At present, the Lactobacillus fermentum 90 TC-4 strain is widely used for production of probiotics, dietary supplements, and food. It is for this reason that it is topical to study this strain using modern molecular genetic methods. The biochemical properties of the strain were examined using the API 50 CHL test system (BioMerieux, France), genome sequencing was carried out using the MiSeq (Illumina) platform, and de novo genome assembly was performed using the Spades, MIRA 4.0, and Newbler 2.6 software. Genome annotation was carried out with the help of the Prokka v. 1.11 utility and RAST and BASys genomic servers. The main characteristics of the L. fermentum 90 TC-4 genome were established. It was proven that the genome does not have any determinants of pathogenicity, virulence or antibiotic resistance. It was shown that the low saccharolytic ability of the strain is associated with the absence of appropriate transport systems—the sucrose-specific phosphonolpyruvate system PTS_ScrA and ribose-specific RbsD permease—as well as several enzymes. The CRISPR-Cas locus of the strain was analyzed, unique spacers (which in future can be used for strain indication) were revealed, and molecular mechanisms of antibiotic resistance of the strain were studied. Using the MLST scheme presented in the scientific literature, allelic profiles of housekeeping genes were established. It was also found that the allelic profile obtained for the L. fermentum 90 TC-4 strain does not correspond to any of the previously described sequence types. Since L. fermentum 90 TC-4 does not have determinants of antibiotic resistance, pathogenicity, virulence, or integrated plasmids, the strain does not pose any hazard in terms of spread of these determinants and can be used as a probiotic producer strain. The observed features of the CRISPR locus and allelic profile can further be used to indicate the strain.

中文翻译：

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发酵乳杆菌90 TC-4生产菌株基因组的生物信息学分析

目前，发酵乳杆菌 90 TC-4 菌株广泛用于益生菌、膳食补充剂和食品的生产。正是出于这个原因，使用现代分子遗传学方法研究该菌株是热门话题。菌株的生化特性采用API 50 CHL检测系统（BioMerieux，France）进行检测，基因组测序采用MiSeq（Illumina）平台进行，基因组de novo组装采用Spades、MIRA 4.0和Newbler进行2.6 软件。基因组注释是在 Prokka v. 1.11 实用程序以及 RAST 和 BASys 基因组服务器的帮助下进行的。确定了发酵乳杆菌 90 TC-4 基因组的主要特征。已证明基因组不具有致病性、毒力或抗生素抗性的任何决定因素。结果表明，该菌株的低糖分解能力与缺乏适当的转运系统（蔗糖特异性膦酰丙酮酸系统 PTS_ScrA 和核糖特异性 RbsD 通透酶）以及几种酶有关。分析了该菌株的 CRISPR-Cas 基因座，揭示了独特的间隔区（将来可用于菌株指示），并研究了该菌株抗生素耐药性的分子机制。使用科学文献中提出的 MLST 方案，建立了看家基因的等位基因图谱。还发现为发酵乳杆菌 90 TC-4 菌株获得的等位基因谱不对应于任何先前描述的序列类型。由于发酵乳杆菌 90 TC-4 不具有抗生素抗性、致病性、毒力的决定因素，或整合质粒，该菌株不会对这些决定因素的传播造成任何危害，并可用作益生菌生产菌株。观察到的 CRISPR 基因座特征和等位基因谱可进一步用于指示菌株。