to continue its expansion in the years to come, for the benefit of all and the planet.” – Elisabeth Claverie de Saint-Martin, Philippe Mauguin, and Valérie Verdier, respective CEOs of CIRAD, INRAE, and IRD
“The question is not whether there will be a new pandemic, but when and where it will occur,” reminds Thierry Caquet. Over 30 new human pathogens have been identified in the past thirty years, of which 75% are of animal origin, with Ebola, Nipah, avian flu, and Covid-19 being the most documented.
These emergences result from converging dynamics. As deforestation, agricultural expansion, and urbanization reduce wildlife habitats and climate change redistributes species’ ranges, interactions between wildlife, livestock, and humans increase, paving the way for pathogens previously confined to distant ecosystems. Approximately 1.7 million unknown viruses currently circulate in wildlife, and without profound changes in prevention strategies, the pandemics they could trigger will appear more frequently, spread faster, and kill more people than Covid-19, as warned by IPBES experts in 2020.
However, Thierry Caquet points out a structural difficulty in public action: “Prevention, by nature, is inconspicuous. As long as no crisis occurs, it may appear as unjustified cost, but when a crisis erupts, its absence becomes evident.” The IPBES report estimated the economic cost of pandemics to be up to 100 times higher than prevention policies.
In the field, One Health community surveillance systems are already active thanks to PREZODE in 16 low- or middle-income countries, funded by €25 million from AFD (PREACTS program financing 15 projects in total in Africa, Asia, and South America). 9 PEPR research projects, representing also €25 million, are underway, in France including several in overseas French territories and internationally. PREZODE has also played an active role in the negotiations for the international pandemic agreement, advocating common North-South positions, and has initiated a global inventory of One Health initiatives in member countries in this context.
These two initiatives are part of the same One Health vision, now structuring for INRAE, and represent a scaling change in addressing these challenges. Their international dimension “brings together scientific communities around common benchmarks, raises new research questions, and generates projects that no single institution could carry alone,” as Thierry Caquet analyzes. They also align research with action-oriented mechanisms and public policies. “We do not implement One Health on principle. We do it because there are human communities involved.” From prevention made visible, measurable, and governable.
