School of Basic Courses, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China.
School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
Probiotics Antimicrob Proteins. 2018 Dec;10(4):748-754. doi: 10.1007/s12602-017-9337-z.
Bacterial species of Bacillus, Lactobacillus, and Bifidobacterium in the intestinal tract have been used as probiotics. Selections for probiotic candidates by the culture-based approaches are time-consuming and labor-consuming. The aim of this study was to develop a new method based on sequencing strategies to select the probiotic Bacillus, Lactobacillus, and Bifidobacterium. The Illumina-based sequencing strategies with different specific primers for Bacillus, Clostridium, and Bifidobacterium were applied to analyze diversity of the genera in goat feces. The average number of different Bacillus, Clostridium, and Bifidobacterium OTUs (operational taxonomic units) at the 97% similarity level ranged from 1922 to 63172. The coverage index values of Bacillus, Clostridium, and Bifidobacterium calculated from the bacterial OTUs were 0.89, 0.99, and 1.00, respectively. The most genera of Bacillus (37.9%), Clostridium (53%), and Bifidobacterium (99%) were detected in goat feces by the Illumina-based sequencing with the specific primers of the genera, respectively. Higher phylogenetic resolutions of the genera in goat feces were successfully established. The results suggest that the selection for probiotic Bacillus, Clostridium, and Bifidobacterium based on the Illumina sequencing with their specific primers is reliable and feasible, and the core Bacillus, Clostridium, and Bifidobacterium species of healthy goats possess the potentials as probiotic microbial consortia.
肠道中的细菌物种如芽孢杆菌、乳杆菌和双歧杆菌已被用作益生菌。基于培养的方法选择益生菌候选物既费时又费力。本研究旨在开发一种基于测序策略的新方法，用于选择益生菌芽孢杆菌、乳杆菌和双歧杆菌。本研究应用基于 Illumina 的测序策略，使用针对芽孢杆菌、梭菌和双歧杆菌的不同特异性引物，分析山羊粪便中属的多样性。在 97%相似性水平上，不同芽孢杆菌、梭菌和双歧杆菌 OTU（操作分类单位）的平均数量范围为 1922 至 63172。从细菌 OTU 计算得到的芽孢杆菌、梭菌和双歧杆菌的覆盖指数值分别为 0.89、0.99 和 1.00。通过使用属特异性引物的 Illumina 测序，分别检测到山羊粪便中芽孢杆菌（37.9%）、梭菌（53%）和双歧杆菌（99%）的属数最多。成功建立了山羊粪便中属的更高系统发育分辨率。结果表明，基于 Illumina 测序及其特异性引物选择益生菌芽孢杆菌、梭菌和双歧杆菌是可靠和可行的，健康山羊的核心芽孢杆菌、梭菌和双歧杆菌具有作为益生菌微生物群落的潜力。
