Preclinical Safety Assessment of Bacillus subtilis BS50 for Probiotic and Food Applications

Whole genome sequencing of the poly-γ-glutamic acid-producing novel Bacillus subtilis Tamang strain, isolated from spontaneously fermented kinema

Kinema, a traditional fermented soybean food from the Himalayas, is well-liked for its sticky texture and flavourful umami taste. Among 175 bacterial strains from spontaneously fermented kinema samples, Bacillus subtilis Tamang strain stood out for its high stickiness and viscosity. The strain's Poly-γ-glutamic acid (γ-PGA) contains various groups of glutamic acid and has a molecular weight of 660 kDa. It demonstrates the ability to solubilize iron, preserve ferritin in Caco-2 cells, and exhibit antibacterial properties. The genome of B. subtilis Tamang is devoid of plasmid elements but does feature nine insert elements. Noteworthy is the presence of unique secondary metabolites with potential antimicrobial effects, such as amyloliquecidin GF610, bogorol A, and thermoactinoamide A. A total of 132 carbohydrate-active enzymes (CAZy) were identified, hinting at possible prebiotic characteristics. The genome analysis revealed genes responsible for γ-PGA production via the capBCA complex. Furthermore, genes associated with fibrinolytic activity, taste enhancement, biopeptides, immunomodulators, and vitamins like B12 and K2 were found, along with probiotics and various health benefits. The genetic material for L-asparaginase production, known for its anti-cancer properties, was also detected, as well as CRISPR-Cas systems. The absence of virulence factors and antimicrobial resistance genes confirms the safety of consuming B. subtilis Tamang as a food-grade bacterium.

Engineered Bacillus subtilis as oral probiotics to enhance clearance of blood lactate

Elevated lactate concentrations are implicated in various acute and chronic diseases such as sepsis and mitochondrial dysfunction, respectively. Conversely, ineffective lactate clearance is associated with poor clinical prognoses and high mortality in these diseases. While several groups have proposed using small molecule inhibitors and enzyme replacement to reduce circulating lactate, there are few practical and effective ways to manage this condition. Recent evidence suggests that lactate is exchanged between systemic circulation and the gut, allowing bidirectional modulation between the gut microbiota and peripheral tissues. Inspired by these findings, this work seeks to engineer spore-forming probiotic B. subtilis strains to enable intestinal delivery of lactate oxidase as a therapeutic enzyme. After strain optimization, we showed that oral administration of engineered B. subtilis spores to the gut of mice reduced elevations in blood lactate in two different mouse models involving exogenous challenge or pharmacologic perturbation without disrupting gut microbiota composition, liver function, or immune homeostasis. Taken together, through the oral delivery of engineered probiotic spores to the gastrointestinal tract, our proof-of-concept study offers a practical strategy to aid in the management of disease states with elevated blood lactate and provides a new approach to 'knocking down' circulating metabolites to help understand their roles in host physiological and pathological processes.

Biological Characterization and Whole-Genome Analysis of Bacillus subtilis MG-1 Isolated from Mink Fecal Samples

Bacillus subtilis is an important part of the gut microbiota and a commonly used probiotic. In the present study, to assess the biological characteristics and probiotic properties of B. subtilis derived from mink, we isolated B. subtilis MG-1 isolate from mink fecal samples, characterized its biological characteristics, optimized the hydrolysis of casein by its crude extract, and comprehensively analyzed its potential as a probiotic in combination with whole-genome sequencing. Biological characteristics indicate that, under low-pH conditions (pH 2), B. subtilis MG-1 can still maintain a survival rate of 64.75%; under the conditions of intestinal fluid, gastric acid, and a temperature of 70 °C, the survival rate was increased by 3, 1.15 and 1.17 times compared with the control group, respectively. This shows that it can tolerate severe environments. The results of hydrolyzed casein in vitro showed that the crude bacterial extract of isolate MG-1 exhibited casein hydrolyzing activity (21.56 U/mL); the enzyme activity increased to 32.04 U/mL under optimized reaction conditions. The complete genome sequencing of B. subtilis MG-1 was performed using the PacBio third-generation sequencing platform. Gene annotation analysis results revealed that B. subtilis MG-1 was enriched in several Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways, and most genes were related to Brite hierarchy pathways (1485-35.31%) and metabolism pathways (1395-33.17%). The egg-NOG annotation revealed that most genes were related to energy production and conversion (185-4.10%), amino acid transport and metabolism (288-6.38%), carbohydrate transport and metabolism (269-5.96%), transcription (294-6.52%), and cell wall/membrane/envelope biogenesis (231-5.12%). Gene Ontology (GO) annotation elucidated that most genes were related to biological processes (8230-45.62%), cellular processes (3582-19.86%), and molecular processes (6228-34.52%). Moreover, the genome of B. subtilis MG-1 was predicted to possess 77 transporter-related genes. This study demonstrates that B. subtilis MG-1 has potential for use as a probiotic, and further studies should be performed to develop it as a probiotic additive in animal feed to promote animal health.

