Complete genome sequencing of exopolysaccharide-producing <i>Lactobacillus plantarum</i> K25 provides genetic evidence for the probiotic functionality and cold endurance capacity of the strain

Jiang, Yunyun; Zhang, Jian; Zhao, Xiao; Zhao, Wen; Yu, Ziming; Chen, Chao; Yang, Zhennai

doi:10.1080/09168451.2018.1453293

Cited by 25 publications

(12 citation statements)

References 57 publications

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“…Therefore, due to their industrial and economic importance, efforts are constantly being made to fully sequence and annotate genomes of these taxa [ 126 , 127 , 128 , 129 ]. In recent years though, genomics studies included NSLAB as well, due to their considerable impact on flavor development in cheese [ 98 , 130 , 131 , 132 , 133 , 134 , 135 , 136 , 137 , 138 , 139 , 140 ].…”

Section: Omics Insights Into Flavor Formation In Cheesementioning

confidence: 99%

Omics Approaches to Assess Flavor Development in Cheese

Anastasiou

Κάζου

Georgalaki

et al. 2022

Foods

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Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.

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Section: Omics Insights Into Flavor Formation In Cheesementioning

confidence: 99%

Omics Approaches to Assess Flavor Development in Cheese

Anastasiou

Κάζου

Georgalaki

et al. 2022

Foods

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“…To date, more than 50 complete genome sequences of L. plantarum strains are available in the GenBank database (http://www.ncbi.nlm.nih.gov/genome/). Genomic diversity and versatility of L. plantarum have been reported (Siezen and van Hylckama Vlieg 2011;Jiang et al 2018;Evanovich et al 2019). Nevertheless, among these strains, only L. plantarum ST-III has been reported to be able to survive in De Man Rogosa and Sharp (MRS) medium with 7.5% NaCl .…”

Section: Introductionmentioning

confidence: 99%

Identification of salt tolerance-related genes of Lactobacillus plantarum D31 and T9 strains by genomic analysis

et al. 2020

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Purpose: The aim of this study was to identify salt tolerance-related genes of Lactobacillus plantarum D31 and T9 strains, isolated from Chinese traditional fermented food, by genomic analysis. Methods: Tolerance of L. plantarum D31 and T9 strains was evaluated at different stress conditions (temperatures, acid, osmolality, and artificial gastrointestinal fluids). Draft genomes of the two strains were determined using the Illumina sequencing technique. Comparative genomic analysis and gene transcriptional analysis were performed to identify and validate the salt tolerance-related genes.Results: Both L. plantarum D31 and T9 strains were able to withstand high osmotic pressure caused by 5.0% NaCl, and L. plantarum D31 even to tolerate 8.0% NaCl. L. plantarum D31 genome contained 3,315,786 bp (44.5% GC content) with 3106 predicted protein-encoding genes, while L. plantarum T9 contained 3,388,070 bp (44.1% GC content) with 3223 genes. Comparative genomic analysis revealed a number of genes involved in the maintenance of intracellular ion balance, absorption or synthesis of compatible solutes, stress response, and modulation of membrane composition in L. plantarum D31 and or T9 genomes. Gene transcriptional analysis validated that most of these genes were coupled with the stress-resistance phenotypes of the two strains.Conclusions: L. plantarum D31 and T9 strains tolerated 5.0% NaCl, and D31 even tolerated 8.0% NaCl. The draft genomes of these two strains were determined, and comparative genomic analysis revealed multiple molecular coping strategies for the salt stress tolerance in L. plantarum D31 and T9 strains.

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“…Survival under acidic conditions is one of the critical parameters of LAB strains if intended to be used as probiotic cells. The key regulator of intracellular pH is the F0F1-ATPase system [ 51 , 52 ]. The EggNOG annotation indicates the presence of eight genes belonging to the F0F1-ATPase system in both native strains and reference WCFS1 ( Table 3 ).…”

Section: Resultsmentioning

confidence: 99%

Decoding the Gene Variants of Two Native Probiotic Lactiplantibacillus plantarum Strains through Whole-Genome Resequencing: Insights into Bacterial Adaptability to Stressors and Antimicrobial Strength

Tenea

2022

Genes

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In this study, whole-genome resequencing of two native probiotic Lactiplantibacillus plantarum strains—UTNGt21A and UTNGt2—was assessed in order to identify variants and perform annotation of genes involved in bacterial adaptability to different stressors, as well as their antimicrobial strength. A total of 21,906 single-nucleotide polymorphisms (SNPs) were detected in UTNGt21A, while 17,610 were disclosed in the UTNGt2 genome. The comparative genomic analysis revealed a greater number of deletions, transversions, and transitions within the UTNGt21A genome, while a small difference in the number of insertions was detected between the strains. A divergent number of types of variant annotations were detected in both strains, and categorized in terms of low, moderate, and high modifier impact on the protein effectiveness. Although both native strains shared common specific genes involved in the stress response to the gastrointestinal environment, which may qualify as a putative probiotic (bile salt, acid, temperature, osmotic stress), they were different in their antimicrobial gene cluster organization, with UTNGt21A displaying a complex bacteriocin gene arrangement and dissimilar gene variants that might alter their defense mechanisms and overall inhibitory capacity. The genome comparison revealed 34 and 9 genomic islands (GIs) in the UTNGt21A and UTNGt2 genomes, respectively, with the overrepresentation of genes involved in defense mechanisms and carbohydrate utilization. In addition, pan-genome analysis disclosed the presence of various strain-specific genes (shell genes), suggesting a high genome variation between strains. This genome analysis illustrates that the bacteriocin signature and gene variants reflect a niche-inherent pattern. These extensive genomic datasets will guide us to understand the potential benefits of the native strains and their utility in the food or pharmaceutical sectors.

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Complete genome sequencing of exopolysaccharide-producing Lactobacillus plantarum K25 provides genetic evidence for the probiotic functionality and cold endurance capacity of the strain

Cited by 25 publications

References 57 publications

Omics Approaches to Assess Flavor Development in Cheese

Omics Approaches to Assess Flavor Development in Cheese

Identification of salt tolerance-related genes of Lactobacillus plantarum D31 and T9 strains by genomic analysis

Decoding the Gene Variants of Two Native Probiotic Lactiplantibacillus plantarum Strains through Whole-Genome Resequencing: Insights into Bacterial Adaptability to Stressors and Antimicrobial Strength

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