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Assessment of Genomic and Metabolic Characteristics of Cholesterol-Reducing and GABA Producer Limosilactobacillus fermentum AGA52 Isolated from Lactic Acid Fermented Shalgam Based on “In Silico” and “In Vitro” Approaches

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Abstract

This study aimed to characterize 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 2,001,184 bp, which is predicted to carry 2024 genes, including 50 tRNAs, 3 rRNAs, 3 ncRNAs, 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 analyzed by comparison with the other Lb. fermentum strains. The detected resistome on the genome of AGA52 was found to be intrinsic originated. Besides, it has been determined that AGA52 has an obligate heterofermentative carbohydrate metabolism due to the absence of the 1-phosphofructokinase (pfK) enzyme. Furthermore, the strain is found to have a better antioxidant capacity and to be tolerant to gastrointestinal simulated conditions. It was also observed that the AGA52 has antimicrobial activity against Yersinia enterocolitica ATCC9610, Bacillus cereus ATCC33019, Salmonella enterica sv. Typhimurium, Escherichia coli O157:h7 ATCC43897, Listeria monocytogenes ATCC7644, Klebsiella pneumoniae ATCC13883, and Proteus vulgaris ATCC8427. Additionally, AGA52 exhibited 42.74 ± 4.82% adherence to HT29 cells. Cholesterol assimilation (33.9 ± 0.005%) and GABA production capacities were also confirmed by “in silico” and “in vitro.” Overall, the 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.

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Acknowledgements

Mr. Mehmet Horzum would like to thank the Council of Higher Education of Türkiye (YÖK) due to the 100/2000 PhD scholarship program.

Funding

This study has been financially supported by Erciyes University Scientific Research Projects Coordination Unit under grant number FKB-2020–10551.

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Authors and Affiliations

  1. Food Engineering Department, Faculty of Engineering, Erciyes University, 38030, Kayseri, Turkey

    Ahmet Yetiman

  2. Food Engineering Department, Graduate School of Natural and Applied Sciences, Erciyes University, 38030, Kayseri, Turkey

    Mehmet Horzum

  3. Genkök Genome and Stem Cell Center, Erciyes University, 38030, Kayseri, Turkey

    Dilek Bahar

  4. Department of Biology, Faculty of Science, Erciyes University, 38030, Kayseri, Turkey

    Mikail Akbulut

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All authors contributed to the study’s conception and design. Material preparation, data collection, and analysis were performed by Ahmet E. Yetiman, Mehmet Horzum, and Dilek Bahar. The first draft of the manuscript was written by Ahmet E. Yetiman and was proofread by Mikail Akbulut. All authors read and approved the final manuscript.

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Yetiman, A., Horzum, M., Bahar, D. et al. Assessment of Genomic and Metabolic Characteristics of Cholesterol-Reducing and GABA Producer Limosilactobacillus fermentum AGA52 Isolated from Lactic Acid Fermented Shalgam Based on “In Silico” and “In Vitro” Approaches. Probiotics & Antimicro. Prot. 16, 334–351 (2024). https://doi.org/10.1007/s12602-022-10038-2

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  • DOI: https://doi.org/10.1007/s12602-022-10038-2

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