CRISPR spacers acquired from plasmids primarily target backbone genes, making them valuable for predicting potential...

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Metagenomic studies have identified numerous novel plasmids, but bacterial host information is scarce.
• Current methods often limit host identification to the original isolate, neglecting alternative hosts and plasmid host range.
• Understanding plasmid-host interactions is crucial for ecological and clinical implications, including the spread of antibiotic resistance genes.

Purpose of the Study:

• To develop and validate a method for predicting potential bacterial hosts and host ranges of plasmids using CRISPR spacers.
• To investigate the specificity of CRISPR spacer targeting on plasmid genes.
• To explore plasmid-mediated horizontal gene transfer networks among bacterial taxa.

Main Methods:

• Alignment of plasmids from the PLSDB database with CRISPR spacers from a CRISPR spacers database.
• Comparison of predicted hosts with reported hosts to assess accuracy at family and phylum levels.
• Analysis of targeted plasmid genes by CRISPR spacers.

Main Results:

• Host predictions were generated for 46% of plasmids in the PLSDB database.
• The method achieved 84% concordance with reported hosts at the family level and 99% at the phylum level.
• CRISPR spacers predominantly target plasmid backbone genes, sparing functional genes like antibiotic resistance genes, and multiple potential hosts were frequently identified.

Conclusions:

• The CRISPR spacer alignment method effectively predicts plasmid hosts and host ranges, addressing a critical knowledge gap.
• CRISPR spacer acquisition appears specific to plasmid backbone regions, suggesting a mechanism to control plasmid replication or spread.
• The study reveals plasmid-mediated networks, offering insights into horizontal gene transfer pathways and the dissemination of important genes.