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 objective of Polyfermenthealth is to demonstrate that the genetic diversity contained in collections of lactic acid bacteria can be translated, via fermented food, into diverse and beneficial metabolic profiles in vivo. Polyfermenthealth is a precompetitive project that will pave the road for the development of innovative food products.
The diversity of the human microbiome is positively associated with human health. However, this diversity is endangered by Westernized dietary patterns that are characterized by a decreased nutrient variety. Diversity might potentially be improved by promoting dietary patterns rich in microbial strains. Various collections of bacterial cultures resulting from a century of dairy research are readily available worldwide, and could be exploited to contribute towards this end. We have thus conducted a functional in silico analysis of the metagenome of 24 strains, each representing one of the species in the Liebefeld bacterial culture collection composed of 626 sequenced strains, and compared the pathways potentially covered by this metagenome to the intestinal metagenome of four healthy, although overweight, humans. Remarkably, the pan-genome of the 24 strains covers 89% of the human gut microbiome's annotated enzymatic reactions. We concluded that microbial culture collections derived from dairy research have the genomic potential to complement and restore functional redundancy in human microbiomes.
As the amount of genomic data continues to grow, there is an increasing need for systematic ways to organize, explore, compare, analyze and share this data. Despite this, there is a lack of suitable platforms to meet this need. We have consequently developed the OpenGenomeBrowser (OGB), a self-hostable, open-source platform to manage access to genomic data and drastically simplify comparative genomics analyses. The source code, documentation, tutorials for OGB are available at opengenomebrowser.github.io and is freely accessible at opengenomebrowser.bioinformatics.unibe.ch. To our knowledge, OGB is the first self-hostable, database-independent comparative genome browser.
Genomic screening of bacteria is common practice to select strains with desired properties. However, 40-60% of all bacterial genes are still unknown, making capturing the phenotype an important part of the selection process. While omics-technologies collect high-dimensional phenotypic data, it remains challenging to link this information to genomic data to elucidate the impact of specific genes on phenotype. To this end, we developed Scoary2, an ultra-fast software for microbial genome-wide association studies (mGWAS), enabling integrative data exploration. As proof of concept, we explored the metabolome of 44 yogurts with different strains of Propionibacterium freudenreichii, discovering two genes affecting carnitine metabolism.
Indole derivatives as metabolites of the tryptophan pathway are bioactive microbial compounds with a role in gut immune homeostasis. The aim of our study was to test, in germ-free mice, if maternal intake of a dairy product enriched in indoles, metabolites derived from tryptophan, through fermentation could boost maturation of the intestinal innate immune system in the offspring. 631 LAB from Agroscope’s collection were genetically screened in regard to their potential to produce indole compounds. 135 different strains were chosen to produce yoghurts, the latter of which were screened for their ability to activate their immunomodulatory receptor in a cell line. The most efficient indole yoghurt was fed to germ-free dams during pregnancy and lactation. Analysis of the offspring on postnatal day 14 revealed an increase in intestinal innate immunity in the pups born to dams that had consumed the indole yoghurt compared to a control yoghurt. The selection of specific LABs based on their ability to produce a fermented dairy with bioactive indoles appears to be an effective approach to produce a yoghurt with immunomodulatory properties.
Folate, also known as vitamin B9, is an essential nutrient that cannot be produced by the human body. Folate deficiency in pregnant women can cause neural tube defects in the fetus. More generally, folate deficiency can lead to macrocytic anemia, Alzheimer’s disease, cardiovascular diseases, and may increase the risk of cancer. We have thus created a yoghurt rich in folate and tested its effect on gnotobiotic mice as well as germ-free mice, with a particular focus on intestinal immunity. Following the genetic pre-selection of bacterial strains from the Liebefeld culture collection with OGB the folate production of 163 yoghurts fermented with one additional strain was measured using a microbiological assay. Milk and yoghurt made from starter strains only contained very similar amounts of folate. The amounts of folate in eight yoghurts were increased at least threefold, with three of them exhibiting a fivefold increase. Determination of the absolute amounts of folate in the folate yoghurt are ongoing. Also, analysis of the immune intestinal cells is pending. A manuscript will be finalized and submitted for publication as soon as this information is available.
Both nutritional diversity and gut microbial diversity are positively associated with human health. Along this line of thoughts, we decided to use the Polyfermenthealth pipeline to design a yoghurt with high taxonomic as well as metabolomic diversity and to evaluate the impact of the ingestion of such product on the metabolism of mice, in particular intestinal gene expression as well as the blood metabolome. We decided to add 5 strains, each from a different species to the yoghurt in addition to the starter culture. We selected these additional strains based on two criteria: (i) we wanted to increase the chance of the strains being able to engraft in the gut; (ii) new strains would be added iteratively to maximize the metabolic diversity of the yoghurt. The yoghurt was called “polydiverse” because it consisted of different species. We indeed succeeded to significantly increase the molecular diversity present in classical yoghurt with five additional strains selected for their ability to produce additional molecules upon fermentation of milk. In the mice trial, the polydiverse yoghurt was compared to a yoghurt with only starter strains. Preliminary results in mice indicate that, compared to the control yoghurt, the increase in bacterial and molecular diversity in the polydiverse yoghurt modified intestinal gene expression as well as blood and milk composition in the mice having ingested this product. An in-depth analysis of the data is ongoing.

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