Comprehensive scanning of prophages in Lactobacillus: Distribution, diversity, antibiotic resistance genes, and linkages with CRISPR-Cas systems

Pei, Zhangming, Sadiq, Faizan Ahmed ORCID: https://orcid.org/0000-0003-1596-4155, Han, Xiao, Zhao, Jianxin, Zhang, Hao, Ross, R. Paul, Lu, Wenwei and Chen, Wei 2021. Comprehensive scanning of prophages in Lactobacillus: Distribution, diversity, antibiotic resistance genes, and linkages with CRISPR-Cas systems. mSystems 6 (3) , 01211-20. 10.1128/msystems.01211-20

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Abstract

Prophage integration, release, and dissemination exert various effects on host bacteria. In the genus Lactobacillus, they may cause bacteriophage contamination during fermentation and even regulate bacterial populations in the gut. However, little is known about their distribution, genetic architecture, and relationships with their hosts. Here, we conducted prophage prediction analysis on 1,472 genomes from 16 different Lactobacillus species and found prophage fragments in almost all lactobacilli (99.8%), with 1,459 predicted intact prophages identified in 64.1% of the strains. We present an uneven prophage distribution among Lactobacillus species; multihabitat species retained more prophages in their genomes than restricted-habitat species. Characterization of the genome features, average nucleotide identity, and landscape visualization presented a high genome diversity of Lactobacillus prophages. We detected antibiotic resistance genes in more than 10% of Lactobacillus prophages and validated that the occurrence of resistance genes conferred by prophage integration was possibly associated with phenotypic resistance in Lactobacillus plantarum. Furthermore, our broad and comprehensive examination of the distribution of CRISPR-Cas systems across the genomes predicted type I and type III systems as potential antagonistic elements of Lactobacillus prophage.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Dentistry
Publisher:	American Society for Microbiology
ISSN:	2379-5077
Last Modified:	08 May 2024 10:00
URI:	https://orca.cardiff.ac.uk/id/eprint/168606

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