Harnessing the power of microbiomes
Microbiomes — omnipresent, complex communities of microorganisms such as bacteria, fungi and viruses — have major impacts on the health of humans, animals, plants and environments. Learning how they function, and how to predict the effects of changing or deploying microbiomes at a large scale, will open up avenues to many new applications in agriculture, healthcare and the food industry.
Individual microbiomes together form ‘holomicrobiomes’ that span all domains. The Holomicrobiome Initiative aims for studying microbiomes as part of such holomicrobiomes and creating tools that predict effects and side effects of potential interventions across domains. That will enable companies to develop and market a wide range of innovative, effective and safe microbiome products and services aimed at better health and sustainability.
Our food system: many microbiomes, one holomicrobiome
People
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.
Animals
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.
Plants
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.
Soils
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.
Water
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 a metro system. In countless ways, bacteria, fungi, viruses, microbial genes and gene products travel along over the network. Changes in a microbiome at one station can have impacts elsewhere.
Soil bacteria travel via vegetables to the guts of consumers; antibiotics-resistant bacteria from patients use waste flows to reach the environment.
New treatments for gut microbiomes, or innovative ways to use microbiomes for recycling of residual flows, can have impacts elsewhere in the network. Without a good metro map, effects as well as side effects are difficult to predict.
Institute, database and predictive modelling
The Holomicrobiome Initiative aims to establish the Holomicrobiome Institute, a public/private institute that will focus growing microbiome research in the Netherlands on mapping the interactions within and between microbiomes in domains that are now often studied separately: people, animals, plants, soil, and water. The new institute aims for a complete ‘holomicrobiome’: that of the Dutch food system, which extends from fields, wastewater and crops to farm animals, food, consumers and patients.
By centrally initiating, coordinating, bundling and integrating research towards a shared goal, the institute will build a unique, cross-domain database filled with large amounts of data from existing and new microbiome research. With its partner institutions, the institute will set up and coordinate large-scale, cross-domain, long-term cohort and field studies as well.
On top of this database, helped by artificial intelligence (AI) and computational modelling, the institute will also build virtual models of microbiomes. With these models, we will be able to predict how localised interventions in microbiomes have desirable, but possibly less desirable effects as well throughout the holomicrobiome. That will offer great opportunities for identifying, testing, and validating promising concepts for innovative new products and services targeted at microbiomes across all domains.
Examples of innovative products, interventions, and services
Outcomes from the work of the Holomicrobiome Institute will be of tremendous value to innovative companies, scientists, governments and society at large. By establishing a validated theoretical framework for proving the efficacy and safety of countless innovative interventions, they will form the foundation under, 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 microbiomes, food components and people’s health status will be established. Microbiome tests will detect health risks earlier; and treatments (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 will come into focus. Methods to fertilize crops with microbes can be developed. Impacts of chemicals and plant microbiomes down the food chain can be better measured and managed.
Circular economy
Using the diversity and potential of microbiomes to treat manure, waste water, contaminated air, and other organic residual flows to win back valuable nutrients and/or rid them from harmful components before they are recycled back into the food system.
Clean water
The microbiological quality of sewage and waste water will be easier to measure and monitor. With new microbial treatments we will be better able to clean waste, surface and industrial water bodies and keep drinking water safe for consumption.