SUMMARY Tractable microbial communities are needed to bridge the gap between observations of patterns of microbial diversity and mechanisms that can explain these patterns. We developed cheese rinds as model microbial communities by characterizing in situ patterns of diversity and by developing an in vitro system for community reconstruction. Sequencing of 137 different rind communities across 10 countries revealed 24 widely distributed and culturable genera of bacteria and fungi as dominant community members. Reproducible community types formed independent of geographic location of production. Intensive temporal sampling demonstrated that assembly of these communities is highly reproducible. Patterns of community composition and succession observed in situ can be recapitulated in a simple in vitro system. Widespread positive and negative interactions were identified between bacterial and fungal community members. Cheese rind microbial communities represent an experimentally tractable system for defining mechanisms that influence microbial community assembly and function.
Microbial succession during Parmigiano-Reggiano cheesemaking was monitored by length heterogeneity PCR (LH-PCR), considering the intact and lysed cells at different stages of cheese production and ripening. When starter species underwent autolysis, species coming from milk were able to grow. For the first time, the LH-PCR technique was applied to study a fermented food.Parmigiano-Reggiano (PR) is a protected-designation-of-origin cheese, produced in specific areas of Northern Italy. It is a hard-textured, cooked, and long-ripened cheese made from raw cow's milk supplemented with natural whey starter rich in thermophilic lactic acid bacteria (LAB). Microbiological features of PR have been studied, isolating on traditional growth media a large number of strains from a large amount of samples representative of production and of the earlier and advanced stages of ripening (2, 3). Other studies have focused on the biodiversity of different strains of Lactobacillus helveticus isolated from natural whey cultures (6, 7). These previous studies showed the microbial biodiversity of PR but not its real microbial succession during production and ripening, and the use of culture-dependent methods could have underestimated the less-abundant components of microflora, which are equally important for cheese ripening and flavor development (15). Thus, the microbial ecology of PR still appears not to be completely understood. From this perspective, a detailed knowledge of LAB dynamics during the manufacturing and ripening stages is necessary for a deeper insight into the complex processes which contribute to the development of this appreciated cheese.In the present study, length heterogeneity PCR (LH-PCR) was used to monitor the microbial dynamics during 24 months of PR ripening for both the whole and lysed cells. The availability of PR twin wheels allowed us to have samples representative of the subsequent stages of the same cheesemaking process.In our opinion, the new findings in this article contribute to a better understanding of microbial dynamics in a complex fermented ecosystem.Cheesemaking. A unique cheese factory was selected for its equipment and technological conditions in order to obtain a suitable number of PR twin wheels. The same milk was distributed in equal volumes in eight vats and was worked according to PR production standards.Thirty-four liters of natural whey starter was added in each vat, containing 1,070 liters of milk (525 liters of partially skimmed evening milk and 545 liters of whole morning milk), bringing the pH of the mixture to 6.20. After cheesemaking and molding, the wheels, two from each vat, were held for 3 days and frequently turned to enable complete whey drainage. They were then salted by immersion in brine at 300 g NaCl ⅐ liter Ϫ1 for 23 days. Ripening was carried out in aging rooms with 85% relative humidity and a temperature of about 18°C for 24 months.Cheese sampling and bacterial recovery. Samples were collected from milk to cheese ripened for 24 months. Aliquots of the total mass of raw...
Aims: The aim of this work was to obtain a deeper insight into the knowledge of microbial composition of Parmigiano Reggiano natural whey starters through different culture‐independent methods. Methods and Results: Eighteen different Parmigiano Reggiano natural whey starters sampled from three different provinces of this cheese production area and the nonacidified wheys from which they arose have been studied by length heterogeneity polymerase chain reaction (LH‐PCR) and fluorescent in situ hybridization (FISH). A high microbial composition variability between different samples has been observed. Conclusions: Revealing different images of the same community, LH‐PCR and FISH have given a more accurate view of the not well‐known Parmigiano Reggiano whey starter ecosystem. Significance and Impact of the Study: New lights have been shed on Parmigiano Reggiano natural whey starters microbial composition, highlighting how culture‐independent approach could be used and improved to study this and other food ecosystems.
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