Genomic Insight Into Lacticaseibacillus paracasei SP5, Reveals Genes and Gene Clusters of Probiotic Interest and Biotechnological Potential

Abstract

The Lacticaseibacillus paracasei species is comprised by nomadic bacteria inhabiting a wide variety of ecological niches, from fermented foodstuffs to host-associated microenvironments. Lc. paracasei SP5 is a novel strain, originally isolated from kefir grains that presents desirable probiotic and biotechnological attributes. In this study, we applied genomic tools to further characterize the probiotic and biotechnological potential of the strain. Firstly, whole genome sequencing and assembly, were performed to construct the chromosome map of the strain and determine its genomic stability. Lc. paracasei SP5 carriers several insertion sequences, however, no plasmids or mobile elements were detected. Furthermore, phylogenomic and comparative genomic analyses were utilized to study the nomadic attributes of the strain, and more specifically, its metabolic capacity and ability to withstand environmental stresses imposed during food processing and passage through the gastrointestinal (GI) tract. More specifically, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-active enzyme (CAZymes) analyses provided evidence for the ability of the stain to utilize an array of carbohydrates as growth substrates. Consequently, genes for heat, cold, osmotic shock, acidic pH, and bile salt tolerance were annotated. Importantly bioinformatic analysis showed that the novel strain does not harbor acquired antimicrobial resistance genes nor virulence factors, in agreement with previous experimental data. Putative bacteriocin biosynthesis clusters were identified using BAGEL4, suggesting its potential antimicrobial activity. Concerning microbe-host interactions, adhesins, moonlighting proteins, exopolysaccharide (EPS) biosynthesis genes and pilins mediating the adhesive phenotype were, also, pinpointed in the genome of Lc. paracasei SP5. Validation of this phenotype was performed by employing a microbiological method and confocal microscopy. Conclusively, Lc. paracasei SP5 harbors genes necessary for the manifestation of the probiotic character and application in the food industry. Upcoming studies will focus on the mechanisms of action of the novel strain at multiple levels.

Genomic Analysis and In Vitro Investigation of the Hop Resistance Phenotype of Two Novel Loigolactobacillus backii Strains, Isolated from Spoiled Beer

“…Indeed, a cluster for F0-F1ATPase proton pump ( atpABCDEFGH ) and a sodium–proton antiporter ( nhaK ) involved in acid tolerance were found in the genome of the strains. These genes are widespread in LAB strains adapted to acidified matrices, including potential probiotic strains, able to withstand the gastrointestinal conditions of the host [ 52 ]. Accordingly, genes coding for cold-shock proteins ( cspC ), members of the universal stress protein family ( uspA ) and of the UvrABC DNA damage system were annotated, among others, in the genome of the strains.…”

Distribution and ecology of the generalist lactic acid bacterium Carnobacterium maltaromaticum in different freshwater habitats: Metabolic and antagonistic abilities

“…Furthermore, antagonistic interactions appeared to play a limited role in this context with only the piscicolin 126‐producing cultures 17‐2 and 43‐1 and the H 2 O 2 ‐producing culture 3Ba‐2‐II showing a significant degree of antagonistic activity. Other generalist (nomadic) LAB species, L. plantarum and Lacticaseibacillus casei are of interest as probiotic cultures (Fidanza et al, 2021; Kiousi et al, 2022; Kokou et al, 2019). This study shows that desirable probiotic traits such as antagonism towards bacterial pathogens are not necessarily a feature of a generalist lifestyle, which may limit the potential application of C. maltaromaticum as a fish probiotic.…”

Genetic and phenotypic assessment of the antimicrobial activity of three potential probiotic lactobacilli against human enteropathogenic bacteria

“…paracasei SP5 effectively co-aggregated and managed to significantly limit adherence of the pathogenic cells. The adhesion capacity of this putative probiotic strain has been previously reported, while proteins involved in attachment on host mucosa have been predicted in its genomic sequence ( Kiousi et al., 2022 ). Competitive exclusion may be induced by non-specific interactions with the epithelium and pathogens or by competition for host receptors by homologous proteins expressed at the surface of lactobacilli and pathogenic species that determine their adhesion in the gut niche, as reported in previous studies ( Chen et al., 2007 ; van Zyl et al., 2020 ).…”

“…plantarum L125 ( Tegopoulos et al., 2021 ) and Lc. paracasei SP5 ( Kiousi et al., 2022 ) have been previously published. Thus, here, we sought to expand the bioinformatic analysis and validate the antimicrobial potential of the strains, against clinical isolates of Staphylococcus aureus, Salmonella enterica ssp enterica serovar Enteritidis and Escherichia coli.…”