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A healthier holomicrobiome

Microbiomes — omnipresent communities of microorganisms such as bacteria, fungi and viruses — have major impacts on human, animal, plant and environmental health. In our food system, the many separate microbiomes together form one large and tight network: a ‘holomicrobiome’.

The Holomicrobiome Initiative aims to map an entire holomicrobiome and, with the help of artificial intelligence, analyse and predict how all the contributing parts interact. That will lead to new, better products and services for agriculture, food production and healthcare, and thus to a society with better health and more sustainability.

Our food system: many microbiomes, one holomicrobiome

From agricultural fields, surface water and livestock farming to food companies, consumers and patients, microbiomes are all around us and play often invisible but very important leading roles. In the holomicrobiome of our food system, all those microbiomes are closely interconnected.
Billions of microbes, fungi, and viruses (A) together form microbiomes (B), which interact with each other in one big holomicrobiome (C).


Microbiomes on our skin and in our digestive system are essential to our health — they comprise 99% of all the genes in and on our bodies! But the effects of unhealthy microbiomes are also becoming increasingly clear, including serious intestinal or brain diseases.


Microbiomes in the guts of chickens, pigs and cows are crucial for animal production end welfare but also contribute to the release of nutrients into the environment. Through animal feed and medicines, they influence food safety and outbreaks of animal disease.


Microbiomes help food crops to obtain crucial nutrients from the soil and from the air, but also to prevent damage from insects and plant diseases. These same microbiomes also end up in farm animals, however, or directly on our plates.


Soil microbiomes are essential for our agriculture. They determine soil life, influence absorption and leakage of fertilizers, and help prevent plant diseases. And chemicals in the soil will eventually seep into the entire food system.


Healthy microbiomes are vital to water quality. They clean our waste, waste waters and surface waters. Conversely, however, micro-organisms, microbial genes or residues can also seriously threaten the quality and safety of water.

The holomicrobiome as a metro system

The holomicrobiome of the food system could be compared to an intricate metro network.

Bacteria, fungi, viruses, microbial genes and gene products, as well as other chemicals, travel as passengers over the rails between many stations along the network. All of them eventually affect the metro system as a whole.

Every day, society introduces countless disruptions on this metro network, for example with pesticides, medicines or altered microbiomes. Until now, we do this without  accurate metro maps or timetables.

Knowledge institutions
Knowledge organisations
Innovation partners

Institute, database and 'digital twin'

The Holomicrobiome Initiative aims to establish the Holomicrobiome Institute, a public/private institute that will focus much of microbiome research in the Netherlands on mapping the interactions between microbiomes in domains that are now often studied separately: people, animals, plants and soil, and water. The new institute is the first to map a complete holomicrobiome: that of the Dutch food system, which extends from fields, wastewater and crops to farm animals, food, consumers and patients.

Bundling and coordinating lots of research, the institute will build a unique, cross-domain Food System Holomicrobiome Database. It will fill that database with large amounts of data from newly launched microbiome research as well as some studies that are ongoing. The institute will set up and coordinate large-scale, cross-domain, long-term cohort and field research via partner institutions.

With the help of artificial intelligence (AI), mathematical modelling and other computational sciences, the new database will be used to create a virtual model (a digital twin) of the holomicrobiome. The digital model will make it possible to predict how positive or negative effects of localised interventions will spread throughout the entire holomicrobiome. This will offer great opportunities for testing and developing innovative and better products and services. As of now companies are encouraged to join the initiative one way or the other.

Examples of innovative products, interventions, and services

The Holomicrobiome Database and Digital Twin will be of tremendous value to innovative companies*, scientists, governments and society at large. They are the basis for, for example, new diagnostic tests and innovative prebiotic and probiotic prevention and treatment interventions, in health care and food production, animal feed production, animal husbandry, veterinary health care, agriculture and soil and water management – major international sectors and markets. Governments will gain a firmer foundation for cross-sectoral policies and new options for refining and enforcing regulation.

Human health

Relationships between, for example, microbes, chemicals or food components and human health will be demonstrated. Microbiome tests will detect risks; preventive and clinical interventions (such as pre- and probiotic nutrition or microbiota transplants) will be developed.

Animal husbandry

The effects of using chemicals and pharmaceuticals in livestock farming will come more into focus. Safer and more effective veterinary alternatives will be developed. Microbiomes in livestock will be modified through feed to reduce environmental damage and food safety risks.

Sustainable agriculture

Adverse effects of fertilizers and pesticides on root microbiomes of food crops will become more clear. Alternative, less harmful cultivation methods will be developed. Effects of chemicals and plant microbiomes further down the food chain can be better measured and managed.

Healthier soils

The condition of microbiomes in agricultural lands and adjacent natural areas will become measurable. Newly developed methods will make soils healthier and farming on those soils safer, more sustainable, and more efficient.

Cleaner water

The microbiological quality of sewage and waste water will be easier to measure and can be monitored more completely. With optimized microbiomes we will better be able to clean waste and surface water and to purify drinking water.