Assessment of the safety and probiotic characteristics of Lactobacillus salivarius CGMCC20700 based on whole-genome sequencing and phenotypic analysis

Impact of maternal Lactiplantibacillus plantarum S58 supplementation on offspring rat immunity and gut health

Pregnancy and lactation provide several opportunities for maternal dietary interventions to confer health benefits to newborns. However, the effects of maternal probiotic supplementation during pregnancy and lactation on offspring immunity and intestinal health remain largely unknown. This study aimed to investigate the effects of supplementation with the probiotic Lactiplantibacillus plantarum S58 (LP.S58) during pregnancy and lactation on the intestinal health and immunity of rat offspring. The results demonstrated that LP.S58 was effectively transmitted to the gastrointestinal tissues of offspring rats following maternal supplementation during pregnancy, lactation, or both, without affecting the normal development of individual organs. Furthermore, maternal LP.S58 supplementation significantly increased the serum levels of IL-4, IL-10, SOD, and T-AOC, while reducing those of TNF-α, IL-1β, IL-6, LPS, and NOS in the offspring. Additionally, it upregulated the mRNA expression of tight junction proteins and downregulated pro-inflammatory factors in the offspring rats, thereby improving intestinal health. More importantly, LP.S58 supplementation significantly increased the levels of beneficial gut bacteria, including Akkermansia and Lactobacillus, in the offspring rats. In conclusion, these findings indicate that maternal supplementation with specific probiotics during pregnancy and lactation may positively influence the immune function and intestinal development of offspring.

Complete genome sequence, metabolic profiling and functional studies reveal Ligilactobacillus salivarius LS-ARS2 is a promising biofilm-forming probiotic with significant antioxidant, antibacterial, and antibiofilm potential

Background

Probiotics restore microbial balance and prevent gut-inflammation. Therefore, finding out novel probiotic strains is a demand. As gut-microbe, benefits of Ligilactobacillus salivarius (LS) are established. However, strain-specific detailed studies are limited. Here, we illustrate probiotic attributes of novel LS-ARS2 for its potential application as food-supplement and/or therapeutic to improve gut-health.

Methods

Whole genome sequencing (WGS) and phylogenetic analysis confirm the strain as LS. To establish probiotic properties, acid-bile tolerance, auto-aggregation, cell-surface-hydrophobicity, biofilm-formation, and adhesion-assays are performed. To ensure safety attributes, antibiotic-susceptibility, hemolytic, DNase, trypan-blue, and MTT assays are done. ABTS, DPPH, superoxide, hydroxyl free radical scavenging assays are used to determine anti-oxidant potential. Antibacterial assays, including co-culture assay with pathogen and pathogenic biofilm-inhibition assays, are performed to explore antibacterial efficacy. To characterize metabolic-profile of LS-ARS2-derived cell-free-supernatant (CFS), HRMS analysis are carried out. Consequently, WGS-analyses predict potential molecular associations related to functional outcomes.

Results

We find LS-ARS2 a remarkable fast-growing strain that shows acid and bile tolerance (>60% survival rate), indicating promising gut-sustainability. High auto-aggregation capacity (>80%), robust cell-surface hydrophobicity (>85%), and adhesion efficacy to Caco-2 cells illustrate significant potential of LS-ARS2 for gut colonization. Fascinatingly, LS-ARS2 is able to form biofilm within 24 h (p < 0.0001), rare among LS strains, indicating the potential of the strain for efficient stay in the gut. The strain ensures safety attributes. LS-ARS2-WGS analysis recognizes probiotic-specific determinants, predicts genomic stability, identifies orthologous-clusters for diverse functions, and predicts metabolites and bacteriocins. HRMS-studies with LS-ARS2-CFS further validate the presence of diverse beneficial metabolites with antimicrobial and immunomodulatory potential. LS-ARS2 shows significant antioxidant properties in ABTS (>60%), DPPH (>10 U/mL), superoxide (>70%), and hydroxyl free radical scavenging assays (>70%). Further, LS-ARS2 shows antimicrobial activities against Gram-positive Methicillin-resistant Staphylococcus aureus (MRSA) and Gram-negative multidrug-resistant clinical strains enterotoxigenic Escherichia coli, Vibrio cholerae, and Shigella flexneri. Anti-Salmonella effect of LS-ARS2 is prominent (p < 0.0001). Most interestingly, LS-ARS2-CFS inhibits MRSA-biofilm (p < 0.0001), again rare among LS strains.

