Genome analysis of food-processing stressful-resistant probiotic Bifidobacterium animalis subsp. lactis BF052, and its potential application in fermented soymilk

Probiotic potential and safety properties of Limosilactobacillus fermentum A51 with high exopolysaccharide production

Introduction

Exopolysaccharides (EPS) produced by Lactic acid bacteria have many health benefits and unique physicochemical properties. They are widely used in the food industry to improve viscosity, mouthfeel, and textural properties of foods. In our previous studies, Limosilactobacillus fermentum A51 (L. fermentum A51) isolated from yak yogurt exhibited high EPS production capacity and was applied to improve the texture of yogurt. In this study, whole genome sequencing analysis and corresponding in vitro assays were performed to investigate the probiotic potential and safety properties of L. fermentum A51.

Results

Scanning electron microscopy (SEM) observed that L. fermentum strain A51 adhered into clusters and its colony exhibited the obvious silk drawing phenomenon. Whole genome mapping revealed that L. fermentum A51 genome is 2,188,538 bp, and with an average guanine and cytosine (GC) content of 51.28%. PGAAP annotation identified 2,152 protein-encoding genes and 58 rRNAs, 15 tRNAs, and 5 5sRNAs. Hemolysis and antibiotic resistance tests, combined with the analysis of genes involved in antibiotic resistance, virulence factor, and hemolysins, suggested that L. fermentum A51 is safe. Fifty-one carbohydrate active enzyme genes in the whole genome sequence of L. fermentum A51 were annotated by carbohydrate active enzymes (CAZymes). Furthermore, L. fermentum A51 possesses adhesion, acid tolerance, bile salt tolerance, and heat tolerance genes (srtA, tuf, Bsh, nhaC, Ntn, cfa), antioxidant (nrfA, npr, nox2, tps), antibacterial genes (Idh and Dld) EPS synthesis-related genes (glf, epsG, gtf, Wzz, Wzx, Wzy), and signal molecule A1-2 synthesis-related genes (luxS, pfs). These probiotic genes were verified by quantitative real-time PCR. In vitro assays confirmed that L. fermentum A51 showed good tolerance to simulated gastrointestinal tract (8.49 log CFU/mL), 0.3% bile salt (39.06%), and possessed adhesion (86.92%), antioxidant (70.60-89.71%), and antimicrobial activities, as well as EPS and signaling molecule AI-2 synthesis capacities.

Conclusion

Collectively, our findings have confirmed that L. fermentum A51 is safe and exhibits good probiotic properties, thus recommending its potential application in the production of value-added fermented dairy products.

Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics

Members of the genus Bifidobacterium are found in a wide-range of habitats and are used as important probiotics. Thus, exploration of their functional traits at the genus level is of utmost significance. Besides, this genus has been demonstrated to exhibit an open pan-genome based on the limited number of genomes used in earlier studies. However, the number of genomes is a crucial factor for pan-genome calculations. We have analyzed the pan-genome of a comparatively larger dataset of 215 members of the genus Bifidobacterium belonging to different habitats, which revealed an open nature. The pan-genome for the 56 probiotic and human-gut strains of this genus, was also found to be open. The accessory- and unique-components of this pan-genome were found to be under the operation of Darwinian selection pressure. Further, their genome-size variation was predicted to be attributed to the abundance of certain functions carried by genomic islands, which are facilitated by insertion elements and prophages. In silico functional and host-microbe interaction analyses of their core-genome revealed significant genomic factors for niche-specific adaptations and probiotic traits. The core survival traits include stress tolerance, biofilm formation, nutrient transport, and Sec-secretion system, whereas the core probiotic traits are imparted by the factors involved in carbohydrate- and protein-metabolism and host-immunomodulations.