Comparative genomic analysis of bacteriocin genes in Lactobacillus crispatus strains

Abstract

Lactobacillus crispatus, a key member of the vaginal microbiota, exhibits strain-specific diversity with important implications for host-microbe interactions and probiotic potential. This study investigates the genomic relationships and bacteriocin diversity across 95 L. crispatus strains to elucidate the mechanisms underlying strain-specific adaptation and microbial competitiveness. Using publicly available data from NCBI, we applied BAGEL4 and core genome multilocus sequence typing (cgMLST) approaches to identify and characterize bacteriocin genes, revealing a high level of conservation of major bacteriocins among strains. Analysis of nucleotide polymorphisms within bacteriocin-encoding sequences showed that these genes are generally conserved, likely due to strong purifying selection. These findings suggest that bacteriocins in L. crispatus are functionally conserved, underscoring their potential role in maintaining vaginal health through microbial competition and pathogen exclusion.

Keywords: Lactobacillus crispatus; Antimicrobial peptides; Bacteriocins; Vaginal microbiota.

Fig. 1

Phylogenetic tree of Lactobacillus crispatus genomes and associated bacteriocins. The circular phylogenetic tree represents the relationship between 91 genomes of Lactobacillus crispatus. Branch lengths are indicative of evolutionary distances and the inner circle indicates the host, with red dots representing human-derived strains, green dots for animal-derived strains, and grey dots for strains with unknown origins. The outer colored blocks denote the presence of bacteriocin genes for every genome, and the colors correspond to the bacteriocin name listed in the legend. The bacteriocins includes: SakT alpha, Enterolysin A, Helveticin J, Bacteriocin Helveticin J, Penocin A, LAPs, Amyrovicin, Lanthipeptide class IV, Lanthipeptide class I, Bovicin 255, Lacticoccin 972, Coagulin, Ericin S and Thermophilin A. Light gray spaces indicate the absence of these bacteriocin genes.

Fig. 2

Heat map of copy number variation of bacteriocin genes in Lactobacillus crispatus genomes. The heat map represents the copy number variation of different bacteriocin genes across different L. crispatus genomes. The intensity of the red color corresponds to the presence of multiple copies of a specific bacteriocin. The deeper red indicates the maximum number of copies, i.e. four. White indicates the absence of the bacteriocin gene in the genome.

Fig. 3

Mutations and allelic variation of the most represented bacteriocins. The figure illustrates the sequence variations observed in different bacteriocin genes found in L. crispatus genomes using BAGEL4. Each panel (a–d) corresponds to a different bacteriocin gene, with the wild-type allele shown at the top as the most represented reference. Enterolisyn A, Helveticin J and Bacteriocin Helveticin J have different non-overlapping sequences and are therefore identified in different genes. Below the reference gene, the following rows represent different alleles with specific mutations indicated by blue circles for point mutations, pink bars for deletions and orange triangles for insertions. Each allele is associated with a frequency (percentage) in the total number of genomes containing the bacteriocin.