Genome mining of Lactiplantibacillus plantarum PA21: insights into its antimicrobial potential

Abstract

Background: The dramatic increase of antimicrobial resistance in the healthcare realm has become inexorably linked to the abuse of antibiotics over the years. Therefore, this study seeks to identify potential postbiotic metabolites derived from lactic acid bacteria such as Lactiplantibacillus plantarum that could exhibit antimicrobial properties against multi-drug resistant pathogens.

Results: In the present work, the genome sequence of Lactiplantibacillus plantarum PA21 consisting of three contigs was assembled to a size of 3,218,706 bp. Phylogenomic analysis and average nucleotide identity (ANI) revealed L. plantarum PA21 is closely related to genomes isolated from diverse niches such as dairy products, food, and animals. Genome mining through the BAGEL4 and antiSMASH database revealed four bacteriocins in a single cluster and four regions of biosynthetic gene clusters responsible for the production of bioactive compounds. The potential probiotic genes indirectly responsible for postbiotic metabolites production were also identified. Additionally, in vitro studies showed that the L. plantarum PA21 cell-free supernatant exhibited antimicrobial activity against all nine methicillin-resistant Staphylococcus aureus (MRSA) and three out of 13 Klebsiella pneumoniae clinical isolates tested.

Conclusion: Results in this study demonstrates that L. plantarum PA21 postbiotic metabolites is a prolific source of antimicrobials against multi-drug resistant pathogens with potential antimicrobial properties.

Keywords: Lactiplantibacillus plantarum; Antimicrobial; Antimicrobial resistance; Genome mining; Postbiotic.

Fig. 1

The prevalence and mean relative abundance of L. plantarum across different environments

Fig. 2

The heatmap depicts the average nucleotide identity (ANI) whole-genome comparison of other 75 Lactiplantibacillus plantarum genomes corresponding to its isolation sources

Fig. 3

Phylogenomic maximum likelihood tree of 75 other Lactiplantibacillus genomes with L. plantarum PA21 and the outgroup, Bacillus cereus (accession: GCF_021655335.1). The branch lengths have been ignored and circled blue icon indicated bootstrap support for the depicted nodes in display. Binary data representing distinct shapes are used to denote the isolation source of the genome

Fig. 4

Pangenome plot of 16 genomes of L. plantarum generated through Anvio. Dark brown and light brown layer represent genomes from two clusters demarcated based on the ANI clustering (top right corner). Presence/absence of gene clusters represent by the presence/absence of dark/light brown box. The genomes are clustered based on the presence/absence of the gene clusters

Fig. 5

Bacteriocin gene cluster organisation and its localization on genome map