Shamsuzzaman Md, Dahal Ram Hari, Kim Shukho, Kim Jungmin
Department of Biomedical Science, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
Front Microbiol. 2023 Jul 6;14:1225282. doi: 10.3389/fmicb.2023.1225282. eCollection 2023.
Three bacterial strains, B5-R-101, TA-R-1, and BL-R-1, were isolated from the feces of a healthy Korean individual. Cells of these strains were Gram-stain-positive, facultatively anaerobic, oxidase-negative, catalase-positive, rod-shaped, and non-motile. They were able to grow within a temperature range of 10-42°C (optimum, 32-37°C), at a pH range of 2.0-10.0 (optimum, pH 5.5-8.0), and at NaCl concentration of 0.5-10.5% (w/v). All the three strains exhibited 2,2-Diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activities ranging from 58 ± 1.62 to 79 ± 1.46% (% inhibition). These strains survived in lower pH (2.0) and in 0.3% bile salt concentration for 4 h. They did not show hemolytic activity and exhibited antimicrobial activity against pathogenic bacteria, such as , , , and . The genomic analysis presented no significant concerns regarding antibiotic resistance or virulence gene content, indicating these strains could be potential probiotic candidates. Phylogenetic analysis showed that they belonged to the genus , with 98.5-99.0% 16S rRNA gene sequence similarities to other members of the genus. Their major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The abundant cellular fatty acids were C, C9, and anteiso-C. Genomic analysis of these isolates revealed the presence of genes necessary for their survival and growth in the gut environment, such as multi-subunit ATPases, stress response genes, extracellular polymeric substance biosynthesis genes, and antibacterial genes. Furthermore, the genome of each strain possessed biosynthetic gene clusters with antioxidant and antimicrobial potentials, including terpenes, saccharides, polyketides, post-translationally modified peptides (RIPPs), and non-ribosomal peptides (NRPs). DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values were lower than the thresholds to distinguish novel species. Based on phenotypic, genomic, phylogenomic, and phylogenetic analysis, these potential probiotic strains represent novel species within the genus , for which the names sp. nov. (type strain B5-R-101 = CGMCC 1.19408 = KCTC 49761), sp. nov. (type strain TA-R-1 = CGMCC 1.60014 = KCTC 49742), and sp. nov. (type strain BL-R-1 = KCTC 49735 = TBRC 17331) are proposed.
从一名健康韩国人的粪便中分离出三株细菌菌株，即B5-R-101、TA-R-1和BL-R-1。这些菌株的细胞革兰氏染色呈阳性，兼性厌氧，氧化酶阴性，过氧化氢酶阳性，杆状，无运动性。它们能够在10-42°C的温度范围内生长（最适温度为32-37°C），pH范围为2.0-10.0（最适pH为5.5-8.0），NaCl浓度为0.5-10.5%（w/v）。这三株菌株均表现出2,2-二苯基-1-苦基肼（DPPH）自由基清除活性，范围为58±1.62%至79±1.46%（抑制率）。这些菌株在较低pH（2.0）和0.3%胆盐浓度下存活4小时。它们没有表现出溶血活性，并且对致病性细菌如[此处原文缺失具体细菌名称]表现出抗菌活性。基因组分析显示在抗生素抗性或毒力基因含量方面没有重大问题，表明这些菌株可能是潜在的益生菌候选菌株。系统发育分析表明它们属于[此处原文缺失具体属名]属，与该属的其他成员16S rRNA基因序列相似性为98.5-99.0%。它们的主要极性脂质是二磷脂酰甘油和磷脂酰甘油。丰富的细胞脂肪酸是C、C9和anteiso-C。对这些分离株的基因组分析揭示了它们在肠道环境中生存和生长所需的基因，如多亚基ATP酶、应激反应基因、细胞外聚合物生物合成基因和抗菌基因。此外，每个菌株的基因组都拥有具有抗氧化和抗菌潜力的生物合成基因簇，包括萜类、糖类、聚酮类、翻译后修饰肽（RIPPs）和非核糖体肽（NRPs）。DNA-DNA杂交（dDDH）和平均核苷酸同一性（ANI）值低于区分新物种的阈值。基于表型、基因组、系统基因组和系统发育分析，这些潜在的益生菌菌株代表了[此处原文缺失具体属名]属内的新物种，为此提出了新物种名称[此处原文缺失具体新物种名称] sp. nov.（模式菌株B5-R-101 = CGMCC 1.19408 = KCTC 49761）、[此处原文缺失具体新物种名称] sp. nov.（模式菌株TA-R-1 = CGMCC 1.60014 = KCTC 49742）和[此处原文缺失具体新物种名称] sp. nov.（模式菌株BL-R-1 = KCTC 49735 = TBRC 17331）。
