Genomic Scale Analysis Foresees Enteroprotective and Butyrogenic Properties in Brazilian Isolates of Lactiplantibacillus plantarum.

Abstract

Probiogenomics offers a rapid and comprehensive approach to characterizing the beneficial properties of microorganisms, allowing the identification and selection of specific strains for improving human health. The species Lactiplantibacillus plantarum is highly ubiquitous and presents great genetic diversity making it difficult to conduct massive screening of probiotic strains when using conventional methods. Hence, this work aimed to taxonomically and functionally characterize the complete genomes of six novel L. plantarum strains isolated in Brazil through high-standard NGS. The taxonomy of strains E6, E10, E14, E18, Lpl2, and Lpl4 was investigated through average nucleotide identity analysis using the genome of L. plantarum SK151 from the GENBANK database as a reference. Moreover, multilocus phylogenetic analyses were performed to investigate their genetic relatedness to probiotic L. plantarum strains using a total of 225 complete genomes from the same database. To investigate specific health-promoting and safety properties, the isolates from Brazil were analyzed using several bioinformatic tools to predict antimicrobials and anti-inflammatory biomolecules and potential risk factors including drug resistance, virulence genes, and genetic mobility elements. The results confirmed that all six isolates belong to the species L. plantarum and the phylogenetic analysis suggests high proximity to known probiotics and strains that have demonstrated protective effects against inflammation and pathogens. Several bacteriocin genes were identified in the Brazilian isolates, mostly plantaricins, suggesting antimicrobial properties, especially in the strain E14 that presented 9 bacteriocins genes. Furthermore, the study revealed the potential capacity of these strains to produce anti-inflammatory compounds including metabolites such as butyrate through the fermentation of fructan sugars, and IL-10 stimulation activity mediated by adhesin proteins from the bacterial cell wall. The lpl4 strain glutamate decarboxylase (GADB) gene showed a high degree of genetic and structural conservation prediction and increased stabilization of the predicted protein compared to a functional homologous GADB from L. plantarum Taj-Apis362, suggesting lpl4 potential for the modulation of the gut-brain axis functions by the production of GABA. Regarding the presence of virulence and resistance genes, only one resistance island was observed in strain E6 genome. In conclusion, it is possible to suggest that most of the evaluated strains are safe and we highlight the strains Lpl4 and E14 for presenting outstanding enteroprotective properties such as the potential production of GABA and several bacteriocins.