{"title":"LIMOSILACTORBACILUS PONTIS 菌株的比较基因组学:特定生态区的变异和适应性","authors":"Xueyan Lei, Qing Liu, Weicheng Li, Yu Li, Lixia Zhao, Wenjun Liu","doi":"10.3390/d16070380","DOIUrl":null,"url":null,"abstract":"Limosilactobacillus pontis (L. pontis) is a species of lactic acid bacteria (LAB) found in various products, including fermented milk, sourdough, and broiler chickens’ gastrointestinal tracts. However, the evolutionary strategies and genomic features of the species remain unknown, which limits its application. In this study, whole-genome sequencing was carried out to investigate the genomic characteristics and evolutionary strategies of L. pontis, combined with a comparative genomic approach, providing the necessary theoretical basis for its application. The genomic sequences in this study included three published genomic sequences and two strains isolated from fermented milk in our lab in Inner Mongolia, China. The mean genome size of the five L. pontis strains was 1.70 Mb, and the mean DNA G + C content was 53.06%. L. pontis was a species with higher G + C content in LAB. The phylogenetic evolutionary tree for the core genes showed that the strains from the same sources were aggregated into a cluster. There were some differences in the genomic information and phylogenetic relationships amongst L. pontis from different sources. An analysis of the annotation results identified differences in the functional genes, carbohydrate-active enzymes, and bacteriocins amongst different isolated strains, which were related to the environment. L. pontis was rich in glycosyltransferases, especially in strains isolated from fermented milk, indicating that they had higher sugar synthesis abilities. It is worth mentioning that only the L. pontis strains isolated in our laboratory identified the bacteriocin operon, which may increase its application potential. The genomic characteristics and evolutionary process of L. pontis were analyzed by comparative genomics, and this study explored the differences in the functional genes amongst the strains, aiming to provide new insights into the genetic characteristics and niche adaptations of L. pontis.","PeriodicalId":501149,"journal":{"name":"Diversity","volume":"229 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Comparative Genomics of Limosilactobacillus pontis Strains: Niche-Specific Variations and Adaptations\",\"authors\":\"Xueyan Lei, Qing Liu, Weicheng Li, Yu Li, Lixia Zhao, Wenjun Liu\",\"doi\":\"10.3390/d16070380\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Limosilactobacillus pontis (L. pontis) is a species of lactic acid bacteria (LAB) found in various products, including fermented milk, sourdough, and broiler chickens’ gastrointestinal tracts. However, the evolutionary strategies and genomic features of the species remain unknown, which limits its application. In this study, whole-genome sequencing was carried out to investigate the genomic characteristics and evolutionary strategies of L. pontis, combined with a comparative genomic approach, providing the necessary theoretical basis for its application. The genomic sequences in this study included three published genomic sequences and two strains isolated from fermented milk in our lab in Inner Mongolia, China. The mean genome size of the five L. pontis strains was 1.70 Mb, and the mean DNA G + C content was 53.06%. L. pontis was a species with higher G + C content in LAB. The phylogenetic evolutionary tree for the core genes showed that the strains from the same sources were aggregated into a cluster. There were some differences in the genomic information and phylogenetic relationships amongst L. pontis from different sources. An analysis of the annotation results identified differences in the functional genes, carbohydrate-active enzymes, and bacteriocins amongst different isolated strains, which were related to the environment. L. pontis was rich in glycosyltransferases, especially in strains isolated from fermented milk, indicating that they had higher sugar synthesis abilities. It is worth mentioning that only the L. pontis strains isolated in our laboratory identified the bacteriocin operon, which may increase its application potential. The genomic characteristics and evolutionary process of L. pontis were analyzed by comparative genomics, and this study explored the differences in the functional genes amongst the strains, aiming to provide new insights into the genetic characteristics and niche adaptations of L. pontis.\",\"PeriodicalId\":501149,\"journal\":{\"name\":\"Diversity\",\"volume\":\"229 1\",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-06-29\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Diversity\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.3390/d16070380\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Diversity","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.3390/d16070380","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
摘要
庞氏乳酸菌(Limosilactobacillus pontis,L. pontis)是一种乳酸菌(LAB),存在于发酵牛奶、酸面团和肉鸡胃肠道等多种产品中。然而,该物种的进化策略和基因组特征仍然未知,这限制了其应用。本研究通过全基因组测序,结合比较基因组学方法,研究了蓬莱藻的基因组特征和进化策略,为其应用提供了必要的理论基础。本研究的基因组序列包括三个已发表的基因组序列和我们在中国内蒙古实验室从发酵乳中分离的两个菌株。五株L. pontis菌株的平均基因组大小为1.70 Mb,平均DNA G + C含量为53.06%。L.pontis是LAB中G + C含量较高的物种。核心基因的系统进化树显示,相同来源的菌株聚集成一个群集。不同来源的 L. pontis 在基因组信息和系统进化关系上存在一些差异。对注释结果的分析发现,不同分离菌株的功能基因、碳水化合物活性酶和细菌素存在差异,这与环境有关。庞氏梭菌富含糖基转移酶,尤其是从发酵牛奶中分离的菌株,这表明它们具有较高的糖合成能力。值得一提的是,只有本实验室分离的蓬菌菌株鉴定出了细菌素操作子,这可能会增加其应用潜力。本研究通过比较基因组学分析了蓬球菌的基因组特征和进化过程,探讨了菌株间功能基因的差异,旨在为了解蓬球菌的遗传特征和生态位适应性提供新的视角。
Comparative Genomics of Limosilactobacillus pontis Strains: Niche-Specific Variations and Adaptations
Limosilactobacillus pontis (L. pontis) is a species of lactic acid bacteria (LAB) found in various products, including fermented milk, sourdough, and broiler chickens’ gastrointestinal tracts. However, the evolutionary strategies and genomic features of the species remain unknown, which limits its application. In this study, whole-genome sequencing was carried out to investigate the genomic characteristics and evolutionary strategies of L. pontis, combined with a comparative genomic approach, providing the necessary theoretical basis for its application. The genomic sequences in this study included three published genomic sequences and two strains isolated from fermented milk in our lab in Inner Mongolia, China. The mean genome size of the five L. pontis strains was 1.70 Mb, and the mean DNA G + C content was 53.06%. L. pontis was a species with higher G + C content in LAB. The phylogenetic evolutionary tree for the core genes showed that the strains from the same sources were aggregated into a cluster. There were some differences in the genomic information and phylogenetic relationships amongst L. pontis from different sources. An analysis of the annotation results identified differences in the functional genes, carbohydrate-active enzymes, and bacteriocins amongst different isolated strains, which were related to the environment. L. pontis was rich in glycosyltransferases, especially in strains isolated from fermented milk, indicating that they had higher sugar synthesis abilities. It is worth mentioning that only the L. pontis strains isolated in our laboratory identified the bacteriocin operon, which may increase its application potential. The genomic characteristics and evolutionary process of L. pontis were analyzed by comparative genomics, and this study explored the differences in the functional genes amongst the strains, aiming to provide new insights into the genetic characteristics and niche adaptations of L. pontis.