Bioprospecting of the Antarctic Bacillus subtilis strain for potential application in leaching hydrocarbons and trace elements from contaminated environments based on functional and genomic analysis

The production of secondary metabolites including biosurfactants by the Bacillus subtilis ANT_WA51 and the evaluation of its ability to leach metals and petroleum derivatives from the soil, using post-culture medium was investigated. The ANT_WA51 strain isolated from a pristine, harsh Antarctic environment produces the biosurfactants surfactin and fengycin, which reduce the surface tension of molasses-based post-culture medium to 26.6 mN m^-1 at a critical micellization concentration (CMC) of 50 mg L^-1 and a critical micelle dilution (CMD) of 1:19. The presence of biosurfactants and other secondary metabolites in the post-culture medium contributed to significant removal of xenobiotics from contaminated soils in the batch washing experiment - 70% hydrocarbons and 10-23% metals (Zn, Ni and Cu). The isolate's tolerance to different abiotic stresses, including freezing, freeze-thaw cycles, salinity (up to 10%), the presence of metals - Cr(VI), Pb(II), Mn(II), As(V) (up to 10 mM) and Mo(VI) (above 500 mM) and petroleum hydrocarbons (up to 20.000 mg kg^-1) as well as the confirmed metabolic activity of these bacteria in toxic environments in the OxiTop® system indicate that they can be used directly in bioremediation. Comparative genomic analysis of this bacteria revealed a high similarity of its genome to the associated plant strains from America and Europe indicating the wide applicability of plant growth-promoting Bacillus subtilis and that the data can be extrapolated to a wide range of environmental strains. An important aspect of the study was to present the absence of inherent features which would indicate its clear pathogenicity enables its safe use in the environment. Based on the obtained results, we also conclude that the use of post-culture medium, obtained on low-cost byproducts like molasses, for leaching contaminants, especially hydrocarbons, is a promising bioremediation method that can be a replacement for the use of synthetic surfactants and provides a base for further large-scale research but the selection of an appropriate leaching may be dependent on the concentration of contaminants.

Production of a Series of Long-Chain Isomaltooligosaccharides from Maltose by Bacillus subtilis AP-1 and Associated Prebiotic Properties

Bacillus subtilis strain AP-1, which produces α-glucosidase with transglucosidase activity, was used to produce a series of long-chain isomaltooligosaccharides (IMOs) with degree of polymerization (DP) ranging from 2 to 14 by direct fermentation of maltose. A total IMOs yield of 36.33 g/L without contabacillusmination from glucose and maltose was achieved at 36 h of cultivation using 50 g/L of maltose, with a yield of 72.7%. IMOs were purified by size exclusion chromatography with a Superdex 30 Increase column. The molecular mass and DP of IMOs were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS). Subsequently, linkages in produced oligosaccharides were verified by enzymatic hydrolysis with α-amylase and oligo-α-1,6-glucosidase. These IMOs showed prebiotic properties, namely tolerance to acidic conditions and digestive enzymes of the gastrointestinal tract, stimulation of probiotic bacteria growth to produce short-chain fatty acids and no stimulating effect on pathogenic bacteria growth. Moreover, these IMOs were not toxic to mammalian cells at up to 5 mg/mL, indicating their biocompatibility. Therefore, this research demonstrated a simple and economical method for producing IMOs with DP2–14 without additional operations; moreover, the excellent prebiotic properties of the IMOs offer great prospects for their application in functional foods.

Safety Evaluation of Bacillus subtilis IDCC1101, Newly Isolated from Cheonggukjang, for Industrial Applications

The present study aimed to evaluate the safety of Bacillus subtilis (BS) IDCC1101, newly isolated from Cheonggukjang in Korea. Genome sequencing of BS IDCC1101 was performed to investigate the presence of secondary metabolites, virulence, antibiotic resistance, and mobile elements. Its phenotypic safety analyses included antibiotic susceptibility, enzyme activity, carbohydrate utilization, production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and toxicities in HaCaT cells and rats. The genome of BS IDCC1101 consisted of 4,118,950 bp with 3077 functional genes. Among them, antimicrobial and antifungal secondary metabolites were found, such as fengycin, bacillibactin, and bacilysin. Antibiotic resistance and virulence genes did not exhibit transferability since they did not overlap with mobile elements in the genome. BS IDCC1101 was susceptible to almost all antibiotics suggested for assessment of BS's antibiotic susceptibility by EFSA guidelines, except for streptomycin. BS IDCC1101 showed the utilization of a wide range of 27 carbohydrates, as well as enzyme activities such as alkaline phosphatase, esterase, esterase lipase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase, α-glucosidase, and β-glucosidase activities. Additionally, BS IDCC1101 did not exhibit the production of D-/L-lactate and hemolytic activities. Its toxicity in HaCaT cells and rats was also not detected. Thus, these genotypic and phenotypic findings indicate that BS IDCC1101 can be safely used for industrial applications.

