EU-US microbiome strategy: Yakult Europe discloses its role in major initiatives to shape future R&D

01 Dec 2023 --- Four substantial microbiome R&D projects have been set in motion in the European region — Holomicrobiome, MicroHealth, Fermented Foods and DeVenir. Yakult Europe, which has significant stakes in all the projects, grants Nutrition Insight an in-depth interview about the purpose, drive and objective of its futuristic initiatives, aiming to make dietary microbes an official food category. 

The Holomicrobiome is the most comprehensive initiative in the portfolio for which the National Growth Fund has agreed to spend a maximum of €200 million (US$218 million) for the research, which has far-reaching implications. Microbiomes can be found in agricultural fields, surface water and livestock farming to food companies, consumers and patients and are all interconnected.

“The aim is to make a link between chronic diseases, antibiotic resistance, declining water quality and nitrogen emissions. In all of these processes, the microbiome is involved. The holomicrobiome project tries to understand this interconnectedness and the connections between all the different systems. Our interest here is in healthcare,” Dr. Bruno Pot, Ph.D., science director at Yakult Europe, tells us. 

“From the private sector, we hope to play a very prominent role in this because we have a lot of information and contacts that could be useful.” The initiative will be used to reduce harmful greenhouse gas emissions, restore soil and clean drinking and groundwater. 

The proposal was submitted to the Dutch Ministry of Agriculture, Nature and Food Quality. All knowledge institutions (academic institutions and universities) in the Netherlands conducting research into microbiomes are involved in the initiative.

Linking microbiomes across ecosystems
The holomicrobiome, which refers to microbiomes over the entire food system, has been likened to an extensive metro network used by bacteria, fungi, viruses, microbial genes and gene products that include chemicals. Thus far, the “passengers” have been traveling without a map, which will be remedied by these new initiatives, which will also guide future environmental and healthcare decision-making.

A Holomicrobiome Institute will be established to map the microbial interactions within and between the microbiomes of people, animals, plants, soil and water. These were previously studied separately.Lacticaseibacillus casei Shirota, Yakult's signature bacteria (Credit: Yakult Europe).

The institute is building a cross-domain database of the latest microbiome research by bundling and coordinating different research. It will use AI, mathematical modeling and computational sciences to create virtual models of microbiomes and the “holomicrobiome.”

The digital models will predict how localized interventions’ positive and negative effects impact microbiomes and spread across the holomicrobiome. The science will open avenues for developing better products and services.

The project has 16 consortium members, 46 private partners including NIZO, Lesaffre, DSM, Beneficial Microbes Consultancy, Arla Foods, Danone, EkoMenu, NIZO, Yakult Europe, 11 public partners and 19 “supporters” including Bayer, Cargill, Noblebio and Syngenta. 

Microbiomes are important in chronic diseases, antibiotic resistance, declining soil and water quality and nitrogen emissions. Stakeholders can leverage the platform to rapidly create applications such as biological alternatives to fertilizers, chemical plant protection products, antibiotics and chronic disease treatments. It can also be used to develop better products for food production, health care and agricultural services.

Dietary microbes food category
The primary objective of all four projects is to drive the formation of a new food category called “dietary microbes” in the scientific community. The category asserts the importance of live microbes in the diet. The idea is supported by the International Scientific Association for Probiotics and Prebiotics, the Institute for the Advancement of Food and Nutrition Sciences, the Lactic Acid Bacteria Industrial Platform and the International Probiotics Association.

Pot explains: “We chose those projects because they have a link to dietary microbes. Scientists as a whole would like to introduce the dietary microbes food category as a way to communicate to the consumer that if you consider a healthy diet, you also need to consider healthy microbes — the good microbes — the old friends — through fermentation. This could be through probiotics or through prebiotics which promote probiotics.”

Researchers emphasize that it is important for consumers to realize the value of dietary microbes in the same way they understand the importance of dietary fibers or vitamins in promoting good health.

“We think it’s important for the consumer to have access to the knowledge but also healthcare professionals. Dietitians don’t get any training on this at the moment. Molecular doctors don’t get any training. That means a lot of the literature that is appearing now is not accessible to them,” he says.Yakult Europe's production factory (Credit: Yakult). 

The projects will investigate the health aspects of dietary microbes, substantiate the presence and the variety of microbes in the diet and illustrate its gradual loss of diversity due to changes in lifestyle or the environment. They constitute innovative fields of research — microbiota-microbiome, fermented foods and alternative biotics — using modern technologies such as next-generation sequencing (NGS), metabolomics and proteomics.

Exposure to microbes through nature
The aim of the projects, particularly the Fermented Foods project — driven by the University of Amsterdam — is to provide proof-of-concept that fermented foods can improve a dysbiotic gut microbiome. The research will evaluate which microbes are transferred to humans via the soil and their importance in health.

“We are exposed on a daily basis by the environment, by the plants. Everything we do, we get contaminated by microorganisms whether it’s yeast, fungi, bacteria, even parasites. They have an impact on our health,” Pot notes.

Scientific sources have conclusively identified between 50–70 microorganisms present in 95% of the population, which can be considered “old friends,” microbiota that have been passed down from an ancestral lineage. However, more than 2,000 species are known today, and the information about their bigger role in health is scant. 

“One of the things we don’t understand today is when (the microorganisms) become pathogenic and when not. The contact with 'old friends' essentially keeps the immune system alert and prevents non-communicable diseases,” highlights Pot. 

By Inga de Jong