基于比较基因组学研究粪肠球菌乳源分离株的安全性  

Safety Evaluation of Dairy-derived Enterococcus faecalis Isolates Based on Comparative Genomic Analysis

作　　者：沈婷婷 马昕玮 路镜达 李伟程 钟智[1] Shen Tingting;Ma Xinwei;Lu Jingda;Li Weicheng;Zhong Zhi(Inner Mongolia Agricultural University,Key Laboratory of Dairy Biotechnology and Engineering,Ministry of Education,Key Laboratory of Dairy Products Processing,Ministry of Agriculture and Rural Affairs,Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering,Hohhot 010018)

机构地区：[1]内蒙古农业大学,乳品生物技术与工程教育部重点实验室,农业农村部奶制品加工重点实验室,内蒙古自治区乳品生物技术与工程重点实验室,呼和浩特010018

出　　处：《中国食品学报》2024年第5期359-372,共14页Journal of Chinese Institute Of Food Science and Technology

基　　金：内蒙古自然科学基金重点项目(2023ZD17);内蒙古自治区高等学校“青年科技英才支持项目”(NJYT24055)。

摘　　要：粪肠球菌为同型发酵乳酸菌,在食品生产中应用广泛。然而,很多粪肠球菌为条件致病菌,使其在食品中的应用存在很大的争议。本文以粪肠球菌乳源分离株为研究对象,探究粪肠球菌乳源分离株的安全性。采用Illumina Hiseq高通量测序平台对35株粪肠球菌乳源分离株进行全基因组测序,与NCBI数据库中下载的21株粪肠球菌粪便分离株进行比较基因组学分析。结果表明,粪肠球菌整体基因组长度为(2.93±0.13)Mb,GC含量在(37.43±0.13)%,转运RNA(tRNA)有(56±4)个,编码序列(CDS)数量在(2768±146)个。粪肠球菌乳源分离株平均基因组长度与粪便分离株无显著差异,而平均CDS数量显著高于粪便分离株。系统发育树结果显示同分离源的菌株聚类在同一进化分支,该结果与平均核苷酸一致性(ANI)聚类结果基本一致。乳源分离株含有5~11种耐药基因、8~24种毒力因子及18~31个可移动遗传元件,与粪便分离株相比较,乳源分离株平均每株菌少携带3个耐药基因和毒力因子,多2.4个可移动遗传元件。因此即使是在乳制品中分离得到的粪肠球菌,也存在致病的风险,使用前需要经过严格的安全性评价。Enterococcus faecalis(E.faecalis)is a homofermentative lactic acid bacterium widely used in food production.However,many E.faecalis strains are opportunistic pathogens,leading to significant controversy regarding their use in foods.This study focuses on dairy-derived isolates of E.faecalis to explore their safety.Using the Illumina HiSeq high-throughput sequencing platform,we performed whole-genome sequencing on 35 dairy-derived E.faecalis isolates and conducted comparative genomics analysis with 21 fecal isolates downloaded from the NCBI database.The results showed that the overall genome length of E.faecalis was(2.93±0.13)Mb,GC content was(37.43±0.13)%,the number of transfer RNA(tRNA)was 56±4,and the number of coding sequences(CDS)was 2768±146.There was no significant difference in the average genome length of E.faecalis milk isolates from fecal isolates,but the average number of CDS was significantly higher than that of fecal isolates.The phylogenetic tree results showed that the strains of the same segregation were clustered in the same evolutionary branch,which was basically consistent with the average nucleotide identity(ANI)clustering results.Compared with fecal isolates,each strain contained 3 less drug resistance genes and 2.4 more mobile genetic elements.Therefore,even E.faecalis isolated from dairy products has a risk of pathogenic disease and needs to undergo strict safety evaluation before use.

关 键 词：粪肠球菌 比较基因组学 乳制品 安全性评价 

分 类 号：TS201.3[轻工技术与工程—食品科学]