Data for: CRISPR spacers acquired from plasmids primarily target backbone genes, making them valuable for predicting potential hosts and host range

Here we provide the full data which is described and discussed in CRISPR
Spacers Acquired from Plasmids Primarily Target Backbone Genes, Making
Them Valuable for Predicting Potential Hosts and Host Range, submitted to
Microbiology Spectrum. Abstract of the main manuscript: In recent years,
there has been a surge in metagenomic studies focused on identifying
plasmids in environmental samples. While these studies have unearthed
numerous novel plasmids, enriching our understanding of their
environmental roles, a significant gap remains: the scarcity of
information regarding the bacterial hosts of these newly discovered
plasmids. Furthermore, even when plasmids are identified within bacterial
isolates, the reported host is typically limited to the original isolate,
with no insight into alternative hosts or the plasmid’s potential host
range. Given that plasmids depend on hosts for their existence,
investigating plasmids without knowledge of potential hosts offers only a
partial perspective. This study introduces a method for identifying
potential hosts and host ranges for plasmids through alignment with CRISPR
spacers. To validate the method, we compared the PLSDB plasmids database
with the CRISPR spacers database, yielding host predictions for 46% of the
plasmids. When compared to reported hosts, our predictions achieved an 84%
concordance at the family level and 99% concordance at the phylum level.
Moreover, the method frequently identified multiple potential hosts for a
plasmid, thereby enabling predictions of alternative hosts and the host
range. Notably, we found that CRISPR spacers predominantly target plasmid
backbone genes while sparing functional genes, such as those linked to
antibiotic resistance, aligning with our hypothesis that CRISPR spacers
are acquired from plasmid-specific regions rather than insertion elements
from diverse sources. Lastly, we illustrate the network of connections
among different bacterial taxa through plasmids, revealing potential
pathways for horizontal gene transfer. IMPORTANCE: Plasmids are notorious
for their role in distributing antibiotic resistance genes, but they may
also carry and distribute other environmentally important genes. Since
plasmids are not free-living entities and rely on host bacteria for
survival and propagation, predicting their hosts is essential. This study
presents a method for predicting potential hosts for plasmids and offers
insights into the potential paths for spreading functional genes between
different bacteria. Understanding plasmid-host relationships is crucial
for comprehending the ecological and clinical impact of plasmids and
implications for various biological processes.