Post-Graduate Program in Health Sciences, Universidade Federal do Rio Grande - FURG, Faculty of Medicine, Academic Area of the University Hospital, Rio Grande, RS, Brazil.
Bioinformatics Laboratory, Technological Development Center, Federal University of Pelotas, Capão do Leão, Rio Grande do Sul, Brazil.
Braz J Microbiol. 2023 Dec;54(4):2733-2743. doi: 10.1007/s42770-023-01139-3. Epub 2023 Oct 6.
Lactic acid bacteria (LAB) are fermentative microorganisms and perform different roles in biotechnological processes, mainly in the food and pharmaceutical industries. Among the LAB, Lactobacillus acidophilus is a species that deserves to be highlighted for being used both in prophylaxis and in the treatment of pathologies. Most of the metabolites produced by this species are linked to the inhibition of pathogens. In this study, we utilized a pangenomic and metabolic annotation analysis using Roary and BlastKOALA, ML-based probiotic activity prediction with iProbiotic and whole-genome similarity using ANI to identify strains of L. acidophilus with potential probiotic activity. According to the results in BlastKOALA and iProbiotics, L. acidophilus NCTC 13721 had the greatest potential among the 64 strains tested, both in terms of its ability to be a Lactobacillus spp. probiotic, when in the amount of genes involved in the metabolism of organic acids and quorum sensing. In addition, DSM 20079 proved to be promising for prospecting new probiotic Lactobacillus from BlastKOALA analyses, as they presented similar results in the number of genes involved in the production of lactic acid, acetic acid, hydrogen peroxide, except for quorum sensing where the NCTC 13721 strain had 14 more genes. L. acidophilus NCTC 13721 and L. acidophilus La-5 strains showed greater ability to be Lactobacillus spp. probiotic capacity, showing 84.8% and 51.9% capacity in the iProbiotics tool, respectively. When analyzed in ANI, none of the evaluated strains showed genomic similarity with NCTC 13721. In contrast, the DSM 20079 strain showed genomic similarity with all evaluated strains except NCTC 13721. Furthermore, eight strains with characteristics with approximately 100% genomic similarity to La-5 were listed: S20_1, LA-5, FSI4, APC2845, LA-G80-111, DS1_1A, LA1, and BCRC 14065. Therefore, according to the findings in iProbiotics and BlastKoala, among the 64 strains evaluated, NCTC 13721 is the most promising strain to be used for future in vitro studies.
乳酸菌（LAB）是发酵微生物，在生物技术过程中发挥着不同的作用，主要在食品和制药行业。在乳酸菌中，嗜酸乳杆菌是一种值得突出的物种，因为它既可以用于预防又可以用于治疗疾病。该物种产生的大多数代谢物都与抑制病原体有关。在这项研究中，我们使用了 Roary 和 BlastKOALA 进行泛基因组和代谢注释分析，使用 iProbiotic 进行基于 ML 的益生菌活性预测，以及使用 ANI 进行全基因组相似性分析，以鉴定具有潜在益生菌活性的嗜酸乳杆菌菌株。根据 BlastKOALA 和 iProbiotics 的结果，在测试的 64 株菌株中，NCTC 13721 株在涉及代谢有机酸和群体感应的基因数量方面具有最大的潜力，成为乳酸杆菌属益生菌的潜力最大。此外，DSM 20079 株从 BlastKOALA 分析中被证明是有前途的新益生菌乳杆菌的候选者，因为它们在涉及生产乳酸、乙酸、过氧化氢的基因数量方面呈现出相似的结果，除了群体感应，其中 NCTC 13721 株有 14 个更多的基因。嗜酸乳杆菌 NCTC 13721 株和嗜酸乳杆菌 La-5 株在 iProbiotics 工具中分别显示出 84.8%和 51.9%的乳酸杆菌属益生菌能力，表现出更大的成为益生菌的能力。当在 ANI 中进行分析时，没有一株评估的菌株与 NCTC 13721 株显示出基因组相似性。相比之下，DSM 20079 株与除 NCTC 13721 株以外的所有评估菌株显示出基因组相似性。此外，列出了 8 株与 La-5 株具有约 100%基因组相似性的特征的菌株：S20_1、LA-5、FSI4、APC2845、LA-G80-111、DS1_1A、LA1 和 BCRC 14065。因此，根据 iProbiotics 和 BlastKoala 的发现，在评估的 64 株菌株中，NCTC 13721 株是最有希望用于未来体外研究的菌株。
