Genomic characterization and production of antimicrobial lipopeptides by Bacillus velezensis P45 growing on feather by-products

Pangenome analysis of Bacillus velezensis exploring the probiotic potential and plant growth promotion traits of strains isolated from fish intestines

New Bacillus velezensis strains with impressive antimicrobial activities are being continuously described. Here we performed genomic comparisons of five B. velezensis strains isolated from Amazonian fish intestines with other 266 genomes from the RefSeq database through a pangenome approach. We aimed to analyze the commonalities and specificities of each strain within this clade to explore their potential as probiotics and for promoting plant growth (PGP). High-quality draft genome sequences were obtained for strains P7 and P11, with genome metrics confirming their identification as B. velezensis. The evaluation of 271 B. velezensis genome sequences revealed an open pangenome composed of 14,918 homologs, while 16% of them represented the core genome. Therefore, the majority of genes belonged to the accessory variable genome, with many strains harboring numerous unique genes, including the Amazonian strain P45. This strain also stood out as carrying the potential to produce many hydrolytic enzymes and PGP traits. Genome mining of all five Amazonian strains annotated secondary metabolites with unknown identifications. The evaluated probiotic genes are mostly conserved in all B. velezensis strains. Moreover, the investigation of the mobilome, resistome, and virulence factors showed that these strains can be considered safe for probiotic and agricultural applications, corroborating our previous studies. This data will be useful to improve our understanding and biotechnological exploration of these strains and other B. velezensis as well.

The Bioavailability of Solid-State Fermented Feather Meal Using a Novel Feather-Degrading Bacterium Bacillus velezensis PN1 in Broilers

In this study, an effective feather-degrading bacterium was isolated and the solid-state fermentation condition for feather degradation was optimized. The resulting fermented feather meal (FFM) was evaluated for its bioavailability in broilers. Four Bacillus strains were examined for feather degradation rates, with Bacillus velezensis PN1 exhibiting the highest rate (83.24%, p < 0.05). A 3 × 3 × 3 factorial design was used to test substrate moisture content (45%, 55%, 65%), temperature (27 °C, 37 °C, 47 °C), and incubation time (24, 48, 72 h) for optimized fermentation conditions. In vitro pepsin digestibility (IVPD) revealed a significant interaction between temperature and time (p < 0.05), and the optimal performance was achieved at 37 °C for 72 h, followed by 37 °C for 48 h. Considering production time and cost, FFM2 (produced with 65% moisture at 37 °C for 48 h) was further compared with FFM1 (produced under the same conditions but at a lower temperature of 27 °C), and commercial hydrolyzed feather meal (HFM). IVPD did not differ significantly between FFM1, FFM2, and HFM, as they all showed significantly higher digestibility compared to raw feathers (RFs). FFM1, as well as FFM2, had significantly higher histidine and lysine concentrations than RF (p < 0.05), while FFM2 had a significantly lower cysteine content (p < 0.05). Based on fermentation conditions and amino acid composition, FFM2 was considered more suitable for large-scale production and was used in a broiler growth trial. The inclusion of 5% FFM2 in the broiler diet did not significantly affect body weight at 35 days compared to the 5% HFM group (p > 0.05), although both groups showed significantly lower weight gain than the 5% fish meal (FM) group (p < 0.05). The feed conversion ratio and performance efficiency factor did not differ significantly between the FFM2, HFM, and FM groups (p > 0.05). In groups fed diets without supplemental crystalline amino acids, growth performance did not significantly differ between the HFM and FFM2 groups (p > 0.05), although both performed significantly worse than groups with amino acid supplementation. In conclusion, FFM produced by B. velezensis PN1 through solid-state fermentation enhances feather bioavailability in poultry and can completely replace HFM when included at 5% in broiler diets, offering a potential sustainable alternative for poultry nutrition on a commercial scale.

