Genomic profiling of pediococcus acidilactici BCB1H and identification of its key features for Biotechnological innovation, food technology and medicine

Abstract

Lactic acid bacteria has been extensively used in food industry because of widespread properties and Pediococcus is among one of them. This study aims to conduct a comprehensive genomic analysis of Pediococcus acidilactici strain BCB1H to elucidate its genetic composition, functional elements, and potential biotechnological applications. The objectives include identifying key genomic features such as coding sequences, tRNA and rRNA genes, antibiotic resistance genes, and secondary metabolite biosynthetic gene clusters, which will highlight the adaptability and potential of P. acidilactici strain BCB1H for use in a variety of industrial and therapeutic applications. P. acidilactici strain BCB1H was analyzed using whole-genome sequencing, which used advanced sequencing technologies to obtain comprehensive genomic data. Key genomic features, such as coding sequences, tRNA and rRNA genes, antibiotic resistance genes, and secondary metabolite biosynthetic gene clusters, were identified through bioinformatics analyses. The genomic analysis of P. acidilactici strain BCB1H revealed a genome size of approximately 1.92 million base pairs with a GC content of 42.4%. The annotation identified 1,895 genes across 192 subsystems, highlighting the metabolic pathways and functional categories. Notably, specialty genes associated with carbohydrate metabolism, stress response, pathogenicity, and amino acid synthesis were identified, underscoring the versatility and potential applications in food technology and medicine. These findings shed light on the genetic makeup and functional potential of P. acidilactici strain BCB1H, highlighting its flexibility and industrial importance. The genetic traits discovered suggest its prospective use in probiotics, food preservation, and biotechnological advancements.

Keywords: Pediococcus acidilactici; Antibiotic resistance genes; BCB1H; Biosynthetic gene clusters; Metabolic pathways; rRNA genes; tRNA genes.

Fig. 1

Circular representation of the genome of P. acidilactici strain BCB1H, visualized using ProkSee, highlighting annotated features such as such as gene distribution, CDS, and tRNA, rRNA, tmRNA, GC Content and ORFs.

Fig. 2

Heatmap representing the genomic similarity of P. acidilactici strains based on ANIb values. Red indicates high similarity, while blue denotes lower similarity.

Fig. 3

The subsystem coverage and classification of genes in the genome of P. acidilactici BCB1H as determined by Prokka. The analysis reveals that 41% of the genome is covered by well-defined subsystems.

Fig. 4

Cluster Share Analysis of P. acidilactici Strains.

Fig. 5

The genetic diversity of distinct strains of P. acidilactici by Cluster of Orthologous Groups (COG).

Fig. 6

The shared and unique gene clusters across different P. acidilactici strains. The intersections highlight the extent of genetic overlap, revealing both conserved and strain-specific gene clusters within the species.

Fig. 7

SNP-based phylogenetic tree of P. acidilactici strains, including P. acidilactici BCB1H. The tree scale is set at 0.1, with branches representing the genetic distances between strains based on single nucleotide polymorphisms (SNPs). The analysis shows the evolutionary relationships and genetic divergence among the strains.

Fig. 8

The predicted HGT regions in the P. acidilactici genome based on analysis by Aller Hunter. The identified HGT regions, ranging in size from 0.2 Mbp to 1.8 Mbp, highlight areas of the genome that may have been acquired via horizontal gene transfer, potentially contributing to the strain’s genetic diversity and adaptive traits.

Fig. 9

(A) The comparison of P. acidilactici BCB1H Genome with other strains (B) The percentage identity on the basis of comparison for P. acidilactici BCB1H with other strains.

Fig. 10

Visualization of predicted biosynthetic gene clusters (BGCs) using antiSMASH, showing diverse secondary metabolite categories such as RiPPs.