基于全基因组测序解析不同瑞士乳杆菌菌株的遗传差异——以瑞士乳杆菌H9和H10为例

Analysis of Genetic Differences between Lactobacillus helveticus Strains Based on Whole-genome Sequencing,Taking Lactobacillus helveticus H9 and H10 as Example

目的:瑞士乳杆菌是广泛用于干酪、发酵乳饮料等领域的重要发酵剂菌种之一。以瑞士乳杆菌H9和H10为例,解析不同瑞士乳杆菌菌株间的遗传背景和基因组差异,为菌株鉴定和开发应用奠定遗传学基础。方法:以瑞士乳杆菌H9和H10为例,结合NCBI数据库中其它16株瑞士乳杆菌全基因组完成图,通过比较基因组学方法探究不同菌株之间的遗传差异。结果:不同瑞士乳杆菌菌株基因组大小、质粒数量、CDSs、tRNA、rRNA数量均存在差异。系统发育分析结果显示,瑞士乳杆菌H9和H10聚类于不同进化分支。与瑞士乳杆菌H10相比,瑞士乳杆菌H9与工业发酵剂菌株瑞士乳杆菌CNRZ32的系统发育关系更近;平均核苷酸一致性(Average nucleotide identity,ANI)聚类结果与系统发育树基本一致,瑞士乳杆菌H9与H10聚类于不同类群,瑞士乳杆菌发酵乳制品分离株间的基因组序列一致性低于人类肠道/粪便分离株;与参考菌株瑞士乳杆菌DPC4571相比,瑞士乳杆菌H9和H10基因组序列中均有不同程度的片段插入、缺失和倒置;瑞士乳杆菌H9和H10特有功能基因存在差异,瑞士乳杆菌H10的特有功能基因更多涉及氨基酸和能量代谢。结论:通过比较基因组学方法分析瑞士乳杆菌基因组信息,发现不同瑞士乳杆菌菌株间存在遗传差异。

Objective:Lactobacillus(L.)helveticus is one of the important starters and widely used in cheese and fermented milk drink.This study aimed to analysis the genetic background and genomic differences of L.helveticus strains,taking L.helveticus H9 and H10 as example,which would lay the genetic foundation for the identification and development of L.helveticus strains.Method:Taking L.helveticus H9 and H10 as examples,combined with the complete genome of other 16 strains of L.helveticus in the NCBI database,the genetic differences between strains were explored by comparative genomic methods.Result:There were diversity in genome size and the number of plasmid,CDSs,tRNA and rRNA among different L.helveticus strains.Phylogenetic analysis showed that L.helveticus H9 and L.helveticus H10 clustered in different evolutionary branches,and the L.helveticus H9 has closer phylogenetic relationship with industrial starter strains L.helveticus CNRZ32 compared with L.helveticus H10.The average nucleotide identity(ANI)clustering result almost consistent with the phylogenetic tree.L.helveticus H9 and L.helveticus H10 were clustered in different groups and the genomic sequence consistency between fermented dairy product isolates were lower than homo-feces/gut isolates.Comparing with L.helveticus DPC4571,the genomic sequences of L.helveticus H9 and L.helveticus H10 both had certain fragments insertion,deletion and inversion.There were differences between the specific functional genes of L helveticus H9 and L.helveticus H10,which of L.helveticus H10 were more involved in amino acid and energy metabolism.Conclusion:Analysis of L.helveticus genome information by comparative genomic methods found genetic differences among different L.helveticus strains.