Conclusion

LS-ARS2 is a novel, fast-growing, biofilm-forming probiotic with significant antioxidant, antibacterial, and anti-biofilm potentials, suggesting the promising applications of LS-ARS2 for combating pathogenic biofilms and improving gut-health. However, further in vivo studies would facilitate their potential applications.

The Characterization of Lactic Acid Bacteria Strains as Components of a Biopreparation for Chickens for Slaughter

Since 2022, the European Union has banned the use of antibiotics in animal production. We conducted studies to characterize Lactiplantibacillus plantarum (47, AN8, and OK-B) and Ligilactobacillus salivarius (AN9) and evaluate their potential to create a biopreparation based on fermented whey for chickens. The following methods were used: lactic acid bacteria (LAB) culture and storage, crystal violet staining, Koch's plate method, Caco-2 cell culture, hydrophobicity test, and spectrophotometric measurements. All bacteria showed weak adhesion to polystyrene and collagen, and the L. plantarum species demonstrated weak adhesion to mucus. All bacteria showed strong adhesion to the intestinal epithelial cell line Caco-2. LAB showed strong autoaggregation and coaggregation with E. coli ATCC10536. The highest affinity for xylene was exhibited by L. salivarius AN9 (above 30%) while, for chloroform, the highest affinity was exhibited by L. plantarum OK-B (approx. 95%); the affinity for n-hexadecane for all strains was below 20%. The highest survival in the presence of bile salts (0.3%) was demonstrated by L. plantarum 47 (above 54%). The effect of low pH resulted in decreased viability for all strains. Significant differences were demonstrated in the concentration of lactic acid between MRS and whey medium after culturing LAB. These results will aid in qualifying these strains for further research to create a functional feed for chickens.

Probiotic Insights from the Genomic Exploration of Lacticaseibacillus paracasei Strains Isolated from Fermented Palm Sap

This study focused on L. paracasei strains isolated from fermented palm sap in southern Thailand that exhibit potential probiotic characteristics, including antibiotic susceptibility, resistance to gastrointestinal stresses, and antimicrobial activity against various pathogens. However, a thorough investigation of the whole genome sequences of L. paracasei isolates is required to ensure their safety and probiotic properties for human applications. This study aimed to sequence the genome of L. paracasei isolated from fermented palm sap, to assess its safety profile, and to conduct a comprehensive comparative genomic analysis with other Lacticaseibacillus species. The genome sizes of the seven L. paracasei strains ranged from 3,070,747 bp to 3,131,129 bp, with a GC content between 46.11% and 46.17% supporting their classification as nomadic lactobacilli. In addition, the minimal presence of cloud genes and a significant number of core genes suggest a high degree of relatedness among the strains. Meanwhile, phylogenetic analysis of core genes revealed that the strains possessed distinct genes and were grouped into two distinct clades. Genomic analysis revealed key genes associated with probiotic functions, such as those involved in gastrointestinal, oxidative stress resistance, vitamin synthesis, and biofilm disruption. This study is consistent with previous studies that used whole-genome sequencing and bioinformatics to assess the safety and potential benefits of probiotics in various food fermentation processes. Our findings provide valuable insights into the potential use of seven L. paracasei strains isolated from fermented palm sap as probiotic and postbiotic candidates in functional foods and pharmaceuticals.

Anaerobic flora, Selenomonas ruminis sp. nov., and the bacteriocinogenic Ligilactobacillus salivarius strain MP3 from crossbred-lactating goats

This study aimed to examine the distribution of anaerobic bacteria in the rumen fluid of Thai crossbred goats and to screen potential probiotic strains capable of producing antimicrobial compounds and inhibiting bacteria that cause milk fat depression. Thirty-four strains of bacteria from the rumen fluid were divided into 13 groups within 12 genera based on 16S rRNA gene sequences. The RF1-5 and RF5-12 were identified as Streptococcus luteliensis and Bacillus licheniformis, respectively, and demonstrated non-ropy exopolysaccharide. Furthermore, mPRGC5T was closely related to Selenomonas caprae JCM 33725 T (97.8% similarity) based on 16S rRNA gene sequences. It exhibited low average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values with related type strains ranging from 84.9 to 86.0%, 21.3 to 21.8%, and 73.8 to 76.1%, respectively. The genotypic and phenotypic characteristics of mPRGC5T strongly support this strain as a new species of the genus Selenomonas for which the name Selenomonas ruminis mPRGC5T was proposed. The type strain is mPRGC5T (= JCM 33724 T = KCTC 25177 T). Ligilactobacillus salivarius MP3 showed antibacterial activity against Cutibacterium acnes subsp. acnes DSM 1897 T and Kocuria rhizophila MIII. The enterolysin A cluster gene was identified in its genome. The auto-aggregation of L. salivarius MP3 was 93.6 ± 0.2%. Additionally, co-aggregation of L. salivarius MP3 with C. acnes DSM 1897 T and K. rhizophila MIII had 92.2 ± 3.4% and 87.3 ± 4.5%, respectively. The adhesion capacity of strain MP3 was 76.11 ± 2.2%. Probiogenomic analysis revealed that L. salivarius MP3 was nonhazardous to animal supplementation and included acid- and bile-tolerant ability. However, strain MP3 contained three antibiotic resistance genes. Thus, the supplementation of L. salivarius MP3 could increase the milk fat content by suppressing C. acnes DSM 1897 T with antibiotic resistance gene horizontal transfer awareness.

