Evaluation of genomic and metabolic properties of cholesterol-reducing and GABA-producer Limosilactobacillus fermentum strain AGA52 isolated from lactic acid fermented Shalgam by using “in silico” and “in vitro” approaches

The objective of this study is characterization of the genomic and metabolic properties of a novel Lb. fermentum strain AGA52 which was isolated from a lactic acid fermented beverage called “Shalgam”. The genome size of AGA52 was 2,001,084 bp, which is predicted to carry 2,024 genes, including 50 tRNAs, 3 rRNAs, 3ncRNAs, 15 CRISPR repeats, 14 CRISPR spacers, and 1 CRISPR array. The genome has a GC content of 51.82% including 95 predicted pseudogenes, 56 complete or partial transposases and 2 intact prophages. The similarity of the clusters of orthologous groups (COG) was analysed by comparison with the other Lb. fermentum strains. The detected resistome on the genome of AGA52 was found to be intrinsically originated. Based on genome analyses many CAZYmes were identified that are responsible for carbohydrate degradation and adaptation to gastrointestinal conditions. Besides, it has been determined that AGA52 has an obligate heterofermentative carbohydrate metabolism due to the absence of the 1-phosphofructokinase (pfK) enzyme. Additionally, it is determined that the strain has a higher antioxidant capacity and is adaptable to gastrointestinal simulated environments. It was also observed that the AGA52 has antimicrobial activity against Y. Enterocolitica ATCC9610, B. cereus ATCC33019, S. enterica sv. Typhimurium, E.coli O157:h7 ATCC43897, L.monocytogenes ATCC7644, K.pneumoniae ATCC13883, and P. vulgaris ATCC8427. Cholesterol assimilation (33.9±0.005%) and GABA production capacities were also confirmed by “in silico” and “in vitro”. Overall, investigation of genomic and metabolic features of the AGA52 revealed that is a potential psychobiotic and probiotic dietary supplement candidate and can bring functional benefits to the host.