Comparative genomics of four lactic acid bacteria identified with Vitek MS (MALDI-TOF) and whole-genome sequencing.

IF 2.3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Molecular Genetics and Genomics Pub Date : 2024-03-13 DOI:10.1007/s00438-024-02129-2

Özge Kahraman-Ilıkkan

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Abstract

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.

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利用 Vitek MS（MALDI-TOF）和全基因组测序鉴定的四种乳酸菌的比较基因组学。

乳酸菌（LAB）可用作乳制品、肉类和蔬菜发酵中的益生菌或启动培养物。因此，分离和鉴定它们至关重要。近年来，全息技术和高通量测序技术的进步使得细菌的鉴定和表征变得更加容易。本研究首先旨在证明 Vitek MS（MALDI-TOF）系统在鉴定乳酸菌方面的灵敏度，其次利用各种生物信息学方法鉴定细菌的特征。研究了益生菌效力相关基因和次级代谢物生物合成基因簇。Vitek MS（MALDI-TOF）系统能够对所有细菌进行属级鉴定。根据全基因组测序，这些细菌被确认为布氏扁豆乳杆菌、布氏左旋乳杆菌、植物乳杆菌和纳姆雷氏左旋乳杆菌。这些细菌拥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，还检测到一些次生代谢物生物合成基因簇、一些有毒代谢物相关基因和抗生素耐药性相关基因。此外，布氏扁豆乳杆菌 Egmn17 还具有 II-A 型 CRISPR/Cas 系统。植物乳杆菌 Gmze16 含有一种细菌素植物素 E/F。

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来源期刊

Molecular Genetics and Genomics 生物-生化与分子生物学

CiteScore

5.10

自引率

3.20%

发文量

134

审稿时长

1 months

期刊介绍： Molecular Genetics and Genomics (MGG) publishes peer-reviewed articles covering all areas of genetics and genomics. Any approach to the study of genes and genomes is considered, be it experimental, theoretical or synthetic. MGG publishes research on all organisms that is of broad interest to those working in the fields of genetics, genomics, biology, medicine and biotechnology. The journal investigates a broad range of topics, including these from recent issues: mechanisms for extending longevity in a variety of organisms; screening of yeast metal homeostasis genes involved in mitochondrial functions; molecular mapping of cultivar-specific avirulence genes in the rice blast fungus and more.