A Selected Core Microbiome Drives the Early Stages of Three Popular Italian Cheese Manufactures

Abstract

Mozzarella (M), Grana Padano (GP) and Parmigiano Reggiano (PR) are three of the most important traditional Italian cheeses. In the three cheese manufactures the initial fermentation is carried out by adding natural whey cultures (NWCs) according to a back-slopping procedure. In this study, NWCs and the corresponding curds from M, GP and PR manufactures were analyzed by culture-independent pyrosequencing of the amplified V1–V3 regions of the 16S rRNA gene, in order to provide insights into the microbiota involved in the curd acidification. Moreover, culture-independent high-throughput sequencing of lacS gene amplicons was carried out to evaluate the biodiversity occurring within the S. thermophilus species. Beta diversity analysis showed a species-based differentiation between GP-PR and M manufactures indicating differences between the preparations. Nevertheless, all the samples shared a naturally-selected core microbiome, that is involved in the curd acidification. Type-level variability within S. thermophilus species was also found and twenty-eight lacS gene sequence types were identified. Although lacS gene did not prove variable enough within S. thermophilus species to be used for quantitative biotype monitoring, the possibility of using non rRNA targets for quantitative biotype identification in food was highlighted.

Metagenomics insights into food fermentations

“…Genes with high polymorphism within a species can be selected for this application, potentially allowing discrimination between different strains within a species (Ercolini et al ., 2013). In spite of the limitations due to possible sequencing errors, this application was recently exploited for monitoring Streptococcus thermophilus in whey and milk cultures and in cheeses, using lactose permease ( lacS , De Filippis et al ., 2014) and phosphoserine phosphatase ( serB , Parente et al ., 2016b; Ricciardi et al ., 2016) as species‐specific and polymorphic target genes.…”

Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food)

“…Studies on other cheeses, using pyrosequencing to gain insight into their microbiota, have also led to the definition of a common core microbiota in several cheese-making units within the same broad geo-graphic area (De Filippis et al, 2014;Fuka et al, 2013;Quigley et al, 2012). The naturally-selected core microbiome is fundamental for the maturation process in artisanal, regional cheeses.…”

“…These methods have been recently used in other dairy products, demonstrating the feasibility of generating deeply sequenced metagenomes for microbial identification and to study the dynamics of microbial communities (review by Bokulich and Mills, 2012;Ercolini, 2013). Recent studies in microbial diversity in cheeses (De Filippis et al, 2014;Ercolini et al, 2012;Masoud et al, 2011) and more specifically artisanal cheeses (Aldrete-Tapia et al, 2014;Alegría et al, 2012;Fuka et al, 2013;Quigley et al, 2012) have validated the application of this methodology in community screening to unravel the microbial structure and to detect determinants of safety and quality in cheese (Lusk et al, 2012;Montel et al, 2014;O'Sullivan et al, 2013). Pyrosequencing was chose for its sensitivity, which provided great sequence coverage and allowed to obtain a complete picture of the diverse microbial communities involved at the different fermentation times.…”

“…Pyrosequencing was chose for its sensitivity, which provided great sequence coverage and allowed to obtain a complete picture of the diverse microbial communities involved at the different fermentation times. High-throughput sequencing has allowed to detect both the core microbiome (De Filippis et al, 2014) and low-abundance microbiota (Quigley et al, 2012) in cheese samples. Low-abundance OTUs in environmental complex microbial communities make up what has been referred in the literature as the microbial rare biosphere (Pedrós-Alió, 2007;Sogin et al, 2006).…”

Probiotic Potential of Autochthone Microbiota from São Jorge and <i>Parmigiano-Reggiano</i> Cheeses

“…Previous studies performed on these products showed that the dominant microorganisms belong to the lactic acid bacteria [12]- [16]. Therefore, the objective of the current study here to isolate and identify new probiotic candidates in a bacterial collection obtained from São Jorge and Parmigiano-Reggiano cheeses.…”