Abstract
The comparative genome analysis of six Lactiplantibacillus plantarum subsp. argentoratensis strains previously isolated from spontaneously fermented Greek wheat sourdoughs is presented. Genomic attributes related to food safety have been studied according to the European Food Safety Authority (EFSA) suggestions for the use of lactic acid bacteria (LAB) in the production of foods. Bioinformatic analysis revealed a complete set of genes for maltose, sucrose, glucose, and fructose fermentation; conversion of fructose to mannitol; folate and riboflavin biosynthesis; acetoin production; conversion of citrate to oxaloacetate; and the ability to produce antimicrobial compounds (plantaricins). Pathogenic factors were absent but some antibiotic resistance genes were detected. CRISPR and cas genes were present as well as various mobile genetic elements (MGEs) such as plasmids, prophages, and insertion sequences. The production of biogenic amines by these strains was not possible due to the absence of key genes in their genome except lysine decarboxylase associated with cadaverine; however, potential degradation of these substances was identified due to the presence of a blue copper oxidase precursor and a multicopper oxidase protein family. Finally, comparative genomics and pan-genome analysis showed genetic differences between the strains (e.g., variable pln locus), and it facilitated the identification of various phenotypic and probiotic-related properties.
Highlights
Lactic acid bacteria (LAB) are microorganisms that possess important technological characteristics and, are used in food fermentations as starters or even as adjunct cultures providing the desired quality and organoleptic properties and assuring the safety of the fermented products
That the genomes were of high quality they were not closed because it is well known that the genome of lactic acid bacteria contains repeat regions and other mobile elements that make it difficult to finish the genome using only short read sequences [16,17]
Sci. 2022, 23, 2487 and the genome coverage was much higher than the threshold of 60–80× and the recommended 100×) they were not closed because it is well known that the genome of lactic acid bacteria contains repeat regions and other mobile elements that make it difficult to finish the genome using only short read sequences [16,17]
Summary
Lactic acid bacteria (LAB) are microorganisms that possess important technological characteristics and, are used in food fermentations as starters or even as adjunct cultures providing the desired quality and organoleptic properties and assuring the safety of the fermented products. The safety assessment of microbial strains aimed to be used as potential food additives is always timely, and it is highly recommended for investigation [6]. Since they constitute the majority of the respective micro-community, LAB and yeasts play a critical role during sourdough fermentation. Greek wheat sourdoughs collected from various geographical regions were analyzed by using culture-dependent and culture-independent molecular techniques. These six strains, initially identified as L. plantarum by 16S rRNA gene sequencing, were further selected for whole-genome sequencing based on their phenotypic and technological properties [9]. Sequenced genomes of L. plantarum subsp. argentoratensis are not readily available, especially strains isolated from sourdoughs
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