基于比较基因组学解析耐酸乳杆菌G10的多碳源利用特征

Comparative genomics-based analysis of Lactobacillus acetotolerans G10, a strain using multiple carbon sources

摘要:

【背景】耐酸乳杆菌(Lactobacillus acetotolerans)是白酒发酵过程中的优势乳酸菌，对白酒发酵具有重要作用。L. acetotolerans G10是分离自芝麻香型白酒发酵酒醅的一株能够利用多种碳源的菌株。【目的】基于全基因组测序，解析菌株G10多碳源利用机制。【方法】通过三代测序平台Oxford Nanopore完成菌株G10全基因组测序，分别利用Circlator和Prodigal对测序数据进行组装和基因预测；通过细菌基因组分析工具(bacterial pan genome analysis tool，BPGA)进行泛基因组分析。【结果】G10能够利用22种糖类及糖类衍生物，其全基因组大小为1 627 828 bp，含有1 878个编码基因；基于Koyto Encyclopedia of Genes and Genomes (KEGG)数据库注释获得292个碳源代谢相关基因，基于Carbohydrate-Active Enzymes (CAZy)数据库注释获得44个CAZy家族的编码基因。与其他发酵食品来源的耐酸乳杆菌相比，G10基因组最小，但其总基因数量以及淀粉和蔗糖代谢相关基因数量均最多且含有426个独有基因；与发酵食品中植物乳杆菌ATCC 14917^T、发酵乳杆菌ATCC 14931^T、干酪乳杆菌ATCC 393^T、短乳杆菌ATCC 14869^T和布氏乳杆菌ATCC 4005^T等其他主要代表性乳酸菌相比，G10基因组最小，碳水化合物代谢相关基因数占比最高，而且具有glvA、malP和glvC等独有基因。【结论】L. acetotolerans G10底物选择范围广，可利用多种碳源，能够适应碳源种类多变的发酵环境，对L. acetotolerans G10基因组信息的分析为进一步阐明L. acetotolerans的发酵性能提供了遗传学基础。

关键词:耐酸乳杆菌;碳源代谢;全基因组测序;比较基因组分析

Abstract:

[Background] Lactobacillus acetotolerans is the dominant lactic acid bacteria species and plays an important role in Chinese liquor fermentation. L. acetotoleran G10, which was isolated from the fermented grains of sesame-flavor liquor, utilizes multiple carbon sources. [Objective] To analyze the mechanism for the multiple carbon source utilization of G10 based on whole genome sequencing. [Methods] The whole genome of G10 was sequenced by Oxford Nanopore Technologies, a third-generation platform for the sequencing of native DNA strands. Circlator was employed to circularize genome assemblies and Prodigal to predict genes and annotate protein-coding genes. bacterial pan genome analysis tool (BPGA) was used for pan-genome analysis. [Results] G10 was able to utilize 22 sugars and their derivatives. The genome size of G10 was 1 627 828 bp with 1 878 coding genes. G10 contained 292 genes related to carbohydrate metabolism, as annotated by Koyto Encyclopedia of Genes and Genomes (KEGG) annotation, and 44 genes related to Carbohydrate-Active EnZymes (CAZy) according to the CAZy annotation. Compared with other L. acetotolerans from food fermentations, G10 had the smallest genome with the highest numbers of total genes and genes related to starch and sucrose metabolism, and contained 426 unique genes. Compared with Lactiplantibacillus plantarum subsp. plantarum ATCC 14917^T, Limosilactobacillus fermentum ATCC 14931^T, Lacticaseibacillus casei ATCC 393^T, Levilactobacillus brevis ATCC 14869^T and Lentilactobacillus buchneri ATCC 4005^T from food fermentations. The genome of G10 was the smallest. The number of genes related to carbohydrate metabolism accounted for the highest proportion of total genes in G10. It had unique genes such as glvA, malP and glvC. [Conclusion] G10 can use a variety of carbon sources and adapt to various fermentation environments. The analysis of genomic information lays a genetic basis for further illustration of the fermentation performance of L. acetotolerans.

Key words:Lactobacillus acetotolerans;carbon source metabolism;whole genome sequencing;comparative genomics-based analysis