Comparative Genomics of Pediococcus pentosaceus Isolated From Different Niches Reveals Genetic Diversity in Carbohydrate Metabolism and Immune System

Frontiers in Microbiology

R. Paul Ross¹  Wei Chen²  Bo Yang³  Catherine Stanton⁴  Jianxin Zhao⁵  Jie Jiang⁶  Hao Zhang⁸ 

[1] APC Microbiome Ireland, University College Cork, Cork, Ireland;Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China;International Joint Research Center for Probiotics and Gut Health, Jiangnan University, Wuxi, China;Moorepark Teagasc Food Research Centre, Cork, Ireland;National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China;School of Food Science and Technology, Jiangnan University, Wuxi, China;State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China;Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, China;

关键词: Pediococcus pentosaceus;    comparative genomics;    genetic diversity;    carbohydrate utilization;    bacteriocin;    CRISPR/Cas;   

DOI  :  10.3389/fmicb.2020.00253

来源: DOAJ

【 摘 要 】

Pediococcus pentosaceus isolated from fermented food and the gastrointestinal tracts of humans and animals have been widely identified, and some strains have been reported to reduce inflammation, encephalopathy, obesity and fatty liver in animals. In this study, the genomes of 65 P. pentosaceus strains isolated from human and animal feces and different fermented food were sequenced and comparative genomics analysis was performed on all strains along with nine sequenced representative strains to preliminarily reveal the lifestyle of P. pentosaceus, and investigate the genomic diversity within this species. The results reveal that P. pentosaceus is not host-specific, and shares core genes encoding proteins related to translation, ribosomal structure and biogenesis and signal transduction mechanisms, while its genetic diversity relates mainly to carbohydrate metabolism, and horizontally transferred DNA, especially prophages and bacteriocins encoded on plasmids. Additionally, this is the first report of a type IIA CRISPR/Cas system in P. pentosaceus. This work provides expanded resources of P. pentosaceus genomes, and offers a framework for understanding the biotechnological potential of this species.

【 授权许可】

Unknown