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Advisor(s)
Abstract(s)
This study aimed to evaluate the microbiome, resistome and virulome of two types of Portuguese cheese using
high throughput sequencing (HTS). Culture-dependent chromogenic methods were also used for certain groups/
microorganisms. Eight samples of raw ewe’s milk cheese were obtained from four producers: two producers with
cheeses with a PDO (Protected Designation of Origin) label and the other two producers with cheeses without a
PDO label. Agar-based culture methods were used to quantify total mesophiles, Enterobacteriaceae, Escherichia
coli, Staphylococcus, Enterococcus and lactic acid bacteria. The presence of Listeria monocytogenes and Salmonella
was also investigated. The selected isolates were identified by 16S rRNA gene sequencing and evaluated to
determine antibiotic resistance and the presence of virulence genes. The eight cheese samples analyzed broadly
complied with EC regulations in terms of the microbiological safety criteria. The HTS results demonstrated that
Leuconostoc mesenteroides, Lactococcus lactis, Lactobacillus plantarum, Lacticaseibacillus rhamnosus, Enterococcus
durans and Lactobacillus coryniformis were the most prevalent bacterial species in cheeses. The composition of the
bacterial community varied, not only between PDO and non-PDO cheeses, but also between producers, partic-
ularly between the two non-PDO cheeses. Alpha-diversity analyses showed that PDO cheeses had greater bac-
terial diversity than non-PDO cheeses, demonstrating that the diversity of spontaneously fermented foods is
significantly higher in cheeses produced without the addition of food preservatives and dairy ferments. Despite
complying with microbiological regulations, both PDO and non-PDO cheeses harbored potential virulence genes
as well as antibiotic resistance genes. However, PDO cheeses exhibited fewer of these virulence and antibiotic
resistance genes compared to non-PDO cheeses. Therefore, the combination of conventional microbiological
methods and the metagenomic approach could contribute to improving the attribution of the PDO label to this
type of cheese.
Description
Keywords
Raw ewe’s milk cheese Protected Designation of Origin PDO High Throughput Sequencing (HTS) Shotgun metagenomic sequencing
Pedagogical Context
Citation
Salamandane, Acácio, et al. «Metagenomic Analysis of the Bacterial Microbiome, Resistome and Virulome Distinguishes Portuguese Serra Da Estrela PDO Cheeses from Similar Non-PDO Cheeses: An Exploratory Approach». Food Research International, vol. 189, agosto de 2024, p. 114556. https://doi.org/10.1016/j.foodres.2024.114556
Publisher
Elsevier