BioEngineering Department, Faculty of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey.
BMC Genomics. 2022 Dec 5;23(1):803. doi: 10.1186/s12864-022-09053-y.
Lentilactobacillus parabuchneri is of particular concern in fermented food bioprocessing due to causing unwanted gas formation, cracks, and off-flavor in fermented dairy foods. This species is also a known culprit of histamine poisonings because of decarboxylating histidine to histamine in ripening cheese. Twenty-eight genomes in NCBI GenBank were evaluated via comparative analysis to determine genomic diversity within this species and identify potential avenues for reducing health associated risks and economic losses in the food industry caused by these organisms.
Core genome-based phylogenetic analysis revealed four distinct major clades. Eight dairy isolates, two strains from an unknown source, and a saliva isolate formed the first clade. Three out of five strains clustered on clade 2 belonged to dairy, and the remaining two strains were isolated from the makgeolli and Korean effective microorganisms (KEM) complex. The third and fourth clade members were isolated from Tete de Moine and dairy-associated niches, respectively. Whole genome analysis on twenty-eight genomes showed ~ 40% of all CDS were conserved across entire strains proposing a considerable diversity among L. parabuchneri strains analyzed. After assigning CDS to their corresponding function, ~ 79% of all strains were predicted to carry putative intact prophages, and ~ 43% of the strains harbored at least one plasmid; however, all the strains were predicted to encode genomic island, insertion sequence, and CRISPR-Cas system. A type I-E CRISPR-Cas subgroup was identified in all the strains, with the exception of DSM15352, which carried a type II-A CRISPR-Cas system. Twenty strains were predicted to encode histidine decarboxylase gene cluster that belongs to not only dairy but also saliva, KEM complex, and unknown source. No bacteriocin-encoding gene(s) or antibiotic resistome was found in any of the L. parabuchneri strains screened.
The findings of the present work provide in-depth knowledge of the genomics of L. parabuchneri by comparing twenty-eight genomes available to date. For example, the hdc gene cluster was generally reported in cheese isolates; however, our findings in the current work indicated that it could also be encoded in those strains isolated from saliva, KEM complex, and unknown source. We think prophages are critical mobile elements of L. parabuchneri genomes that could pave the way for developing novel tools to reduce the occurrence of this unwanted species in the food industry.
由于在发酵乳制品中会产生不需要的气体、裂缝和异味，扁豆乳杆菌（Lentilactobacillus parabuchneri）在发酵食品生物加工中受到特别关注。由于该物种能够将组氨酸脱羧基生成组胺，因此也是组胺中毒的已知罪魁祸首。在 NCBI GenBank 中评估了 28 个基因组，通过比较分析来确定该物种内的基因组多样性，并确定减少食品工业中由这些生物体引起的与健康相关的风险和经济损失的潜在途径。
基于核心基因组的系统发育分析揭示了四个不同的主要分支。第一个分支由 8 个乳制品分离株、2 个来源不明的菌株和 1 个唾液分离株组成。属于乳制品的 5 个菌株中的 3 个聚集在分支 2 上，其余 2 个菌株分离自 makgeolli 和韩国有效微生物（KEM）复合体。第三和第四个分支成员分别分离自 Tete de Moine 和与乳制品相关的生态位。对 28 个基因组的全基因组分析表明，所有 CDS 的40%在整个菌株中保守，这表明分析的扁豆乳杆菌菌株之间存在相当大的多样性。在将 CDS 分配到其相应功能后，79%的所有菌株被预测携带完整的潜伏噬菌体，并且~43%的菌株携带至少一个质粒；然而，所有菌株都被预测携带基因组岛、插入序列和 CRISPR-Cas 系统。所有菌株中都鉴定出 I-E 型 CRISPR-Cas 亚群，除了 DSM15352，它携带 II-A 型 CRISPR-Cas 系统。20 株被预测编码组氨酸脱羧酶基因簇，该基因簇不仅存在于乳制品中，还存在于唾液、KEM 复合体和来源不明的菌株中。在筛选的所有扁豆乳杆菌菌株中都没有发现细菌素编码基因或抗生素抗性组。
通过比较迄今为止可用的 28 个基因组，本工作深入了解了扁豆乳杆菌的基因组学。例如，hdc 基因簇通常在奶酪分离株中报道；然而，我们在当前工作中的发现表明，它也可以在那些从唾液、KEM 复合体和来源不明的菌株中分离出来的菌株中编码。我们认为噬菌体是扁豆乳杆菌基因组的关键移动元件，可以为开发减少该不受欢迎物种在食品工业中出现的新工具铺平道路。
