Pangenome analysis and “in silico” overview of carbohydrate and vitamin metabolism of Lactiplantibacillus plantarum strain TRA56 obtained from lactic-acid fermented beverage known as Shalgam

Year 2025, Volume: 34 Issue: 1, 1 - 21

Ahmet Yetiman

https://doi.org/10.38042/biotechstudies.1615601

Abstract

Lactiplantibacillus plantarum is a highly adaptable and versatile species that can be found in a diverse range of niches. It can generate bioactive compounds, including riboflavin, folic acid, and exopolysaccharides, which contribute to the functional qualities of fermented foods. This study aimed to provide a brief evaluation of the overall genetic characteristics, as well as the carbohydrate and vitamin metabolisms, of the Lb. plantarum TRA56 (The TRA56). Its genome size was 3,242,215 bp with a 44.41% GC content, including 3.030 coding sequences, 62 tRNA genes, 3 rRNA, 4 ncRNA, 1 CRISPR array, 69 pseudogenes, and 2 intact phages. Its genome had 195 singleton genes that differed from those found in other strains analyzed in the pangenome. Moreover, it has been found that TRA56 possesses a facultative heterofermentive carbohydrate metabolism as a result of the existence of 6-phosphofructokinase (pfk) and fructose-bisphosphate aldolase (fbaA) enzymes. The strain's capacity to synthesize vitamins B2, B5, and B9 has been verified using computational tools. Cholesterol assimilation (46.28±1.6%) and antioxidant activity against DPPH (59.04±0.43%) and ABTS+ (77.76±0.33%) were verified via in vitro tests. The study of the TRA56's genetic and metabolic characteristics demonstrated its potential as a probiotic food supplement, offering functional advantages to the host.

Keywords

Microbial genomics, CAZYmes, Vitamins

Supporting Institution

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

Project Number

FKB-2020–10551

Thanks

I would like to thank the Proofreading & Editing Office of the Dean for Research at Erciyes University for the copyediting and proofreading service for this manuscript.

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