Polyfermenthealth – Linking bacterial diversity in fermented food to metabolic health

A collaboration between Agroscope, Prof. Andrew J. Macpherson, Department for BioMedical Research (DBMR-UNIBE), and Dr. Rémy Brugmann, Interfaculty Bioinforamtics Unit (IBU-UNIBE) of the University of Bern 

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 life styles 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. To this end, a set of >600 sequenced and annotated bacterial strains, mostly lactic acid bacteria, which contains >35’000 orthologue groups of genes, will be screened in silico for their genetic diversity and functional properties. A subset of strains will then be selected and characterized phenotypically. The molecular diversity of ‘monofermented’ (MF) yoghurts prepared with each of these strains will be characterized by untargeted metabolomics. Based on the phenotypic information obtained on the individual strains and the MF yoghurts, ‘polyfermented’ (PF) yoghurts will be designed that combine the strains to potentially maximize the molecular diversity of the yoghurts and introduce specific functional properties, in particular the immune modulatory properties of indoles and folate. The metabolic fate of these products will be tested in different stages of the life cycle, including pregnancy, in a nutritional study in germ-free mice as well as in isobiotic mice possessing a stable microbiota composed of 12 defined bacterial strains. The blood metabolome, the composition of the faecal microbiota, as well as the survival and adhesion of the investigated strains to the gastro-intestinal tract of the mice will be analysed. 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 and to modulate their immune system; (iv) the potential health benefits of each of the PF yoghurts. 

The project Polyfermenthealth received start-up funding from the Gebert Rüf Stiftung.

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