Genomic Characterization of the three Lactiplantibacillus plantarum strains with probiotic potential isolated from Ethiopian traditional cottage cheese
Background: Lactiplantibacillus (L.) plantarum is a versatile species found in a wide range of ecological niches, including dairy products (traditional cottage cheese, yoghurt) and vegetables, and it may also occur naturally in the human gastrointestinal tract (GIT). The precise mechanisms underlying the bene?cial properties of these microbes on their host are also remain obscure. Although Lactic acid bacteria (LAB) are generally regarded as safe, there are rare emergence of some infections and antibiotic resistance by certain probiotics.  Objective: The in silico genome analysis of putative probiotic bacteria was set up to identify strains, predict desirable functional properties, and identify potentially detrimental antibiotic resistance and virulence genes.  Methods and results: In this study, we characterized the genomes of three L. plantarum strains isolated from Ethiopian traditional cottage cheese. Whole-genome sequencing (WGS) was performed using Illumina MiSeq sequencing. We have assessed completeness and quality of the L. plantarum strains genomes through CheckM. Analyses results showed that L. plantarum 54B and 54C are closely related but different strains. This study reveals that the genomes studied do not harbor resistance and virulence factors.  The genomes studied have also ?ve classes of carbohydrate-active enzymes with several important functions. Cyclic lactone autoinducer, terpenes, Type III polyketide synthases (T3PKS), ribosomally synthesized and post-translationally modified peptides (RiPP)-like gene clusters, sactipeptides, plantaricins and all genes required for riboflavin biosynthesis have been identi?ed, evidencing their promising probiotic properties.  Conclusions: Combined, the lack of resistome and virulome and their previous functional capabilities have rendered these strains important. The results also provide better insights into the probiotic potential and safety of these three strains and indicate avenues for further mechanistic studies using these isolates.