母乳源乳双歧杆菌Probio-M8的遗传特征及基因组差异比较分析

Genetic characteristics and functional genes of Bifidobacterium animalis subsp. lactis Probio-M8 from breast milk

摘要:

【目的】母乳源乳双歧杆菌(Bifidobacterium animalis subsp.lactis) Probio-M8具有优良的益生特性，本文拟从全基因组水平解析Probio-M8的遗传特征，并与已有益生功效的乳双歧杆菌的基因组进行比较分析。【方法】本研究基于NCBI已公开的21株乳双歧杆菌和1株模式菌株DSM10140^T的基因组数据，构建了核心基因集与泛基因集，解析该群体的系统发育关系，比较分析Probio-M8的遗传特征及功能基因组。【结果】22株乳双歧杆菌的泛基因集包含1 618个基因，其中核心基因1 514个，占泛基因集的93.57%，表明乳双歧杆菌核心基因集高度保守。以1 514个核心基因构建系统发育树，发现22株乳双歧杆菌分为两个分支，AD011单独为一个分支，Probio-M8和其他菌株与模式菌株DSM10140^T聚在同一分支，且Probio-M8与V9、BB-12、Bi-07、HN019的遗传距离极为接近。进一步分析耐药基因和毒力基因，在Probio-M8与V9、BB-12、Bi-07、HN019基因组上均检测到DfrA43、tetW及rpoB 3种拷贝数完全一致的固有耐药基因，且均不含毒力基因。碳水化合物代谢活性酶注释结果发现，Probio-M8与V9、Bi-07、BB-12和HN019均编码47个碳水化合物代谢相关基因的家族，其中，Bi-07缺少GH49基因，且少一个GH13基因的拷贝，而Probio-M8多一个GH49基因的拷贝，显示Probio-M8与V9、BB-12、Bi-07和HN019具有相似的碳水化合物代谢相关基因。【结论】本研究从全基因组水平完成了对22株乳双歧杆菌的比较分析，发现乳双歧杆菌的核心基因集高度保守，Probio-M8与V9、BB-12、Bi-07和HN019四株益生菌的遗传特征高度相似，基因组差异较小，为Probio-M8的后续研究提供数据支持。

关键词:乳双歧杆菌;比较基因组;碳水化合物酶

Abstract:

[Objective] Breast milk-derived Bifidobacterium animalis subsp. lactis Probio-M8 has excellent probiotic properties. We analyzed the genetic characteristics of Probio-M8 at the genome-wide level and compared the genomes between Probio-M8 and other B.animalis subsp. lactis strains with probiotic efficacy. [Methods] We constructed the core gene set and pan gene set based on the genome data of 21 strains and 1 model strain DSM10140^T of B.animalis subsp. lactis in the NCBI database. Further, we constructed a phylogenetic relationship of this population and analyzed the genetic characteristics and functional genes of Probio-M8. [Results] The pan gene set of the 22 strains contained 1 618 genes, including 1 514 (93.57%) core genes, which indicated the core gene set was highly conserved. A phylogenetic tree was constructed based on the 1 514 core genes, which showed that AD011 was in a single branch, while Probio-M8 and the other strains were in the same clade with the type strain DSM10140^T. Probio-M8 had short genetic distance with V9, BB-12, Bi-07, and HN019. The genomes of Probio-M8, V9, BB-12, Bi-07, and HN019 carried three inherent resistance genes dfrA43, tetW, and rpoB with the same copy number among strains and did not contain virulence genes, which indicated the virulence and resistance genes were conserved. Furthermore, Probio-M8, V9, BB-12, and HN019 all had 47 carbohydrate metabolism-related genes. Bi-07 lacked GH49 gene and one GH13 gene copy, while Probio-M8 had an extra copy of GH49 gene, which indicated that the 5 probiotic strains had similar genes for carbohydrate metabolism. [Conclusion] The core gene set is highly conserved among the 22 strains of B.animalis subsp. lactis. The strains Probio-M8, V9, BB-12, Bi-07, and HN019 have similar genetic characteristics. This article supplies data support for the follow-up studies of Probio-M8.

Key words:Bifidobacterium animalis subsp. lactis;comparative genomics;carbohydrase