Pangenomics of Limosilactobacillus fermentum reveals genomic diversity and bacteriocin activity against Staphylococcus aureus and Escherichia coli

Creative Commons License

KASAPOĞLU M. Z., ACAR I., Gumustop I., Erol I., KURT İ. Ç., Ortakcı F.

Scientific Reports, cilt.16, sa.1, 2026 (SCI-Expanded, Scopus)

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 16 Sayı: 1
  • Basım Tarihi: 2026
  • Doi Numarası: 10.1038/s41598-026-51219-1
  • Dergi Adı: Scientific Reports
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, BIOSIS, Chemical Abstracts Core, EMBASE, MEDLINE, Directory of Open Access Journals, Zoological Record, Academic Search Ultimate (EBSCO), Natural Science Collection (ProQuest), Biological Science Database (ProQuest), Biomedical Reference Collection: Corporate Edition (EBSCO), Health Research Premium Collection (ProQuest)
  • Anahtar Kelimeler: Bacteriocins, Comparative genomics, CRISPR-cas systems, Gamma-aminobutyric acid, Limosilactobacillus fermentum
  • Açık Arşiv Koleksiyonu: AVESİS Açık Erişim Koleksiyonu
  • İstanbul Üniversitesi-Cerrahpaşa Adresli: Evet

Özet

Limosilactobacillus fermentum is a versatile lactic acid bacterium with significant probiotic and biotechnological potential, yet the genomic determinants underlying its ecological adaptation and therapeutic applications remain underexplored. This study performed a comparative genomic analysis of 52 L. fermentum strains, with a focus on the novel strain ATT-06 isolated from traditional Turkish shalgam. We uncovered substantial genetic diversity, evidenced by an open pan-genome (18,647 genes) and a small core genome (718 genes). CRISPR-Cas systems were prevalent (46 strains), with Type-IE and Type-IIA being most common and mutually exclusive from Type-IC. Strain ATT-06, which uniquely produced gamma-aminobutyric acid at 17.74 µg/mL, harbored a Type-IIA CRISPR system and a single prophage. In silico molecular docking and dynamics simulations revealed that the bacteriocin Lactococcin, encoded by strain ATA-LTC-Lf170503, exhibited strong binding affinities (ΔG: –8.1 to –13.0 kcal/mol) against Rho proteins of Staphylococcus aureus and Escherichia coli, outperforming Acidocin A. These findings highlight the genomic plasticity and adaptive mechanisms of L. fermentum, and position strain ATT-06 as a promising probiotic candidate with potential neuroactive and antimicrobial applications.