自然发酵乳中乳酸菌种内微观多样性及其生态驱动因素  

Intraspecific microdiversity and ecological drivers of lactic acid bacteria in naturally fermented milk ecosystem

作　　者：尤利军 靳昊 郭丽如 吕瑞瑞 赵志鑫 孟和毕力格 孙志宏 刘文俊 张和平 Lijun You;Hao Jin;Lai-Yu Kwok;Ruirui Lv;Zhixin Zhao;Menghe Bilige;Zhihong Sun;Wenjun Liu;Heping Zhang(Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering,Inner Mongolia Agricultural University,Hohhot 010018,China;Key Laboratory of Dairy Products Processing,Ministry of Agriculture and Rural Affairs,Inner Mongolia Agricultural University,Hohhot 010018,China;Key Laboratory of Dairy Biotechnology and Engineering,Ministry of Education,Inner Mongolia Agricultural University,Hohhot 010018,China)

机构地区：[1]Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering,Inner Mongolia Agricultural University,Hohhot 010018,China [2]Key Laboratory of Dairy Products Processing,Ministry of Agriculture and Rural Affairs,Inner Mongolia Agricultural University,Hohhot 010018,China [3]Key Laboratory of Dairy Biotechnology and Engineering,Ministry of Education,Inner Mongolia Agricultural University,Hohhot 010018,China

出　　处：《Science Bulletin》2023年第20期2405-2417,M0005,M0006,共15页科学通报（英文版）

基　　金：supported by the National Key R&D Program of China(2022YFD2100700);the National Natural Science Foundation of China(U22A20540 and 31972095);the Inner Mongolia Science&Technology Planning Project(2022YFSJ0017 and 2021PT0005);the earmarked fund for CARS36。

摘　　要：自然发酵乳制品的制作和食用已有数千年历史,其中蕴藏的微生物资源经历了千年的选择与进化,形成了稳定、可遗传的微观生态体系,但是该体系的形成原因和驱动因素尚不清楚.本研究采用培养组学技术和宏基因组学技术对来自5个国家12个地区的12份自然发酵乳制品样本中的乳酸菌微观多样性及其驱动因素进行了系统性的研究.本研究分离并测序了717株代表性的乳酸菌菌株,对自然发酵乳样本进行了深度宏基因组测序,并对其中的214株瑞士乳杆菌、97株乳酸乳球菌乳酸亚种和325株德氏乳杆菌保加利亚亚种进行了系统发育关系的分析.研究发现,同一样本中的乳酸菌菌株具有高度的种内异质性(每个样本平均含有2418~4382个单核苷酸多态性),在进化角度上被分为2~8个进化谱系.绝大多数谱系的碳水化合物和蛋白水解功能具有显著差异.通过对种内特异性基因进行溯源,发现23.93%~53.70%的基因发生水平基因转移事件.此外,样品的微生物组成与各个物种/亚种的核苷酸多样性呈显著负相关关系(r=-0.65,P<0.008).综上所述,本研究发现自然发酵乳种群组成及遗传物质交流是该微观体系的驱动因素,也为自然发酵乳制品的微生物研究提供了生态学见解.Traditional fermented milks are produced by inoculating technique,which selects well-adapted microorganisms that have been passed on through generations.Few reports have used naturally fermented milks as model ecosystems to investigate the mechanism of formation of intra-species microbial diversity.Here,we isolated and whole-genome-sequenced a total of 717 lactic acid bacterial isolates obtained from 12 independent naturally fermented milks collect from 12 regions across five countries.We further analyzed the within-sample intra-species phylogenies of 214 Lactobacillus helveticus isolates,97 Lactococcus lactis subsp.lactis isolates,and 325 Lactobacillus delbrueckii subsp.bulgaricus isolates.We observed a high degree of intra-species genomic and functional gene diversity within-/between-sample(s).Single nucleotide polymorphism-based phylogenetic reconstruction revealed great within-sample intra-species heterogeneity,evolving from multiple lineages.Further phylogenetic reconstruction(presence-absence gene profile)revealed within-sample inter-clade functional diversity(based on carbohydrate-active enzyme-and peptidase-encoding genes)in all three investigated species/subspecies.By identifying and mapping clade-specific genes of intra-sample clades of the three species/subspecies to the respective fermented milk metagenome,we found extensive potential inter-/intra-species horizontal gene transfer events.Finally,the microbial composition of the samples is closely linked to the nucleotide diversity of the respective species/subspecies.Overall,our results contribute to the conservation of lactic acid bacteria resources,providing ecological insights into the microbial ecosystem of naturally fermented dairy products.

关 键 词：自然发酵乳 德氏乳杆菌保加利亚亚种 乳酸乳球菌乳酸亚种 发酵乳制品 瑞士乳杆菌 乳酸菌种 水平基因转移 宏基因组学 

分 类 号：TS252.1[轻工技术与工程—农产品加工及贮藏工程]