Comparative genomics of Pediococcus pentosaceus isolated from different niches reveals genetic diversity in carbohydrate metabolism and immune system

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Date
2020-02
Authors
Jiang Jie
Yang, Bo
Ross, R. Paul
Stanton, Catherine
Zhao, Jianxin
Zhang, Hao
Chen, Wei
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Volume Title
Publisher
Frontiers Media S.A.
Published Version
10.3389/fmicb.2020.00253
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Abstract
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.
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Keywords
Bacteriocin , Carbohydrate utilization , Comparative genomics , CRISPR/Cas , Genetic diversity , Pediococcus pentosaceus , Prophage
Citation
Jiang, J., Yang, B., Ross, R.P., Stanton, C., Zhao, J., Zhang, H. and Chen, W. (2020) ‘Comparative genomics of Pediococcus pentosaceus isolated from different niches reveals genetic diversity in carbohydrate metabolism and immune system’, Frontiers in Microbiology, 11, 253 (22pp). doi: 10.3389/fmicb.2020.00253
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https://hdl.handle.net/10468/14260
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APC Microbiome Ireland - Journal Articles
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© 2020 Jiang, Yang, Ross, Stanton, Zhao, Zhang and Chen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.