Safety Considerations for Natural Products Commonly Used By Patients with Allergic Disease

Natural products are a category of Complementary and Alternative Medicine that includes medicinal plants, vitamins, and dietary supplements. These products are often utilized by patients with allergies in conjunction with, or as an alternative to, their conventional medical therapies. Despite the wide use of these modalities, many clinicians often have limited knowledge and training in their use. It is important for health care providers to know the safety and risks of these products that their patients may use. This Clinical Commentary reviews the side effects and adverse reactions of several natural products commonly used by patients with allergies and gives an overview of the U.S. Food and Drug Administration requirements for manufacturing, advertising and distribution.

The probiotic Bacillus subtilis BS50 decreases gastrointestinal symptoms in healthy adults: a randomized, double-blind, placebo-controlled trial

ABSTRACT

Durable spore-forming probiotics are increasingly formulated into foods, beverages, and dietary supplements. To help meet this demand, the safety and efficacy of daily supplementation of Bacillus subtilis BS50 for 6 weeks was investigated in a randomized, double-blind, placebo-controlled, parallel clinical trial of 76 healthy adults. Before and during supplementation, gastrointestinal symptoms were recorded daily using a multi-symptom questionnaire. Clinical chemistry, hematology, plasma lipids, and intestinal permeability and inflammation markers were measured at baseline and end of study. Compared to placebo, 2 × 10⁹ colony-forming units (CFU) BS50 per day increased the proportion of participants showing improvement from baseline to week 6 in the composite score for bloating, burping, and flatulence (47.4% vs. 22.2%), whereby the odds of detecting an improvement were higher with BS50 (OR [95% CI]: 3.2 [1.1, 8.7], p = .024). Analyses of individual gastrointestinal symptoms indicate that BS50 increased the proportion of participants showing an improvement at week 6 compared to placebo for burping (44.7% vs. 22.2%, p = .041) and bloating (31.6% vs. 13.9%, p = .071), without affecting other symptoms. There were no clinically meaningful changes in clinical chemistry, hematology, plasma lipids and intestinal permeability and other inflammation markers. In conclusion, the results suggest that dietary supplementation of 2 × 10⁹ CFU Bacillus subtilis BS50 per day is a well-tolerated and safe strategy to alleviate gas-related gastrointestinal symptoms in healthy adults.

ABBREVIATIONS

AE adverse event; BHD bowel habits diary; BMI body mass index; BSS Bristol Stool Scale; CFU colony-forming unit; CRP C-reactive protein; FGID functional gastrointestinal disorder; GI gastrointestinal; GITQ Gastrointestinal Tolerance Questionnaire; GLP-1 glucagon-like peptide 1; GSRS Gastrointestinal Symptom Rating Scale; HDL-C high-density lipoprotein-cholesterol; IBS irritable bowel syndrome; IL-10 interleukin-10; ITT intent-to-treat; LBP lipopolysaccharide binding protein; LDL-C low-density lipoprotein-cholesterol; PP per protocol; PYY peptide YY; TG triglyceride; total-C total cholesterol.

2,4-Dichlorophenol biotransformation using immobilized marine halophilic Bacillus subtilis culture and laccase enzyme: application in wastewater treatment

Background

2,4-Dichlorophenol (2,4-DCP) is a very toxic aromatic compound for humans and the environment and is highly resistant to degradation. Therefore, it is necessary to develop efficient remediation and cost-effective approaches to this pollutant. Microbial enzymes such as laccases can degrade phenols, but limited information is known about immobilized bacterial laccase and their reuse.

Methods

Immobilization of marine halophilic Bacillus subtilis AAK cultures via entrapment and adsorption techniques and degradation of different phenolic compounds by immobilized cells were estimated. Partial purification and immobilization of laccase enzymes were carried out. In addition, the biodegradation of 2,4-DCP and others contaminated by wastewater was investigated.

Results

Immobilization of cells and partially purified laccase enzymes by adsorption into 3% alginate increased 2,4-DCP biotransformation compared with free cells and free enzymes. In addition, the reuse of both the immobilized culture and laccase enzymes was evaluated. The highest removal of 2,4-DCP from pulp and paper wastewater samples inoculated by immobilized cells and the immobilized enzyme was 90% and 95%, respectively, at 50 h and 52 h of incubation, compared to free cells and free enzyme.

Conclusion

The results of this study have revealed the immobilization of a biocatalyst and its laccase enzyme as a promising technique for enhancing the degradation of 2,4-DCP and other toxic phenolic and aromatic compounds. The reuse of the biocatalyst and its laccase enzyme enabled the application of this cost-effective bioremediation strategy.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-022-00417-1.