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<p><i>Pediococcus acidilactici</i> is a bacterial species of probiotic interest belonging to the family <i>Lactobacillaceae</i>. The present study aims to analyze publicly available complete genomes of 42 <i>P. acidilactici</i> strains to identify and characterize core, accessory and unique genes, evaluate genomic diversity, and assess their probiotic properties using a reproducible comparative genomics pipeline. The pangenome analysis identified 1,070 core genes, 2,697 accessory genes and 1,253 unique genes. Phylogenetic analysis revealed isolates from similar environments clustered together, suggesting a link between environmental origin and genomic relatedness. The functional annotation indicated that core genes predominantly contribute to essential biological functions, including cellular and developmental processes, reproduction, and transporter activity. The accessory genes were associated with biological regulation, detoxification and antioxidant activity, while unique genes were linked to localization and negative regulation of biological processes. Screening of the pangenome reference for antimicrobial resistance genes resulted in identifying a group of genes (viz<i>., poxtA</i><i>, </i><i>fexB</i><i>, </i><i>vatE</i><i>, </i><i>sdrM</i><i>, </i><i>qacG</i><i>, </i><i>vanT</i><i>, </i><i>tetM</i><i>, </i><i>ermB</i><i>, </i><i>qacJ,</i> and <i>narB</i>) that have been previously reported in various probiotic species. Additionally, Enterolysin A, a bacteriocin belonging to the class of cell wall-degrading antimicrobial proteins, was identified in several strains of <i>Pediococcus acidilactici.</i> Further investigation revealed that <i>Pediococcus</i> genomes did not comprise any virulence factors, supporting that these strains are likely non-pathogenic based on the computational analyses performed. A Snakemake-based bioinformatics pipeline to streamline the analysis was created, automating genome annotation, classification of genes into core, accessory and unique genes, and extraction of their sequences.</p>

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Automated pangenomic profiling of Pediococcus acidilactici genomes via Snakemake: uncovering genomic plasticity and specialized antimicrobial potential

  • 期刊论文

  • 发表日期：

    2026年7月23日

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  • Sowmiya Ezhumalai,
  • Aishwarya Swain,
  • Zircon Basumatary,
  • Sucharita Sen Maiti,
  • Archana Pan

摘要

Pediococcus acidilactici is a bacterial species of probiotic interest belonging to the family Lactobacillaceae. The present study aims to analyze publicly available complete genomes of 42 P. acidilactici strains to identify and characterize core, accessory and unique genes, evaluate genomic diversity, and assess their probiotic properties using a reproducible comparative genomics pipeline. The pangenome analysis identified 1,070 core genes, 2,697 accessory genes and 1,253 unique genes. Phylogenetic analysis revealed isolates from similar environments clustered together, suggesting a link between environmental origin and genomic relatedness. The functional annotation indicated that core genes predominantly contribute to essential biological functions, including cellular and developmental processes, reproduction, and transporter activity. The accessory genes were associated with biological regulation, detoxification and antioxidant activity, while unique genes were linked to localization and negative regulation of biological processes. Screening of the pangenome reference for antimicrobial resistance genes resulted in identifying a group of genes (viz., poxtA, fexB, vatE, sdrM, qacG, vanT, tetM, ermB, qacJ, and narB) that have been previously reported in various probiotic species. Additionally, Enterolysin A, a bacteriocin belonging to the class of cell wall-degrading antimicrobial proteins, was identified in several strains of Pediococcus acidilactici. Further investigation revealed that Pediococcus genomes did not comprise any virulence factors, supporting that these strains are likely non-pathogenic based on the computational analyses performed. A Snakemake-based bioinformatics pipeline to streamline the analysis was created, automating genome annotation, classification of genes into core, accessory and unique genes, and extraction of their sequences.