RESUMO
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.
RESUMO
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.