Genome based analysis of Antibacterial Biosynthetic Clusters in Lactiplantibacillus plantarum C6 and Exploration of their Natural Small Molecules as anti-biofilm in Methicillin-Resistant Staphylococcus aureus

Abstract

This study presents the complete genome characterization of Lactiplantibacillus plantarum C6, a strain isolated from Indian dairy cheese, using Illumina NovaSeq sequencing. The assembled genome (3.22 Mb, 44.5% GC) comprised 3,076 coding sequences, 59 tRNAs, 10 rRNAs, and 2 CRISPR arrays. Phylogenomic and ANI analyses confirmed its identity within the L. plantarum clade (>99% similarity with NMGL2 and DMDL 9010). Functional annotation revealed genes enriched in carbohydrate metabolism (10.7%), stress response, and host-adaptation pathways, supporting its probiotic potential. Bacteriocin biosynthetic gene clusters were identified, including those encoding PlnE, PlnF, PlnJ, PlnK, and PlnN, indicating the strains ability to produce class II plantaricins. A RiPP cluster encoding a cyclic uberolysin-like peptide was also detected, with structural similarity to known lanthipeptides such as Streptococcin A, Nisin Q, and Lacticin 3147 (Tanimoto scores 0.93-1.0), suggesting antimicrobial relevance. CAZy analysis revealed 102 carbohydrate-active enzymes (GHs, GTs), highlighting metabolic flexibility. To evaluate the antibiofilm potential of L. plantarum-derived metabolites, 15 small molecules from cell-free supernatants (CFS) were selected through literature mining and subjected to molecular docking against the MRSA biofilm-associated enzyme poly-{beta}-1,6-N-acetyl-D-glucosamine synthase (encoded by icaA). 2,4-Di-tert-butylphenol (-7.2 kcal/mol) and Indole-3-lactic acid (-7.1 kcal/mol) showed the strongest binding, followed by Cyclo (L-propyl-L-valine) (-6.8 kcal/mol) and DL-4-Hydroxyphenyllactic acid (-6.4 kcal/mol), indicating promising inhibition of MRSA biofilm synthesis. Organic acids like acetic and lactic acid showed weaker interactions but may contribute synergistically through acidification. Overall, L. plantarum C6 combines robust probiotic features, genomic safety, and antimicrobial potential, supported by bacteriocin gene clusters and effective antibiofilm metabolites, highlighting its application in functional foods and novel antimicrobial development.