Abstract
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.
Highlights
Bioprospecting tropical plants to search for beneficial endophytic microorganisms that produce novel biotechnological molecules remains of interest [1,2]
Overall high synteny conservation was observed among the three strains, indicating that L. plantarum has a very stable genomic structure, numerous gene rearrangements were detected, with highly variable regions located between 1000 kb and 2500 kb (Figure 1A,B)
The intersection and connection lines indicate the presence of some regions without Locally Collinear Blocks (LCBs) outlines, suggesting the presence of strain-specific regions; these differences might be related to the differences in the lifestyle islands (Table S1)
Summary
Bioprospecting tropical plants to search for beneficial endophytic microorganisms that produce novel biotechnological molecules remains of interest [1,2]. Microorganisms associated with plants are subjected to constant metabolic and environmental interactions; the diversity of the produced molecules is linked to the host chemical composition [3,4]. Lactobacillus casei strains isolated from different fermented products, showing a limited number of SNPs in the genome, among other features that implied the high similarity among these strains. Botta et al [6] studied the genomes of three L. plantarum strains, indicating that the high flexibility and metabolic versatility of these strains—which can acquire, substitute, or delete genomic regions—are ligated to their distinct environmental niches of origin. Previous research indicates that L. plantarum strains isolated from various niches exhibit high genetic variation and phylogenetic patterns [11]. More recent genomic comparison between several L. plantarum strains originating from pickles, fermented sauce, and human feces indicated that the genetic variation of LAB strains is associated with the host niche [13]. Several species have been identified, the selection of new strains with valuable biotechnological properties remains a topic of interest [16]
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