不同来源植物乳杆菌基因组结构和功能差异的比较研究

Comparative study on the structure and function of Lactobacillus plantarum from different ecology

摘要:

[目的] 本试验研究不同来源植物乳杆菌（Lactobacillus plantarum）基因特点以及在不同环境下其基因多样性，探究2株L.plantarum A8和P9在肠道生境及植物表面适应性的异同，为优良菌株的开发提供理论基础。[方法] 本研究对从动物肠道和植物表面分离获得的L.plantarum A8和L.plantarum P9的基因组进行分析，利用第二代测序技术（NextGeneration Sequencing，NGS），基于Illumina NovaSeq测序平台，同时利用第三代单分子测序技术，基于PacBio Sequel测序平台，对L.plantarum A8和L.plantarum P9进行测序。采用Carbohydrate-active enzymes（CAZy）、Koyto encyclopedia of genes and genomes（KEGG）和Clusters of orthologous genes（COG）数据库对基因组进行功能注释；采用CGView软件绘制菌株的基因组环形图谱。应用比较基因组学与已经公开发表的其他L.plantarum基因组进行比较分析。[结果] 由研究可知L.plantarum A8和L.plantarum P9基因组大小存在差异，通过构建系统发育树发现2株菌与其他来源的L.plantarum分在同一分支，并且L.plantarum P9与母乳来源的L.plantarum WLPL04菌株距离最近，而L.plantarum A8与L.paraplantarum DSM10667距离最近。通过基因家族分析可知，2株菌共有基因为2643个，其中包括一些抗应激蛋白如热休克蛋白、冷休克蛋白。L.plantarum A8和P9独特基因分别为321和336个，L.plantarum A8中独特基因主要参与DNA复制、ABC转运系统（ABC transfer system）、PTS系统（phosphotransferase system）、磺酸盐转运系统、氨基酸生物合成等代谢通路；L.plantarum P9的独特基因以参与碳水化合物的运输和代谢基因居多，例如rpiA基因、lacZ基因、FruA基因等。[结论] 通过比较基因组学方法解析L.plantarum的基因组信息，发现动物肠道来源的L.plantarum具有较好的氨基酸转运能力，植物表面附着的L.plantarum菌株具有较好碳水化合物利用能力，从而为益生菌的开发与利用提供理论依据。

Abstract:

[Objective] This experiment studies the genetic characteristics of Lactobacillus plantarum from different sources and its genetic diversity in different environments, and explores the similarities and differences in the adaptability of two strains of L. plantarum A8 and P9 in the animal intestine and plant surfaces, so as to provide a theoretical basis for the development of excellent strains.[Methods] This study analyzed the genomes of L. plantarum A8 and L. plantarum P9 isolated from the Animal intestines and plant surface. The research uses Next Generation Sequencing (NGS), based on the Illumina NovaSeq sequencing platform, and using the third-generation single-molecule sequencing technology, based on the PacBio Sequel sequencing platform to sequence L. plantarum A8 and L. plantarum P9. Carbohydrate-active enzymes (CAZy), Koyto encyclopedia of genes and genomes (KEGG), and Clusters of orthologous genes (COG) databases are used to annotate the genome function; CGView software is used to draw the genome circle map of the strain. At the same time, comparative genomics was used to compare with other published L. plantarum genomes.[Results] The research shows that the L. plantarum A8 and L. plantarum P9 genomes were different in genome size, the phylogenetic tree showed that the two strains were in the same branch with L. plantarum from other sources, and L. plantarum P9 was the closest to L. plantarum WLPL04 from breast milk, while L. plantarum A8 was the closest to L. paraplantarum DSM 10667. According to gene family analysis, there are 2643 common genes in the two strains, including some anti-stress proteins, such as heat shock proteins and cold shock proteins. There are 321 and 336 unique genes in plantarum A8 and P9, respectively. The unique genes in L. plantarum A8 are mainly involved in DNA replication, ABC transport system, PTS system, sulfonate transport system, amino acid biosynthesis and other metabolic pathways; The unique genes of L. plantarum P9 are mainly involved in carbohydrate transport and metabolism, such as rpiA gene, lacZ gene, fruA gene and so on.[Conclusion] By analyzing the genomic information of L. plantarum with comparative genomics method, it was found that L. plantarum from animal intestine has better amino acid transport ability, and the L. plantarum strain attached to the surface of the plant has good carbohydrate utilization ability, which provides a theoretical basis for the development and utilization of probiotics.