Holomicrobiome Groeifonds Project and InnerBuddies' Role
The holomicrobiome is the idea that microbiomes should be studied as connected ecosystems rather than as isolated parts. In practice, it refers to the interactions between microbial communities in humans, animals, plants, food systems and the environment. That broader view helps researchers understand how changes in one ecosystem may affect another.
The Dutch Holomicrobiome Groeifonds project brings this perspective into a large public-private research program. InnerBuddies is participating in this initiative because it aligns with our focus on gut health, microbiome education and the role microbiome communities may play in supporting healthier food and lifestyle choices.
What is a holomicrobiome?
A holomicrobiome is a systems-level way of looking at microbiome science. Instead of focusing on one microbiome at a time, such as the gut microbiome, it considers the full network of microbial communities across ecosystems.
This includes:
- Human microbiomes, such as the gut, skin and oral microbiomes
- Animal microbiomes, which may influence health and food systems
- Plant and soil microbiomes, which affect agriculture and food production
- Environmental microbiomes, including water and broader ecosystem communities
This approach can support more complete research into how microbiome communities interact, how food ecosystems affect microbial balance, and how predictive tools may eventually help researchers better understand effects and possible side effects of microbiome-based interventions. In short, the holomicrobiome framework looks at the whole microbial network, not just a single sample or single organ system.
Why the holomicrobiome matters for diet and health
The holomicrobiome perspective is relevant to diet and health because food does not exist in isolation from the environment that produces it. Soil health, crop growth, food processing and human digestion are all part of a connected microbiome landscape.
For gut health education, this matters in a few ways:
- It helps explain why the quality of the food ecosystem may influence what reaches the plate.
- It supports a broader understanding of how microbiome communities may relate to digestion, nutrient exposure and resilience.
- It may help researchers explore how microbiomes and disease prevention are connected through diet, environment and lifestyle.
- It opens the door to more careful study of microbiome-based diagnostics and personalized nutrition approaches.
While this research field is promising, it is still developing. Findings from holomicrobiome research may one day help guide better tools and more precise microbiome science, but they do not replace medical care or individual diagnosis.
The Dutch Holomicrobiome Groeifonds project
In March 2024, the Dutch cabinet allocated €200 million from the National Growth Fund to support a public-private consortium focused on microbiome research and applications. The goal is to map, analyze and model relationships between microbiomes across humans, animals, plants and the environment.
The project aims to:
- Advance scientific understanding of microbiome interactions across ecosystems
- Support health and sustainability research
- Encourage innovation in agriculture, healthcare and environmental applications
- Explore microbiome-based diagnostics and broader microbiome tools
This initiative is especially relevant to the holomicrobiome because it treats microbiomes as interconnected communities with potential implications across multiple sectors.
InnerBuddies' role in the project
InnerBuddies is participating as a private sector partner in the Dutch Holomicrobiome Groeifonds project. Our involvement reflects our interest in evidence-based microbiome education and in better understanding how microbiome communities relate to daily life, food and gut health.
The project also connects with our work on InnerSoils, a spinoff focused on agricultural soils. Because the holomicrobiome includes soil microbiomes as well as human and animal microbiomes, this broader research framework creates meaningful links between soil health, food ecosystems and gut health education.
As part of a larger consortium, InnerBuddies contributes to a collaboration that spans research, innovation and practical applications. That collaboration includes academic institutions, medical centers, research organizations, government bodies and other private sector partners such as DSM, Danone, Arla Foods and Genzai.
Who is involved in the Holomicrobiome Groeifonds project?
The consortium includes a wide range of participants across the Netherlands:
Academic institutions
- University of Amsterdam (UvA)
- Vrije Universiteit Amsterdam (VU)
- Radboud University (RU)
- University of Groningen (RUG)
- Delft University of Technology (TUD)
- Utrecht University (UU)
- Maastricht University (UM)
- University of Twente (UT)
- Leiden University (UL)
- Wageningen University & Research (WUR)
University medical centers
- Amsterdam UMC
- Erasmus Medical Center (Erasmus MC)
- Leiden University Medical Center (LUMC)
- Radboud University Medical Center (Radboud UMC)
- University Medical Center Groningen (UMCG)
Research organizations
- Netherlands Institute of Ecology (NIOO-KNAW)
- KWR Water Research Institute
- Wageningen Research
Government participants
- Ministry of Agriculture, Nature and Food Quality (LNV)
- Ministry of Health, Welfare and Sport (VWS)
What kinds of topics will the project explore?
The Holomicrobiome Institute and broader project scope cover several research themes. These include:
- Microbiome interactions across ecosystems and how communities may influence one another
- Microbiomes and disease prevention, including the study of community compositions associated with better health outcomes
- Antibiotic resistance microbiome modulation, including how microbial communities may be involved in resistance mechanisms
- Microbiome-based diagnostics that may one day support earlier or more personalized insights
- Microbiomes in agriculture and sustainability, especially soil and plant microbiomes
- Environmental health, including water systems and ecosystem resilience
- Ethics and regulation, so that future applications are developed responsibly
These areas are still active research topics, and the practical benefits will depend on what future studies show.
FAQ
What is the holomicrobiome in simple terms?
The holomicrobiome is the idea that microbial communities across people, animals, plants, food systems and the environment are connected and should be studied together.
How is the holomicrobiome different from the gut microbiome?
The gut microbiome focuses on microbes in the digestive tract. The holomicrobiome takes a wider view and includes multiple microbiomes across ecosystems, including soil and environmental communities.
Why does the holomicrobiome matter for health?
It may help researchers better understand how diet, environment and microbial communities interact. This could support future research into microbiomes and disease prevention and microbiome-based diagnostics.
Does this project mean microbiome testing can diagnose disease?
No. Microbiome-based diagnostics are still an active research area, and microbiome testing should not be treated as a standalone diagnosis or treatment tool.
What is InnerBuddies doing in the project?
InnerBuddies is participating as a private partner and contributing to the broader research conversation around gut health, soil microbiomes and ecosystem-wide microbiome understanding.
Conclusion
The Dutch Holomicrobiome Groeifonds project is an important step toward studying microbiomes as connected ecosystems. For InnerBuddies, participation in this initiative reflects our commitment to responsible microbiome education and to better understanding how gut health, food ecosystems and environmental microbiomes may fit together. As research continues, the holomicrobiome may become a useful framework for future work in health, agriculture and sustainability.