中国人群格氏乳杆菌的比较分析揭示了一个新的种级分类单元。

Comparative analysis of Lactobacillus gasseri from Chinese subjects reveals a new species-level taxa.

机构信息

State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.

School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.

出版信息

BMC Genomics. 2020 Feb 3;21(1):119. doi: 10.1186/s12864-020-6527-y.

BACKGROUND

Lactobacillus gasseri as a probiotic has history of safe consumption is prevalent in infants and adults gut microbiota to maintain gut homeostasis.

RESULTS

In this study, to explore the genomic diversity and mine potential probiotic characteristics of L. gasseri, 92 strains of L. gasseri were isolated from Chinese human feces and identified based on 16 s rDNA sequencing, after draft genomes sequencing, further average nucleotide identity (ANI) value and phylogenetic analysis reclassified them as L. paragasseri (n = 79) and L. gasseri (n = 13), respectively. Their pan/core-genomes were determined, revealing that L. paragasseri had an open pan-genome. Comparative analysis was carried out to identify genetic features, and the results indicated that 39 strains of L. paragasseri harboured Type II-A CRISPR-Cas system while 12 strains of L. gasseri contained Type I-E and II-A CRISPR-Cas systems. Bacteriocin operons and the number of carbohydrate-active enzymes were significantly different between the two species.

CONCLUSIONS

This is the first time to study pan/core-genome of L. gasseri and L. paragasseri, and compare their genetic diversity, and all the results provided better understating on genetics of the two species.

背景

作为一种益生菌的格氏乳杆菌具有安全食用的历史，广泛存在于婴儿和成人的肠道微生物群中，以维持肠道内环境的稳定。

结果

在这项研究中，为了探索格氏乳杆菌的基因组多样性并挖掘其潜在的益生菌特性，从中国人的粪便中分离出 92 株格氏乳杆菌，并基于 16S rDNA 测序进行鉴定。在进行了草图基因组测序后，通过进一步的平均核苷酸同一性（ANI）值和系统发育分析，将它们重新归类为副格氏乳杆菌（n=79）和格氏乳杆菌（n=13）。确定了它们的全基因组/核心基因组，结果表明副格氏乳杆菌具有一个开放的全基因组。进行了比较分析以鉴定遗传特征，结果表明 39 株副格氏乳杆菌携带 II-A 型 CRISPR-Cas 系统，而 12 株格氏乳杆菌则含有 I-E 和 II-A 型 CRISPR-Cas 系统。两种菌的细菌素基因簇和碳水化合物活性酶的数量存在显著差异。