In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates

Bacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active enZYmes (CAZYme) profiling revealed the presence of genes and a repertoire of probiotics properties promoting enzymes. The isolates BB10.1, BP20.15 (isolated from bee bread), and PY2.3 (isolated from bee pollen) genome mining revealed the presence of several genes encoding acid, heat, cold, and other stress tolerance mechanisms, adhesion proteins required to survive and colonize harsh gastrointestinal environments, enzymes involved in the metabolism of dietary molecules, antioxidant activity, and genes associated with the synthesis of vitamins. In addition, genes responsible for the production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and other toxic compounds were also analyzed. Pan-genome analyses were performed with 180 Bacillus subtilis and 204 Bacillus velezensis genomes to mine for any novel genes present in the genomes of our isolates. Moreover, all three isolates also consisted of gene clusters encoding secondary metabolites.

Benefits and concerns of probiotics: an overview of the potential genotoxicity of the colibactin-producing Escherichia coli Nissle 1917 strain

Recently, the mounting integration of probiotics into human health strategies has gathered considerable attention. Although the benefits of probiotics have been widely recognized in patients with gastrointestinal disorders, immune system modulation, and chronic-degenerative diseases, there is a growing need to evaluate their potential risks. In this context, new concerns have arisen regarding the safety of probiotics as some strains may have adverse effects in humans. Among these strains, Escherichia coli Nissle 1917 (EcN) exhibited traits of concern due to a pathogenic locus in its genome that produces potentially genotoxic metabolites. As the use of probiotics for therapeutic purposes is increasing, the effects of potentially harmful probiotics must be carefully evaluated. To this end, in this narrative review article, we reported the findings of the most relevant in vitro and in vivo studies investigating the expanding applications of probiotics and their impact on human well-being addressing concerns arising from the presence of antibiotic resistance and pathogenic elements, with a focus on the polyketide synthase (pks) pathogenic island of EcN. In this context, the literature data here discussed encourages a thorough profiling of probiotics to identify potential harmful elements as done for EcN where potential genotoxic effects of colibactin, a secondary metabolite, were observed. Specifically, while some studies suggest EcN is safe for gastrointestinal health, conflicting findings highlight the need for further research to clarify its safety and optimize its use in therapy. Overall, the data here presented suggest that a comprehensive assessment of the evolving landscape of probiotics is essential to make evidence-based decisions and ensure their correct use in humans.

Recent and Advanced DNA-Based Technologies for the Authentication of Probiotic, Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) Fermented Foods and Beverages

The authenticity of probiotic products and fermented foods and beverages that have the status of protected designation of origin (PDO) or geographical indication (PGI) can be assessed via numerous methods. DNA-based technologies have emerged in recent decades as valuable tools to achieve food authentication, and advanced DNA-based methods and platforms are being developed. The present review focuses on the recent and advanced DNA-based techniques for the authentication of probiotic, PDO and PGI fermented foods and beverages. Moreover, the most promising DNA-based detection tools are presented. Strain- and species-specific DNA-based markers of microorganisms used as starter cultures or (probiotic) adjuncts for the production of probiotic and fermented food and beverages have been exploited for valuable authentication in several detection methods. Among the available technologies, propidium monoazide (PMA) real-time polymerase chain reaction (PCR)-based technologies allow for the on-time quantitative detection of viable microbes. DNA-based lab-on-a-chips are promising devices that can be used for the on-site and on-time quantitative detection of microorganisms. PCR-DGGE and metagenomics, even combined with the use of PMA, are valuable tools allowing for the fingerprinting of the microbial communities, which characterize PDO and PGI fermented foods and beverages, and they are necessary for authentication besides permitting the detection of extra or mislabeled species in probiotic products. These methods, in relation to the authentication of probiotic foods and beverages, need to be used in combination with PMA, culturomics or flow cytometry to allow for the enumeration of viable microorganisms.