Genomic analysis revealed adaptive mechanism to plant-related fermentation of Lactobacillus plantarum NCU116 and Lactobacillus spp.

Huang, Tao; Xiong, Tao; Peng, Zhen; Xiao, Yazhong; Liu, Zhang-gen; Hu, Min; Xie, Mingyong

doi:10.1016/j.ygeno.2019.05.004

Cited by 29 publications

(16 citation statements)

References 51 publications

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“…Although these strains share a common genetic repertoire with proteins involved in replication, transcription, translation, energy production, carbohydrate transport, and metabolism, a disproportionate distribution of COG categories among L. plantarum strains has been observed ( Botta et al, 2017 ). These results agree with previously published reports ( Huang et al, 2020 ). In addition, one copy of the 23S rRNA gene of 2,919 nucleotides in length was detected in the genome of the native strains, while the reference WCFS1 showed five copies of 23S rRNA.…”

Section: Resultssupporting

confidence: 94%

Bioprospecting of Ribosomally Synthesized and Post-translationally Modified Peptides Through Genome Characterization of a Novel Probiotic Lactiplantibacillus plantarum UTNGt21A Strain: A Promising Natural Antimicrobials Factory

Tenea

Ascanta

2022

Front. Microbiol.

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The present work describes the genome sequencing and characterization of a novel Lactiplantibacillus plantarum strain assigned UTNGt21A isolated from wild Solanum quitoense (L.) fruits. In silico analysis has led to identifying a wide range of biosynthetic gene clusters (BGCs) and metabolic compounds. The genome had a total of 3,558,611 bp with GC of 43.96%, harboring 3,449 protein-coding genes, among which 3,209 were assigned by the EggNOG database, and 240 hypothetical proteins have no match in the BLASTN database. It also contains 68 tRNAs, 1 23S rRNA, 1 16S rRNA, 6 5S rRNA, and 1 tmRNA. In addition, no acquired resistance genes nor virulence and pathogenic factors were predicted, indicating that UTNGt21A is a safe strain. Three areas of interest (AOI) consisting of multiple genes encoding for bacteriocins and ABC transporters were predicted with BAGEL4, while eight secondary metabolite regions were predicted with the antiSMASH web tool. GutSMASH analysis predicted one metabolic gene cluster (MGC) type pyruvate to acetate-formate, a primary metabolite region essential for anaerobe growth. Several lanthipeptides and non-ribosomal peptide synthetase (NRPS) clusters were detected in the UTNGt21A but not the reference genomes, suggesting that their genome diversity might be linked to its niche-specific lineage and adaptation to a specific environment. Moreover, the application of a targeted genome mining tool (RiPPMiner) uncovered a diverse arsenal of important antimicrobial molecules such as lanthipeptides. Furthermore, in vitro analysis indicated that the crude extract (CE) of UTNGt21A exerted a wide spectrum of inhibition against several pathogens. The results indicated that the possible peptide-protein extract (PC) from UTNGt21A induces morphological and ultrastructural changes of Salmonella enterica subsp. enterica ATCC51741, compatible with its inhibitory potential. Genome characterization is the basis for further in vitro and in vivo studies to explore their use as antimicrobial producers or probiotic strains.

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Section: Resultssupporting

confidence: 94%

Bioprospecting of Ribosomally Synthesized and Post-translationally Modified Peptides Through Genome Characterization of a Novel Probiotic Lactiplantibacillus plantarum UTNGt21A Strain: A Promising Natural Antimicrobials Factory

Tenea

Ascanta

2022

Front. Microbiol.

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“…Acetic acid is typically produced through heterofermentive pathways in lactic acid bacteria. While predominantly homofermentive species, genomic studies on L. plantarum have showed the ability to alternate between homo-and heterofermentive routes [43]. On the other hand, citrate metabolism (via citrate lyase) into oxaloacetic acid produces acetate as a by-product [12].…”

Section: Changes In Volatile Profile By Microbial Activity and Strainmentioning

confidence: 99%

“…Both acetoin and diacetyl are produced from pyruvate, which in turn originates from either citrate or carbohydrate metabolism [12]. Acetoin can be further converted to 2,3-butanediol; however, L. plantarum lacks the enzyme for this conversion (2,3-butanediol hydrogenase) [43], possibly explaining why diacetyl and acetoin, but not 2,3-butanediol, were detected in the fermented juices.…”

Section: Changes In Volatile Profile By Microbial Activity and Strainmentioning

confidence: 99%

Impact of malolactic fermentation with Lactobacillus plantarum on volatile compounds of sea buckthorn juice

Markkinen

Laaksonen

Yang

2021

Eur Food Res Technol

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Malolactic fermentation using sea buckthorn (Hippophaë rhamnoides) juice as raw material was performed with six different strains of Lactobacillus plantarum. Increasing juice pH from 2.7 to 3.5 or adapting cells to low pH (i.e., acclimation) prior to inoculation allowed malolactic fermentation with all tested strains. Moreover, reducing pH of the growth medium from 6 to 4.5 with l-malate had little or no impact on biomass production. Volatile profile of sea buckthorn juice was analyzed with HS-SPME–GC–MS before and after fermentation. A total of 92 volatiles were tentatively identified and semi-quantified from sea buckthorn juice, majority of which were esters with fruity odor descriptors. Esters and terpenes were decreased in both inoculated and control juices during incubation. Microbial activity increased the levels of acetic acid (vinegar like), free fatty acids (cheese like), ketones (buttery like), and alcohols with fruity descriptors. Conversely, aldehydes associated with “green” aroma were decreased as a result of fermentation. Juices fermented with DSM 1055 had the highest acid and alcohol content, while fermentation with DSM 13273 resulted in the highest content of ketones. Compared to inoculation with other strains, fermentation with strains DSM 16365 and DSM 100813 resulted in rapid malolactic fermentation, less production of volatile acids, and lower loss of esters and terpenes important for natural sea buckthorn flavor.

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“…The intersection and connection lines indicate the presence of some regions without LCB outlines, suggesting the presence of strain-specific regions; these differences might be related to the differences in the lifestyle islands ( Table S1 ). These events can occur during evolution or horizontal gene transfer (HGT), indicating the plasticity of the L. plantarum genome [ 33 ]. Moreover, a total of 4074 genes were subjected to the pan-genome analysis ( Figure 2 A).…”

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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Genomic analysis revealed adaptive mechanism to plant-related fermentation of Lactobacillus plantarum NCU116 and Lactobacillus spp.

Cited by 29 publications

References 51 publications

Bioprospecting of Ribosomally Synthesized and Post-translationally Modified Peptides Through Genome Characterization of a Novel Probiotic Lactiplantibacillus plantarum UTNGt21A Strain: A Promising Natural Antimicrobials Factory

Bioprospecting of Ribosomally Synthesized and Post-translationally Modified Peptides Through Genome Characterization of a Novel Probiotic Lactiplantibacillus plantarum UTNGt21A Strain: A Promising Natural Antimicrobials Factory

Impact of malolactic fermentation with Lactobacillus plantarum on volatile compounds of sea buckthorn juice

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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