Whole Genome Sequencing of the Novel Probiotic Strain Lactiplantibacillus plantarum FCa3L

Lactiplantibacillus plantarum is best known for its significant adaptive potential and ability to colonize different ecological niches. Different strains of L. plantarum are widely used as probiotics. To characterize the probiotic potential of the novel L. plantarum FCa3L strain isolated from fermented cabbage, we sequenced its whole genome using the Illumina MiSeq platform. This bacterial isolate had a circular chromosome of 3,365,929 bp with 44.3% GC content and a cyclic phage phiX174 of 5386 bp with 44.7% GC content. The results of in vitro studies showed that FCa3L was comparable with the reference probiotic strain L. plantarum 8PA3 in terms of acid and bile tolerance, adhesiveness, H₂O₂ production, and acidification rate. The strain 8PA3 possessed higher antioxidant activity, while FCa3L demonstrated superior antibacterial properties. The antibiotic resistance of FCa3L was more relevant to the probiotic strain than that of 8PA3, although a number of silent antibiotic resistance genes were identified in its genome. Genomic evidence to support adhesive and antibacterial properties, biosynthesis of bioactive metabolites, and safety of FCa3L was also presented. Thus, this study confirmed the safety and probiotic properties of L. plantarum FCa3L via complete genome and phenotype analysis, suggesting its potential as a probiotic, although further in vivo investigations are still necessary.

Investigating the biotechnological potential of lactic acid bacteria strains isolated from different Algerian dairy and farm sources

Currently, consumption of spontaneously fermented milks is common in Algeria, making it a feasible source of diverse lactic acid bacteria (LAB) with the potential to be used as adjunct cultures to improve quality and safety of fermented dairy products. In this context, to select eligible indigenous strains which could be applied as bioprotective and/or starter cultures, the present study aimed to characterize the genomic variability, biotechnological potential, and safety of thirty-eight LAB isolated from Algerian dairy and farm sources of western Algeria. The isolates were unequivocally identified by 16S rRNA gene and fingerprint-based methods. The following species were identified: Enterococcus faecium (n = 15), Enterococcus durans (n = 2), Enterococcus hirae (n = 2), Enterococcus lactis (n = 1), Lactiplantibacillus plantarum (n = 6), Lactococcus lactis (n = 4), Levilactobacillus brevis (n = 3), Lacticaseibacillus paracasei (n = 3), Lacticaseibacillus rhamnosus (n = 1), and Pediococcus acidilactici (n = 1). Among the strains, three of them, L. lactis LGMY8, Lb. plantarum LGMY30 and Lb. paracasei LGMY31 were safe and showed some valuable biotechnological properties, such as high acidification, proteolytic activity, EPS production, and inhibition of undesirable bacteria that made them powerful candidates to be used as starter.

Whole-genome sequencing and genomic-based acid tolerance mechanisms of Lactobacillus delbrueckii subsp. bulgaricus LJJ

The probiotic efficacy and fermentative ability of Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus), a widely used probiotic, is majorly affected by its acid tolerance. Here, we conducted whole-genome sequencing of the high acid-tolerant L. bulgaricus LJJ stored in the laboratory. Compared with the whole genome of low acid-tolerant strain L. bulgaricus ATCC11842, the results show that 16 candidate acid-tolerant genes may be involved in the regulation of the acid tolerance of L. bulgaricus LJJ. Association analysis of candidate acid-tolerant genes and acid-tolerant traits of different L. bulgaricus strains revealed that the three genes dapA, dapH, and lysC are the main reasons for the strong acid tolerance of L. bulgaricus LJJ. The results of real-time quantitative PCR (RT-qPCR) supported this conclusion. KEGG pathway analysis showed that these three acid-tolerant genes are involved in the synthesis of lysine; the synthesis of lysine may confer L. bulgaricus LJJ strong acid tolerance. This study successfully revealed the acid tolerance mechanism of L. bulgaricus LJJ and provides a theoretical basis for the subsequent selection of strains with high acid tolerance for improved probiotic functions. KEY POINTS: • Three genes are identified as acid-tolerant genes, respectively, lysC, dapA, and dapH. • LysC and dapA are the major key genes in the synthesis of lysine. • The synthesis of lysine may confer L. bulgaricus LJJ strong acid tolerance.

Antibiotic Resistance of LACTOBACILLUS Strains

The study provides phenotypic and molecular analyses of the antibiotic resistance in 20 Lactobacillus strains including 11 strains newly isolated from fermented plant material. According to the results of disc diffusion method, 90% of tested lactobacilli demonstrated sensitivity to clindamycin and 95% of strains were susceptible to tetracycline, erythromycin, and rifampicin. Ampicillin and chloramphenicol were found to inhibit all bacteria used in this study. The vast majority of tested strains revealed phenotypic resistance to vancomycin, ciprofloxacin, and aminoglycosides. Most of Lactobacillus strains showed high minimum inhibitory concentrations (MICs) of cefotaxime, ceftriaxone, and cefazolin and therefore were considered resistant to cephalosporins. All the strains exhibited multidrug resistance. The occurrence of resistance genes was associated with phenotypic resistance, with the exception of phenotypically susceptible strains that contained genes for tetracycline (tetK, tetL) and erythromycin (ermB, mefA) resistance. The vanX gene for vancomycin resistance was among the most frequently identified among the lactobacilli (75% of strains), but the occurrence of the parC gene for ciprofloxacin resistance was sporadic (20% of strains). Our results mainly evidence the intrinsic nature of the resistance to aminoglycosides in lactobacilli, though genes for enzymatic modification of streptomycin aadA and aadE were found in 20% of tested strains. The occurrence of extended spectrum beta-lactamases (ESBL) was unknown in Lactobacillus, but our results revealed the blaTEM gene in 80% of strains, whereas blaSHV and blaOXA-1 genes were less frequent (20% and 15% of strains, respectively).