Pseudomonas-derived secondary metabolites in traditional dairy products

Raw milk has a rich microbiota that engages in complex mutualistic or antagonistic interactions. These interactions shape microbial communities in dairy products, influencing fermentation, preservation, and product quality. This thesis investigates the ecological role of microbial natural products in structuring these communities. Mongolia provides a unique ecological and anthropological context for studying these dynamics due to its rich history in dairying and fermentation. The traditional Mongolian dairy product öröm served as a microbial source, leading to the isolation of Pseudomonas sp. SM4, which was found to produce a collection of cyclic lipopeptides (CLPs). The structure of six CLPs was elucidated using a combination of bioinformatic predictions, mass spectrometry, Marfey’s analysis, NMR spectroscopy, and X-ray crystallography. Milk-based bioassays and metabarcoding analyses revealed changes in the microbial composition of milk due to the addition of the CLP tensin A and allowed the identification of a novel function in promoting the growth of Candida zeylanoides, a yeast commonly found in dairy environments. This represents the first report of a CLP directly stimulating yeast growth, suggesting a novel ecological role for CLPs in dairy environments. Transcriptomic analysis linked this effect to glyoxylate metabolism. Psychrotolerant Pseudomonas species are a predominant part of the microbiota in milk and dairy products and thrive in these environments due to various adaptation features. To investigate whether milk-associated Pseudomonas strains have adapted their metabolism to milk, a pan-genome analysis was performed. This thesis aimed to determine whether specific genetic traits enable Pseudomonas species to adapt to milk, whether these traits are widespread or species-specific, and whether the heat-resistant alkaline metallopeptidase AprX offers a competitive advantage in this environment.