Genome Characterization of Lactiplantibacillus plantarum Strain UTNGt2 Originated from Theobroma grandiflorum (White Cacao) of Ecuadorian Amazon: Antimicrobial Peptides from Safety to Potential Applications

Abstract

The genome characterization of the Lactiplantibacillus plantarum strain UTNGt2, isolated from wild copoazu or white cacao (Theobroma grandiflorum), is described. A total of 31 contigs is assembled with a total length of 3,264,448 bases, with all contigs matching the core genome of different groups in the database. The genome size is 3,540,752 bases with GC content of 44.53% and the genome repeat sequences constitute around 457,386 bases of the assembly. The UTNGt2 matches the Lactiplantibacillus plantarum genome with 99% identity. The genome contains 3115 genes, 3052 protein-coding genes, assigned with the EggNOG database. On the basis of the results, 745 proteins are classified with an unknown function, from which 128 proteins have no match in the BLASTN database. It also contains 57 tRNAs, 5 copies of 5S rRNA, and 1 copy of tmRNA. Based on gene prediction and annotation results, 9.4% of proteins are involved in carbohydrate transport and metabolism and 8.46% in transcription, 2.36% are responsible for defense mechanisms, 0.5% are responsible for the biosynthesis of secondary metabolites, transport, and catabolism, while 25.11% have an unknown function. The genome revealed the presence of genes involved in riboflavin and folate production, the presence of CRISPR/Cas genes, phage sequences, the absence of acquired antibiotics resistance genes, virulence, and pathogenic factors, suggesting that UTNGt2 is a safe strain. Its highly antimicrobial capacity is related to the presence of two bacteriocin clusters (class IIc) of the sactipeptide class (contig 4) and plantaricin E class (contig 22), as detected by the BAGEL 4 webserver. Several RiPP-like peptides (non-bactericidal ribosomally produced and post-translationally modified peptides), polyketides (PKs), and terpenes were predicted. Whole-genome sequencing analysis revealed that the UTNGt2 strain has diverse bacteriocins with a high inhibitory capacity, thus it is a bacteriocinogenic strain. Considering the safety profile, UTNGt2 is a nonpathogenic, nonvirulent strain with valuable biotechnological traits and can be further exploited for its probiotic and antimicrobial potential in the food industry or as a potential producer strain of antimicrobial peptides as an alternative to conventional antibiotics.

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

“…Lactiplantibacillus plantarum UTNGt21A and UTNGt2 strains were isolated from wild fruits of Solanum quitoense Lam. (naranjilla) and Theobroma grandiflorum (white cacao), following the procedure described in [ 19 ]. The genome assembly data of the UTNGt2 and UTNUTNGt21A strains were previously deposited to the NCBI database under the BioProject PRIJNA705232 with BioSample SAMN18053630 on 26 February 2021, and BioProject PRIJNA740042 with BioSample SAMN19816459 on June 23, 2021.…”

“…The Illumina HiSeq X Ten platform was used for sequencing using a custom assay by the design service (Macrogen Inc., Seoul, Korea). The detailed construction procedure, sequencing library, cluster generation, quality control, and statistical analyses summarized the basic characteristics of the read contig, and assembly was as described in previous studies [ 19 , 20 ]. To map the reads obtained from the sequencing, the Burrows–Wheeler aligner (BWA) (v0.7.17) and Burrows–Wheeler transform (BWT) ( , accessed on 11 September 2020) algorithms were used [ 21 ].…”

“…Previously, we prospected the microbiota of several wild fruits of the Ecuadorian Amazon [ 19 ] to select potential probiotic and antimicrobial LAB producers. Among these unique biological niches, two strains of Lactiplantibacillus plantarum —UTNGt21A and UTNGt2—were selected, and their genomes were characterized.…”

Retención de vitamina C en el procesamiento de la pulpa de copoazú (Theobroma grandiflorum) enlatada

“…Se desconocen trabajos enfocados en la retención de vitamina C durante el procesamiento de enlatado de la pulpa de copoazú o del género Theobroma, a pesar de que la literatura muestra publicaciones disímiles en diferentes periodos. De ellas, al 2021, según la base de datos de Web of Science, se publicaron trabajos de Das Neves Selis et al, 2021;De Oliveira et al, 2021;Silva et al, 2021;Tenea & Ortega, 2021. No obstante, existen antecedentes de que se ha evaluado la retención de vitamina C en frutas como naranja (Maeda & Mussa, 1986), mango (Ahmed et al, 2005), manzana anacardo (Emelike & Ebere, 2015), papaya (Avila-Gaxiola et al, 2016) y albaricoque (Adkison et al, 2018). A partir de este panorama, se planteó la siguiente hipótesis: el procesamiento adecuado de la pulpa de copoazú enlatado garantiza el uso comercial en empresas agroindustriales, además de permitir la reducción óptima de la vitamina C.…”

Distribution of bacteriocin genes in the lineages of Lactiplantibacillus plantarum

“…Lactiplantibacillus plantarum is known to produce class I and II bacteriocins, including Plns A-Y, NC81F, NC8HK, and NC8βα 11 . A new L. plantarum strain harboring genes coding for different bacteriocins rather than conventional plantaricins and showing broad inhibitory spectrum is discovered recently 12 . The bacteriocins produced by L. plantarum are known to reduce the gastrointestinal diseases by inhibiting the growth of pathogens like as Staphylococcus aureus and Listeria 13 and also known to possess antagonist effects against food spoilage 14 .…”