Functional diversity is a key element of human biology providing the organism with dynamic structures, which allow robust and resilient responses to external stimuli. To maintain this ‘mosaic physiology’ the organism must literally be fed with a wide range of nutrients and societal wisdom has accordingly long recognized the importance of diverse dietary patterns to promote and maintain health. The last decade has also discovered the association between the gut microbial diversity and health as well as the important contribution of the gastrointestinal microbes to the metabolism of the nutrients ingested by humans. In that context, Westernized lifestyles are increasingly being characterized by a lower diversity in dietary patterns and gut microbial composition, both phenomena being associated with detrimental effects on human health.
Fermented foods offer a strategic opportunity to promote health by delivering both nutrient and microbial diversity to the human organism. The Polyfermenthealth project will use the bacterial collection of Agroscope Liebefeld composed of > 10’000 strains and cow milk as the food matrix for producing and delivering molecular and bacterial diversity to the organism of mice as animal model.
An integrative analysis of the data will evaluate (i) the extent to which the genetic diversity available in bacteria can be transferred to food in the form of nutrient diversity; (ii) the extent to which nutrient diversity introduced by bacteria in food can be transferred systemically, after processing by the gastrointestinal tract, to the organism of mice; (iii) the ability of selected bacterial strains formulated in the milk matrix to stably integrate the gastrointestinal tract of the mice; (iv) the potential health benefits of polyfermented yoghurts.
What is special about the project?
Polyfermenthealth is an interdisciplinary project combining integrative bioinformatics with biomedical and dairy research for a targeted and synergetic use of bacterial resources to deliver health-promoting nutrients, bacteria, and products of bacterial metabolism to the human organism via food matrices.
In addition to the innovative approach, the unique mix of resources of the project is noteworthy, including (i) access to a highly divers strain collection, the Agroscope Liebefeld collection composed of > 10’000 strains, which has been built over decades of dairy research; (ii) the possibility to study the influence of the delivered bacteria and nutrients on an immunological level in sophisticated mice models; (iii) access to metabolomics and next generation sequencing platforms to examine the effects in their entirety.
The vision of Polyfermenthealth is to contribute to the introduction of fermented foods into the Food Pyramid as a specific category of food, which provides beneficial nutrients to the human organism across all major food groups.
The 631 sequenced strains of the Liebefeld collection were functionally annotated. Subsequently, a functional analysis of the metagenome of 24 strains was conducted, each representing one of the species available in the sequenced Liebefeld collection. The pathways potentially covered by this metagenome were then compared to the intestinal metagenome of four healthy humans. The findings were presented in a manuscript entitled “The metagenome of a microbial culture collection derived from dairy environment covers the genomic content of the human microbiome” (submitted for publication).
An interactive webtool was created to efficiently explore the genomic data in the database of the Liebefeld collection. This webtool will be the foundation for a new genome database management website that is currently being developed and will be published in an international peer-reviewed journal.
Two groups of metabolites, indoles and folate (vitamin B9), were chosen as targets due to their role in immunity and gut-microbiome interactions. Two hundred new ‘mono-fermented’ yoghurts have been produced, each targeting these two groups of metabolites with a different bacterial strain.
In order to evaluate the impact of the indole and folate produced in yoghurt on the immunity of germ-free mice, the billions of colony forming units present in these products had to be removed by sterilization. Also, the fermented products had to be formulated in pellets. A pilot experiment has showed that the germ-free mice consumed the pellets and remained sterile thereafter.
In order to screen the yoghurt samples for aryl hydrocarbon receptor activity triggered by indoles, a human hepatic cell-based assay has been adapted. The screening for folate is performed using a microbiological test, which is currently being optimized for yoghurt samples.
13.9.2018, Swiss Society for Infectious Diseases, Interlaken, Switzerland: Polyfermenthealth – Thomas Roder, Andrew J. Macpherson, Rémy Bruggmann, Guy Vergères (oral presentation);
20.5.2019, Microbiome Announcement: The metagenome of a microbial culture collection derived from dairy environment covers the genomic content of the human microbiome – Thomas Roder, Daniel Wüthrich, Zahra Sattari, Ueli von Ah, Cornelia Bär, Francesca Ronchi, Andrew J. Macpherson, Stephanie C. Ganal-Vonarburg, Rémy Bruggmann, Guy Vergères – Microbiome Announcement (manuscript submitted);
10.9.2019, NuGOweek 2019, Bern, Switzerland: The metagenome of a microbial culture collection derived from dairy environment covers the genomic content of the human microbiome – Thomas Roder, Daniel Wüthrich, Zahra Sattari, Ueli von Ah, Cornelia Bär, Francesca Ronchi, Andrew J. Macpherson, Stephanie C. Ganal-Vonarburg, Rémy Bruggmann, Guy Vergères. (poster presentation);
10.9.2019, NuGOweek 2019, Bern, Switzerland: Polyfermenthealth – Linking bacterial diversity in fermented food to metabolic health – Zahra Sattari, Thomas Roder, Ueli von Ah, Cornelia Bär, Francesca Ronchi, Andrew J. Macpherson, Stephanie C. Ganal-Vonarburg, Rémy Bruggmann, Guy Vergères (poster presentation).
None so far
Persons involved in the project
Prof. Dr. Guy Vergères
, project leader, Agroscope Dr. rer. nat. Cornelia Bär
, AgroscopeDr Rémy Bruggmann
, group leader at the Swiss Institute of Bioinformatics and head of the Interfaculty Bioinformatics Unit of the University of Bern (IBU-UNIBE), Baltzerstrasse 6 CH-3012 Bern, Switzerland
Dr. rer. nat. Stephanie Ganal-VonarburgProf Dr med Andrew J. Macpherson
, professor of medicine and chief of Gastroenterology at the University Hospital of Bern, Department for BioMedical Research, (DBMR-UNIBE), BHH D117, Inselspital, CH-3010 Bern, Switzerland Thomas Roder
, PhD student, IBU
Zahra Sattari, PhD student, DBMRDr. sc. techn. Ueli von Ah
Last update to this project presentation 28.01.2021