Evaluation of bacterial communities of Grana Padano cheese by DNA metabarcoding and DNA fingerprinting analysis

Bacterial Community of Grana Padano PDO Cheese and Generical Hard Cheeses: DNA Metabarcoding and DNA Metafingerprinting Analysis to Assess Similarities and Differences

“…The 10-g cheese slices were treated as described by Zago et al [18]. Briefly, the samples were homogenized twice in a Stomacher 400 Circulator (Seward Laboratory, London, UK) with sterile sodium citrate (NaCt 2% w/v, pH 7.5).…”

“…Total DNA extracted from the 119 GP and the 49 HC samples was subjected to DNA metabarcoding analysis (IGATech, Udine, Italy) by sequencing of the variable V3-V4 regions of the 16S rRNA gene using an Illumina MiSeq platform, as described previously [18].…”

“…RAPD-PCR from total DNA of each sample was carried out according to Zago et al [18]. PCR products were separated by QIAxcel electrophoresis using dedicated DNA Screening Gel Cartridges (Qiagen, Milan, Italy).…”

“…Statistical differences (p value ≤ 0.05) and evaluation of the influence of the two cheese samplings on the microbial indexes were evaluated by ANOVA followed by the Tukey HSD test. Relative abundance for each OTU across all cheeses was calculated, and "subdominant" and "dominant" OTUs were discriminated according to Zago et al [18]. Taxonomic analysis was carried out through "reshape2" and "ggplot2" packages [22,23].…”

“…In other studies, geographic or technological differences were observed in the microbiota of cheese, suggesting it as a possible tool to establish cheese authenticity and diversity [14][15][16][17]. In a previous study, the bacterial taxa present in GP were highlighted by 16S rRNA gene sequencing (DNA metabarcoding) [18]. In the present study, the usefulness of the cheese microbiota to distinguish GP cheese from generical hard cheeses, i.e., cheeses whose appearance could be confused with Grana Padano PDO cheese, was investigated.…”