PORTFOLIO

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 uses the bacterial collection of Agroscope composed of > 10’000 strains (Liebefeld collection) 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 aims to 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.

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 the highly diverse 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 published in an article entitled “In Silico Comparison Shows that the Pan-Genome of a Dairy-Related Bacterial Culture Collection Covers Most Reactions Annotated to Human Microbiomes” (Microorganisms 2020, 8, 966; doi:10.3390/microorganisms8070966). The results were also submitted to the Frontiers for Young Minds’ collection “New ways to understand how foods affect me and my health!”. The journal targets kids from 8 to 14 y.o. and allows researchers to share their discoveries in a language that is accessible for young readers.
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; it was presented at the 2021 [BC]2 Basel Computational Biology Conference, the Swiss Society for Microbiology annual meeting and the 13th International Symposium on Lactic Acid Bacteria. It has also been submitted for publication in an international peer-reviewed journal.
Two groups of metabolites, indole derivatives and folate (vitamin B9), were chosen as targets due to their role in immunity and gut-microbiome interactions. 187 new yoghurts have been produced, each targeting one these two groups of metabolites with a different bacterial strain.
To identify indoles-containing yoghurts, the 187 yoghurts were screened according to their ability to activate the transcription factor Aryl Hydrocarbon Receptor (AhR). AhR is an activator of IL22 production by intestinal group 3 innate lymphoid cells (ILC3), and for which many indoles derivatives are ligands. The screening was performed in vitro using HepG2-AhR-Luc cell line and a combination of two strains producing the highest AhR gene expression was selected The immunomodulatory properties of the indole-rich yoghurt were tested in pups after feeding the test yoghurt to pregnant germ-free mice. To do so, sterile yoghurt-containing pellets have been developed, and we have shown that germ-free mice remained sterile after their consumption. After feeding the test yoghurt to the pregnant mother for 14 days and 10 days postnatal, a significant increase in the frequency of NKp46+ILC3+ ILC3s was observed in the pups compared to a conventional yoghurt. This result was confirmed in a second experiment. In addition, a metabolomics analysis targeting indole derivatives was conducted on the test and control products. Thirty-eight indoles derivatives were investigated, 22 were detected in the products, seven were significantly different between the conventional (control) yoghurt and the test yoghurt; each of them showing a higher concentration in the test product. Among the significant compounds, indole-3-aldehyde and indole-3-ethanol were particularly of interest as they have been reported in a recent study as being regulators of the gut barrier function via AhR in mice. The results were presented during an oral presentation at the NuGOweek 2021 and will be submitted for publication in an international peer-reviewed journal.
The ability of the strains to produce folate was evaluated by microbiological assay. A strain producing an elevated activity was selected and pellets containing the folate-rich yoghurt were produced. The immunomodulatory properties of the folate-rich yoghurt will be tested in germ-free and gnotobiotic adult mice.
In addition to indole derivatives and folate, other bioactive metabolites of nutritional interest were searched in the 187 yoghurts using untargeted metabolomics datasets from LC-MS and GC-MS analyses. The preliminary results indicate significant differences between the new yoghurts for various compounds relevant to human health. These molecules include, but are not limited to, D-tagatose, branched-chain amino acids, and short-chain fatty acids. A second experiment aimed at replicating these results is in progress.
Finally, in addition to targeting specific bioactive metabolites, the diversity of metabolites present in milks fermented with an increasing number of lactic acid bacteria strains is evaluated using both LCMS-based metabolomics and in silico predictions. The ability of the most “diverse” yoghurt (‘polydiverse yoghurt’) to increase the blood metabolic diversity and modulate the composition of the gut microbiome of gnotobiotic mice will be assessed in a third experiment.

08.2021, Can eating bacteria from fermented foods support your health? – Thomas Roder, Grégory Pimentel, Cornelia Bär, Ueli von Ah, Rémy Bruggmann, Guy Vergères. Frontiers for Young Minds, section Human Health. (in press);
27.06.2020, In Silico Comparison Shows that the Pan-Genome of a Dairy-Related Bacterial Culture Collection Covers Most Reactions Annotated to Human Microbiomes – Thomas Roder, Daniel Wüthrich, Zahra Sattari, Ueli von Ah, Cornelia Bär, Francesca Ronchi, Andrew J. Macpherson, Stephanie C. Ganal-Vonarburg, Rémy Bruggmann, Guy Vergères – Microorganisms 2020, 8, 966; doi:10.3390/microorganisms8070966