Filamentous fungi in artisanal cheeses: A problem to be avoided or a market opportunity?

Deciphering microbial communities of three Savoyard raw milk cheeses along ripening and regarding the cheese process

Different Savoyard cheeses are granted with PDO (Protected Designation or Origin) and PGI (Protected Geographical Indication) which guarantees consumers compliance with strict specifications. The use of raw milk is known to be crucial for specific flavor development. To unravel the factors influencing microbial ecosystems across cheese making steps, according to the seasonality (winter and summer) and the mode of production (farmhouse and dairy factory ones), gene targeting on bacteria and fungus was used to have a full picture of 3 cheese making technologies, from the raw milk to the end of the ripening. Our results revealed that Savoyard raw milks are a plenteous source of biodiversity together with the brines used during the process, that may support the development of specific features for each cheese. It was shown that rinds and curds have very contrasted ecosystem diversity, composition, and evolution. Ripening stage was selective for some bacterial species, whereas fungus were mainly ubiquitous in dairy samples. All ripening stages are impacted by the type of cheese technologies, with a higher impact on bacterial communities, except for fungal rind communities, for which the technology is the more discriminant. The specific microorganism's abundance for each technology allow to see a real bar-code, with more or less differences regarding bacterial or fungal communities. Bacterial structuration is shaped mainly by matrices, differently regarding technologies while the influence of technology is higher for fungi. Production types showed 10 differential bacterial species, farmhouses showed more ripening taxa, while dairy factory products showing more lactic acid bacteria. Meanwhile, seasonality looks to be a minor element for the comprehension of both microbial ecosystems, but the uniqueness of each dairy plant is a key explicative feature, more for bacteria than for fungus communities.

Genomic, transcriptomic, and ecological diversity of Penicillium species in cheese rind microbiomes

Although Penicillium molds can have significant impacts on agricultural, industrial, and biomedical systems, the ecological roles of Penicillium species in many microbiomes are not well characterized. Here we utilized a collection of 35 Penicillium strains isolated from cheese rinds to broadly investigate the genomic potential for secondary metabolism in cheese-associated Penicillium species, the impact of Penicillium on bacterial community assembly, and mechanisms of Penicillium-bacteria interactions. Using antiSMASH, we identified 1558 biosynthetic gene clusters, 406 of which were mapped to known pathways, including several mycotoxins and antimicrobial compounds. By measuring bacterial abundance and fungal mRNA expression when culturing representative Penicillium strains with a cheese rind bacterial community, we observed divergent impacts of different Penicillium strains, from strong inhibitors of bacterial growth to those with no impact on bacterial growth or community composition. Through differential mRNA expression analyses, Penicillium strains demonstrated limited differential gene expression in response to the bacterial community. We identified a few shared responses between the eight tested Penicillium strains, primarily upregulation of nutrient metabolic pathways, but we did not identify a conserved fungal response to growth in a multispecies community. These results in tandem suggest high variation among cheese-associated Penicillium species in their ability to shape bacterial community development and highlight important ecological diversity within this iconic genus.

Neoteric Biofilms Applied to Enhance the Safety Characteristics of Ras Cheese during Ripening

The milk's natural flora, or the starter, can preserve cheesemaking and allow for microbial competition. This investigation aimed to improve cheese safety and assess its characteristics using probiotic cell pellets (LCP) or cell-free extracts (CFS). Cheese samples were collected from different areas to investigate the current contamination situation. Six CFSs of probiotics were assessed as antifungal against toxigenic fungi using liquid and solid media and their aflatoxin reduction impact. The most effective CFS was chosen for cheese coating in nanoemulsion. Coated cheese with CFS, LCP, and LCP-CFS was assessed against control for changes in chemical composition, ripening indications, rheological properties, and microbiology. Results showed significant contamination levels in the collected samples, and toxic fungi were present. Lactobacillus rhamnosus CFS has aflatoxins reducibility in liquid media. During cheese ripening, uncoated cheese showed higher fat, protein, salt content, soluble nitrogen, total volatile fatty acids, tyrosine, and tryptophan contents than coated samples, except for LCP-coating treatment. Cheese rheology indicated that coating treatments had the lowest hardness, cohesiveness, gumminess, chewiness, and springiness compared to uncoated cheese. Uncoated cheese had the highest yeast and mold counts compared to the treated ones. The LCP-CFS-coated cheese showed no Aspergillus cells for up to 40 days. Uncoated Ras cheese recorded slightly lower flavor, body, texture, and appearance scores than coated cheeses. In conclusion, coating cheese with L. rhamnosus nanoemulsion has antifungal and antiaflatoxigenic properties, even for LCP, CFS, and CFS-LCP, which could extend cheese shelf life.