Analysis of Probiotic Bacteria Genomes: Comparison of CRISPR/Cas Systems and Spacer Acquisition Diversity

Kahraman-Ilıkkan, Özge

doi:10.1007/s12088-021-00971-1

Cited by 9 publications

(3 citation statements)

References 46 publications

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“…As depicted in Supplementary Figure S1 , subtype II-A encompasses Cas2, Cas1, Cas9, and the characteristic Cas gene (Csn2). Consistent with earlier research, the outcomes suggested the prevalence of subtype II-A in LAB ( Yang et al, 2020 ; Kahraman Ilıkkan, 2022 ; Panahi et al, 2022 ). Previous studies have focused on identifying and characterizing CRISPR-Cas systems in diverse bacteria ( Van Der Oost et al, 2014 ; Hidalgo-Cantabrana et al, 2019 ).…”

Section: Resultssupporting

confidence: 86%

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CRISPR-Cas systems feature and targeting phages diversity in Lacticaseibacillus rhamnosus strains

Panahi,

Dehganzad,

Nami

2023

Front. Microbiol.

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One of the most important adaptive immune systems in bacteria against phages is clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (CAS) genes. In this investigation, an approach based on genome mining was employed to characterize the CRISPR-Cas systems of Lacticaseibacillus rhamnosus strains. The analysis involved retrieving complete genome sequences of L. rhamnosus strains, and assessing the diversity, prevalence, and evolution of their CRISPR-Cas systems. Following this, an analysis of homology in spacer sequences from identified CRISPR arrays was carried out to investigate and characterize the range of target phages. The findings revealed that 106 strains possessed valid CRISPR-Cas structures (comprising CRISPR loci and Cas genes), constituting 45% of the examined L. rhamnosus strains. The diversity observed in the CRISPR-Cas systems indicated that all identified systems belonged to subtype II-A. Analyzing the homology of spacer sequences with phage and prophage genomes discovered that strains possessing only CRISPR-Cas subtype II targeted a broader spectrum of foreign phages. In summary, this study suggests that while there is not significant diversity among the CRISPR-Cas systems identified in L. rhamnosus strains, there exists notable variation in subtype II-A systems between L. rhamnosus and other lactobacilli. The diverse nature of these CRISPR-Cas systems underscores their natural activity and importance in adaptive immunity.

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Section: Resultssupporting

confidence: 86%

“…These repeats separated by unique sequences called spacers. The spacer sequences are obtained often from an invasive plasmid or bacteriophage and are incorporated into the bacterial crisper ( Kahraman Ilıkkan, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

CRISPR-Cas systems feature and targeting phages diversity in Lacticaseibacillus rhamnosus strains

Panahi,

Dehganzad,

Nami

2023

Front. Microbiol.

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show abstract

“…Researchers have found that the CRISPR/Cas system, which uses spacers derived from invading elements to control the immune response in a sequence-specific way, protects prokaryotes from viruses ( Barrangou and Horvath, 2012 ). As a result, the spacer repertoire might represent the lifestyle of bacteria ( Ilıkkan and Özge, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Molecular and bacteriological investigations for the co-existence CRISPR/Cas system and β-lactamases of types extended-spectrum and carbapenemases in Multidrug, extensive drug and Pandrug-Resistant Klebsiella pneumoniae

Owaid,

Al-Ouqaili

2024

Saudi Journal of Biological Sciences

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Insights from metagenome-assembled genomes on the genetic stability and safety of over-the-counter probiotic products

2023

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Analysis of Probiotic Bacteria Genomes: Comparison of CRISPR/Cas Systems and Spacer Acquisition Diversity

Cited by 9 publications

References 46 publications

CRISPR-Cas systems feature and targeting phages diversity in Lacticaseibacillus rhamnosus strains

CRISPR-Cas systems feature and targeting phages diversity in Lacticaseibacillus rhamnosus strains

Molecular and bacteriological investigations for the co-existence CRISPR/Cas system and β-lactamases of types extended-spectrum and carbapenemases in Multidrug, extensive drug and Pandrug-Resistant Klebsiella pneumoniae

Insights from metagenome-assembled genomes on the genetic stability and safety of over-the-counter probiotic products

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