Ecology of lactobacilli present in Italian cheeses produced from raw milk.

Among the bacterial genera that are employed for cheese production, Lactobacillus is a key taxon of high industrial relevance being commonly present in commercial starter cultures for dairy fermentations. Certain lactobacilli play a defining role in the development of the organoleptic features during the ripening stages of particular cheeses. We performed an in depth 16S rRNA gene-based microbiota analysis coupled with ITS-mediated Lactobacillus compositional profiling of 21 common Italian cheeses produced from raw milk in order to evaluate the ecological distribution of lactobacilli associated with this food matrix. Statistical analysis of the collected data revealed the existence of putative Lactobacillus Community State Types (LCSTs), which consist of clusters of Lactobacillus (sub)species. Each LCST is dominated by one or two taxa that appear to represent key stone elements of an elaborate network of positive and negative interactions with minor components of the cheese microbiota. The results obtained in this study reveal the existence of peculiar cheese microbiota assemblies that represent intriguing targets for further functional studies aimed at dissecting the species-specific role of bacteria in cheese manufacturing. Importance The microbiota is known to play a key role in the development of the organoleptic features of dairy products. Lactobacilli have been reported to represent one of the main components of the non-starter bacterial population, i.e. bacteria that are not deliberately added to the milk, harbored by cheese, although the species-level composition of this microbial population has never been assessed in detail. In the current study, we applied a recently developed metagenomic approach that employs the Internally Transcribed Spacer to profile the Lactobacillus population harbored by cheese produced from raw milk at (sub)species level. The obtained data revealed the existence of particular Lactobacillus Community State Types (LCSTs) consisting of clusters of Lactobacillus (sub)species that tend to co-occur in the screened cheeses. Moreover, analysis of co-variances between members of this genus indicate that these taxa form an elaborate network of positive and negative interactions that define specific Clusters of Covariant Lactobacilli (CCL).