Kahraman-Ilıkkan Özge
Department of Food Processing, Baskent University, Ankara, Türkiye.
Mol Genet Genomics. 2024 Mar 13;299(1):31. doi: 10.1007/s00438-024-02129-2.
Lactic acid bacteria (LAB) can be used as a probiotic or starter culture in dairy, meat, and vegetable fermentation. Therefore, their isolation and identification are essential. Recent advances in omics technologies and high-throughput sequencing have made the identification and characterization of bacteria. This study firstly aimed to demonstrate the sensitivity of the Vitek MS (MALDI-TOF) system in the identification of lactic acid bacteria and, secondly, to characterize bacteria using various bioinformatics approaches. Probiotic potency-related genes and secondary metabolite biosynthesis gene clusters were examined. The Vitek MS (MALDI-TOF) system was able to identify all of the bacteria at the genus level. According to whole genome sequencing, the bacteria were confirmed to be Lentilactobacillus buchneri, Levilactobacillus brevis, Lactiplantibacillus plantarum, Levilactobacillus namurensis. Bacteria had most of the probiotic potency-related genes, and different toxin-antitoxin systems such as PemIK/MazEF, Hig A/B, YdcE/YdcD, YefM/YoeB. Also, some of the secondary metabolite biosynthesis gene clusters, some toxic metabolite-related genes, and antibiotic resistance-related genes were detected. In addition, Lentilactobacillus buchneri Egmn17 had a type II-A CRISPR/Cas system. Lactiplantibacillus plantarum Gmze16 had a bacteriocin, plantaricin E/F.
乳酸菌（LAB）可作为益生菌或发酵剂用于乳制品、肉类和蔬菜发酵。因此，对它们的分离和鉴定至关重要。组学技术和高通量测序的最新进展已实现细菌的鉴定和表征。本研究首先旨在证明Vitek MS（基质辅助激光解吸电离飞行时间质谱）系统在乳酸菌鉴定中的敏感性，其次使用各种生物信息学方法对细菌进行表征。检测了与益生菌效力相关的基因和次级代谢产物生物合成基因簇。Vitek MS（基质辅助激光解吸电离飞行时间质谱）系统能够在属水平上鉴定所有细菌。根据全基因组测序，这些细菌被确认为布氏扁豆乳杆菌、短乳杆菌、植物乳杆菌、那慕尔乳杆菌。这些细菌具有大多数与益生菌效力相关的基因，以及不同的毒素-抗毒素系统，如PemIK/MazEF、Hig A/B、YdcE/YdcD、YefM/YoeB。此外，还检测到一些次级代谢产物生物合成基因簇、一些与有毒代谢产物相关的基因以及与抗生素抗性相关的基因。此外，布氏扁豆乳杆菌Egmn17具有II-A型CRISPR/Cas系统。植物乳杆菌Gmze16具有一种细菌素，即植物乳杆菌素E/F。
