The ecology and viability of the microbiota of a Grana type cheese produced in the North West of Italy, was evaluated throughout manufacturing and ripening. While the microbiota diversity was evaluated by denaturing gradient gel electrophoresis (DGGE) and rRNA-based high-throughput sequencing, the enumeration of bacteria was carried out by the use of quantitative PCR (qPCR). Three different cheese productions from the same dairy plant were analysed. The application of the qPCR protocol during manufacture of the cheese until the tenth month of ripening underlined the presence of 7 Log CFU/ml in raw milk, while during ripening bacterial loads varied from 6 to 8 Log CFU/ml. The natural whey starter showed the same microbiota composition in the three productions, characterized by the presence of Lactobacillus helveticus, Lactobacillus acidophilus and Lactobacillus delbrueckii. Beta-diversity analysis of the 16S rRNA sequencing data and rRNA-DGGE showed a clear separation between the three cheese productions probably driven by the different milk used. Substantial differences among the three raw milks used in the cheese making were described, characterized by the presence of several contaminants such as Propionibacterium acnes, Acinetobacter, Pseudomonas and non starter lactic acid bacteria (NSLAB). Predicted metagenomes confirmed differences between the three batches and indicated that the presence of certain contaminants OTUs belong to milks can increased the abundance of specific metabolic pathways related to the spoilage. The present study provides a more integrated view on the viable bacterial communities during cheese manufacturing and highlights the impact of the milk quality in the development of the microbiota during the ripening.
RNA-based study of the microbiota of an Italian hard cheese during manufacture and ripening
ALESSANDRIA, Valentina;FERROCINO, ILARIO;RANTSIOU, KALLIOPI;COCOLIN, Luca Simone
2016-01-01
Abstract
The ecology and viability of the microbiota of a Grana type cheese produced in the North West of Italy, was evaluated throughout manufacturing and ripening. While the microbiota diversity was evaluated by denaturing gradient gel electrophoresis (DGGE) and rRNA-based high-throughput sequencing, the enumeration of bacteria was carried out by the use of quantitative PCR (qPCR). Three different cheese productions from the same dairy plant were analysed. The application of the qPCR protocol during manufacture of the cheese until the tenth month of ripening underlined the presence of 7 Log CFU/ml in raw milk, while during ripening bacterial loads varied from 6 to 8 Log CFU/ml. The natural whey starter showed the same microbiota composition in the three productions, characterized by the presence of Lactobacillus helveticus, Lactobacillus acidophilus and Lactobacillus delbrueckii. Beta-diversity analysis of the 16S rRNA sequencing data and rRNA-DGGE showed a clear separation between the three cheese productions probably driven by the different milk used. Substantial differences among the three raw milks used in the cheese making were described, characterized by the presence of several contaminants such as Propionibacterium acnes, Acinetobacter, Pseudomonas and non starter lactic acid bacteria (NSLAB). Predicted metagenomes confirmed differences between the three batches and indicated that the presence of certain contaminants OTUs belong to milks can increased the abundance of specific metabolic pathways related to the spoilage. The present study provides a more integrated view on the viable bacterial communities during cheese manufacturing and highlights the impact of the milk quality in the development of the microbiota during the ripening.
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