Genomic and phenotypic assessment of functional and safety properties of Lacticaseibacillus rhamnosus PMK4 isolated from Cameroonian infant faeces

The gut microbiota is a complex community of microorganisms that plays a crucial role in maintaining short- and long-term health. However, a perturbed microbial ecosystem is associated with a range of diseases, including increased risk of infections. Probiotic-based strategies may help restore microbiome function, but candidate strains require robust functional and safety evaluation. Here, we performed integrated genomic and phenotypic characterisation of beneficial properties of Lacticaseibacillus rhamnosus PMK4, isolated from the stool of a healthy Cameroonian infant. Whole-genome sequencing and comparative pangenomic analysis against 13 L. rhamnosus genomes were used to infer functional potential, with in silico safety screening conducted using ResFinder, CARD and VFDB. Beneficial-relevant phenotypes were assessed through tolerance to simulated gastrointestinal conditions, adhesion-associated traits (hydrophobicity, aggregation), antimicrobial activity, nutrients utilisation profiling and safety-related assays. The L. rhamnosus PMK4 genome (2,935,039 bp), contains strain-specific loci predicted to support acid stress tolerance and epithelial adhesion. Functional annotation indicated the presence of genetic potential for carbohydrate metabolism, stress response, adhesion-related functions, and biosynthesis of secondary metabolites including acids, terpenes and vitamins. No acquired antibiotic resistance determinants or virulence genes were detected. Consistent with genomic predictions, PMK4 showed high survival under simulated gastrointestinal conditions, strong auto-aggregation capacity, moderate hydrophobicity and co-aggregation, and broad antagonistic activity against a range of enteropathogens. The strain also utilised a wide range of substrates, including complex carbohydrates and proteins, suggesting metabolic versatility relevant to microbe-microbe and microbe-host interactions in the gut. Together, these data support L. rhamnosus PMK4 as a promising indigenous probiotic candidate with a favourable safety profile and functional potential.