Genomic and Functional Characterization of Three Probiotic Strains with Features Relevant to Cholesterol and Choline-TMAO Metabolism: Rationale for a Cardiometabolic Formulation

Background/Objectives: The gut microbiota acts on two cardiovascular risk factors that are open to intervention: circulating cholesterol and TMAO, which derives from bacterial conversion of dietary choline to trimethylamine. We characterised Bifidobacterium breve BR03 (DSM 16604), Lactiplantibacillus plantarum LP14 (DSM 33401) and Limosilactobacillus reuteri LRE11 (DSM 33827), candidate components of a cardiometabolic formulation. Genomic profiling across seven functional categories was combined with an in vitro assessment of cholesterol removal. Methods: Whole-genome screening was used to identify genes related to oxidative stress resistance, adhesion, cholesterol-related functions (including bsh), folate biosynthesis, immune-interface functions and degradation of anti-nutritional factors. In addition, an in vitro assay assessed cholesterol removal from the medium. Results: All three strains carry bsh at 90.7–100% identity, along with core adhesion determinants and antioxidant systems, and all three are genetically incapable of generating trimethylamine: neither cutC nor cntA is present in assemblies that are essentially complete (100% for LP14, 99.5% for LRE11, closed and optically validated for BR03). The three repertoires then diverge. LP14 provides near-complete folate biosynthesis, the broadest set of surface and immune-interface genes, a choline kinase homologue at 99.6% and putative matches to choXWV. BR03 contributes the widest range of enzymes degrading anti-nutritional factors. BR03 and LRE11 remove the most cholesterol in vitro. Conclusions: The three strains cover complementary metabolic and surface functions while sharing a safety-relevant feature: none can contribute to TMAO formation. This profile makes them suitable candidates for a combined cardiometabolic formulation, whose clinical application will be tested in a planned clinical study.