Next-Generation Sequencing for Whole-Genome Characterization of Weissella cibaria UTNGt21O Strain Originated From Wild Solanum quitoense Lam. Fruits: An Atlas of Metabolites With Biotechnological Significance

Abstract

The whole genome of Weissella cibaria strain UTNGt21O isolated from wild fruits of Solanum quitoense (naranjilla) shrub was sequenced and annotated. The similarity proportions based on the genus level, as a result of the best hits for the entire contig, were 54.84% with Weissella, 6.45% with Leuconostoc, 3.23% with Lactococcus, and 35.48% no match. The closest genome was W. cibaria SP7 (GCF_004521965.1) with 86.21% average nucleotide identity (ANI) and 3.2% alignment coverage. The genome contains 1,867 protein-coding genes, among which 1,620 were assigned with the EggNOG database. On the basis of the results, 438 proteins were classified with unknown function from which 247 new hypothetical proteins have no match in the nucleotide Basic Local Alignment Search Tool (BLASTN) database. It also contains 78 tRNAs, six copies of 5S rRNA, one copy of 16S rRNA, one copy of 23S rRNA, and one copy of tmRNA. The W. cibaria UTNGt21O strain harbors several genes responsible for carbohydrate metabolism, cellular process, general stress responses, cofactors, and vitamins, conferring probiotic features. A pangenome analysis indicated the presence of various strain-specific genes encoded for proteins responsible for the defense mechanisms as well as gene encoded for enzymes with biotechnological value, such as penicillin acylase and folates; thus, W. cibaria exhibited high genetic diversity. The genome characterization indicated the presence of a putative CRISPR-Cas array and five prophage regions and the absence of acquired antibiotic resistance genes, virulence, and pathogenic factors; thus, UTNGt21O might be considered a safe strain. Besides, the interaction between the peptide extracts from UTNGt21O and Staphylococcus aureus results in cell death caused by the target cell integrity loss and the release of aromatic molecules from the cytoplasm. The results indicated that W. cibaria UTNGt21O can be considered a beneficial strain to be further exploited for developing novel antimicrobials and probiotic products with improved technological characteristics.

Complete Genome Sequence of Weissella cibaria NH9449 and Comprehensive Comparative-Genomic Analysis: Genomic Diversity and Versatility Trait Revealed

“…We found 27 matches of putative virulence factor genes in the NH9449 genome, including tufA (elongation factor Tu), lisR (two-component response regulator), hasC (DP-glucose pyrophosphorylase) and SMU_322c (glucose-1-phosphate uridylyltransferase). These genes were previously reported in W. hellenica 0916-4-2 ( Panthee et al, 2019 ), and W. cibaria UTNGt21O ( Tenea and Hurtado, 2021 ). W. confusa FS54 encodes 133 virulence-associated genes, which is the highest number in this genus.…”

“…For instance, W. cibaria can produce bacteriocins such as weissellicin 110, which has strong activity against Gram-positive bacteria ( Srionnual et al, 2007 ; Wu et al, 2015 ). Some W. cibaria strains were reported to encode and harbor several genes with useful biotechnological properties ( Carlosama Adriana et al, 2021 ; Tenea and Hurtado, 2021 ). They also play an important role in heterofermentative metabolism and CO 2 production from carbohydrate metabolism, which makes them suitable for use in fermentation processes ( Ricciardi et al, 2009 ; Kang et al, 2016 ).…”

Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species

“…With due caution, this may represent an exploitable feature if probiotics and antibiotics are coadministered to prevent gastrointestinal disorders due to the antibiotic treatment ( 59 ). We should underline that antibiotic resistance studies on Weissella and Periweissella are limited ( 16 , 61 ), and to date, no reference cutoff values are established to determine their antibiotic resistance. Here, we assessed the MIC values of the six Weissella and Periweissella type strains analyzed, evaluating antibiotic concentrations even 10-fold higher than the ones reported by the FEEDAP panel in the guidance on the assessment of bacterial susceptibility to antimicrobials of human and veterinary importance ( 62 ).…”

Safety Evaluation of Weissella cibaria JW15 by Phenotypic and Genotypic Property Analysis

“…As a result, the COGs were classified into 26 functional categories except for Nohit against the COG database and of the 2556 protein-coding genes, 2259 genes (88.39%) were assigned to COGs categories. The W. cibaria UTNGt21O strain (1635 genes) reported by Tenea and Hurtado [39] was less than the W. cibaria JW15 strain. We found that the essential genes from the functional subcategories with the COG codes G (Carbohydrate transport and metabolism, 7.75%), J (Translation, ribosomal structure, and biogenesis, 7.67%), K (Transcription, 5.95%), L (Replication, recombination and repair, 4.38%), H (Coenzyme transport and metabolism, 3.44%), and I (Lipid transport and metabolism, 3.4%).…”