LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal; Faculdade de Ciências de Saúde, Universidade Lúrio, Campus Universitário de Marrere, Nampula 4250, Mozambique.
Teagasc Food Research Centre, Fermoy, Cork, Ireland.
Food Res Int. 2024 Aug;189:114556. doi: 10.1016/j.foodres.2024.114556. Epub 2024 May 27.
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, particularly between the two non-PDO cheeses. Alpha-diversity analyses showed that PDO cheeses had greater bacterial 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.
本研究旨在使用高通量测序（HTS）评估两种葡萄牙奶酪的微生物组、抗性组和毒力组。还使用基于培养的显色方法来检测某些菌群/微生物。从四个生产商处获得了 8 个生羊奶奶酪样本：两个生产商的奶酪带有 PDO（受保护的原产地名称）标签，另外两个生产商的奶酪则没有 PDO 标签。基于琼脂的培养方法用于定量总需氧菌、肠杆菌科、大肠杆菌、葡萄球菌、肠球菌和乳酸菌。还调查了李斯特菌和沙门氏菌的存在情况。通过 16S rRNA 基因测序对所选分离株进行鉴定，并评估其抗生素抗性和毒力基因的存在情况。对这 8 个奶酪样本进行了分析，结果表明，从微生物安全标准方面来看，这些奶酪均广泛符合欧盟法规的要求。HTS 结果表明，肠膜明串珠菌、乳球菌乳脂亚种、植物乳杆菌、鼠李糖乳杆菌、耐久肠球菌和乳杆菌科乳杆菌是奶酪中最常见的细菌物种。细菌群落的组成不仅在 PDO 和非 PDO 奶酪之间存在差异，而且在生产商之间也存在差异，特别是在两种非 PDO 奶酪之间。α多样性分析表明，PDO 奶酪的细菌多样性大于非 PDO 奶酪，这表明在没有添加食品防腐剂和乳制品发酵剂的情况下，自发发酵食品的多样性显著更高。尽管符合微生物学法规，但 PDO 和非 PDO 奶酪都携带有潜在的毒力基因和抗生素抗性基因。然而，与非 PDO 奶酪相比，PDO 奶酪携带的这些毒力基因和抗生素抗性基因较少。因此，将传统微生物学方法与宏基因组方法相结合，可能有助于提高此类奶酪的 PDO 标签的归属。
