Genomic insights into prophage and CRISPR-Cas system present in Lactobacillus delbrueckii subsp. bulgaricus strains.
- 2026-03
- Food research international (Ottawa, Ont.) 227
- PubMed: 41652748
- DOI: 10.1016/j.foodres.2025.118213
Study Design
- Sample size
- n = 1,704
- Population
- 119 L. bulgaricus strains
- Methods
- Bioinformatics analysis to investigate the distribution of prophages and the structure of the CRISPR-Cas system in 119 L. bulgaricus strains, and explored the targeting relationship between them and annotated the functional genes of targeted prophages
As a key starter culture for yogurt fermentation, Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) was subjected to bioinformatics analysis to investigate the distribution of prophages and the structure of the CRISPR-Cas system in 119 L. bulgaricus strains, and explored the targeting relationship between them and annotated the functional genes of targeted prophages. A total of 1704 prophage fragments were identified, of which 8.74 % (149/1704) were classified as complete prophages, none of them carried virulence factor genes and antibiotic resistance genes. Among all complete prophage genomes, the GC content was significantly affected by geographical sources (Asia, Europe, and North America) of host bacteria (P < 0.01). The 123 CRISPR-Cas systems detected in L. bulgaricus, type I-E (69) and type II-A (40) systems were predominant. Spacers-prophages targeting analysis revealed a negative correlation (P < 0.05), with 23.43 % (1055/4503) spacers showing homology to prophages. Functional gene annotation revealed that the diversity of prophage functional genes showed significant differences in under different grouping conditions (P < 0.05). Nevertheless, in-depth analysis of targeted prophage genomes revealed a conserved functional gene--ABC transporter. This study provides data support for exploring the genomic diversity and adaptive evolution mechanism of prophages in L. bulgaricus, and providing insights for screening phage-resistant strains and developing novel anti-phage strategies in dairy industry.
Research Insights
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