Genomic Evidence of Ecological Flexibility and Cross-Niche CRISPR Spacerome Targeting Phage-Plasmid Hybrids in Latilactobacillus Curvatus

Abstract

Background Latilactobacillus curvatus is a lactic acid bacterium with a remarkable ability to persist in diverse niches, including fermented foods and gut. Despite its industrial and potential probiotic relevance, the genomic underpinnings of its cross-niche adaptability remain poorly characterized.Methods We conducted a species-contextualized comparative genomic analysis of 53 L. curvatus strains from food and gut isolates. This analysis integrated pangenome structure, metabolic repertoire, CRISPR-Cas immunity profiles, and mobilome analysis. Additionally, binding mode predictions and dynamics simulations were used to evaluate the theoretical binding energies of bacteriocins to the BamA target.Results Phylogenomics revealed a polyphyletic population structure, indicating that long-term evolution is not strictly niche-specific. In contrast, genome-wide similarity showed clustering by isolation source, highlighting horizontal gene transfer (HGT) as a plausible contributor to niche adaptation. We identified a highly active mobilome, encompassing diverse plasmids, IS elements, and multiple intact prophages, reflecting high genomic plasticity characteristic of a multihabitat lifestyle. CRISPR-Cas systems were widespread, and analysis of 2,029 spacers revealed a broad immune repertoire targeting mobile genetic elements represented in fermented food, gut, and environmental datasets. We also identified spacer matches to phage-plasmid hybrid-like elements, highlighting the diversity of mobile genetic elements associated with the L. curvatus spacerome.Conclusion Our study reveals genomic features consistent with ecological flexibility in L. curvatus, including high genomic plasticity and a broad CRISPR spacer repertoire. Rather than demonstrating strict niche-specific evolution or a causal mechanism for cross-niche persistence, these findings support the hypothesis that this species has experienced diverse interactions with mobile genetic elements across multiple ecological contexts.