Optimization and purification of bioproducts from Bacillus velezensis PhCL fermentation and their potential on industrial application and bioremediation

Bioproduction is considered a promising alternative way of obtaining useful and green chemicals. However, the downstream process of biomolecules has been one of the major difficulties in upscaling the application of bioproducts due to the high purification cost. Acid precipitation is the most common method for purifying biosurfactants from the fermentation broth with high purity. However, the use of strong acids and organic solvents in solvent extraction has limited its application. Hence, in this study, a new strain of Bacillus velezensis PhCL was isolated from phenolic waste, and its production of amylase had been optimized via response surface methodology. After that, amylase and biosurfactant were purified by sequential ammonium sulfate precipitation and the result suggested that even though the purified crude biosurfactant had a lower purification fold compared to the acid precipitation, the yield was higher and both enzymes and biosurfactant also could be recovered for lowering the purification cost. Moreover, the purified amylase and crude biosurfactant were characterized and the results suggested that the purified crude biosurfactant would have a higher emulsion activity and petroleum hydrocarbon removal rate compared to traditional surfactants. This study provided another approach for purifying bioactive compounds including enzymes and biosurfactants from the same fermentation broth and further explored the potential of the crude purified biosurfactant in the bioremediation of polycyclic aromatic hydrocarbons and petroleum hydrocarbons.

Response surface methodology based optimization of keratinase from Bacillus velezensis strain ZBE1 and nanoparticle synthesis, biological and molecular characterization

The increasing demands of keratinases for biodegradation of recalcitrant keratinaceous waste like chicken feathers has lead to research on newer potential bacterial keratinases to produce high-value products with biological activities. The present study reports a novel keratinolytic bacterium Bacillus velezensis strain ZBE1 isolated from deep forest soil of Western Ghats of Karnataka, which possessed efficient feather keratin degradation capability and induced keratinase production. Production kinetics depicts maximum keratinase production (11.65 U/mL) on 4th day with protein concentration of 0.61 mg/mL. Effect of various physico-chemical factors such as, inoculum size, metal ions, carbon and nitrogen sources, pH and temperature influencing keratinase production were optimized and 3.74 folds enhancement was evidenced through response surface methodology. Silver (AgNP) and zinc oxide (ZnONP) nanoparticles with keratin hydrolysate produced from chicken feathers by the action of keratinase were synthesized and verified with UV-Visible spectroscopy that revealed biological activities like, antibacterial action against Bacillus cereus and Escherichia coli. AgNP and ZnONP also showed potential antioxidant activities through radical scavenging activities by ABTS and DPPH. AgNP and ZnONP revealed cytotoxic effect against MCF-7 breast cancer cell lines with IC50 of 5.47 µg/ml and 62.26 µg/ml respectively. Characterizations of nanoparticles were carried out by Fourier transform infrared spectroscopy, scanning electron microscopy with energy dispersive X-ray, X-ray diffraction, thermogravimetric analysis and atomic force microscopy analysis to elucidate the thermostability, structure and surface attributes. The study suggests the prospective applications of keratinase to trigger the production of bioactive value-added products and significant application in nanotechnology in biomedicine.

Genetic Evidences of Biosurfactant Production in Two Bacillus subtilis Strains MB415 and MB418 Isolated From Oil Contaminated Soil

Biosurfactants are a diverse group of amphiphilic compounds obtained from microbes. In the present study, the genomic analysis of biosurfactant-producing Bacillus subtilis MB415 and MB418 obtained from oil-contaminated soil was performed. Initially, the strains were screened for biosurfactant production by hemolytic assay, emulsification index, and oil displacement. Further FTIR analysis of extracted biosurfactants revealed the presence of lipopeptides. The sequenced genomes of MB415 and MB418 were of 4.2 Mbps with 43% GC content. Among more than 4,500 protein-coding genes, many were involved in virulence, metal/multidrug resistances, flagella assembly, chemotactic response, and aromatic ring hydroxylating dioxygenases. An annotation analysis revealed that both genomes possessed non-ribosomal synthetase gene clusters for the lipopeptide synthetases srf and fen responsible for surfactin and fengycin production. Comparative studies of both genomes highlighted variability in gene operons mainly for surfactin biosynthesis.

Aspergillus carbonarius-derived ochratoxins are inhibited by Amazonian Bacillus spp. used as a biocontrol agent in grapes

Bacillus spp. have been used as a biocontrol strategy to eliminate/reduce toxic fungicides in viticulture. Furthermore, the presence of fungi that are resistant to commonly used products is frequent, highlighting the need for new biocontrol strains. Aspergillus carbonarius can produce ochratoxins, including ochratoxin A (OTA), which has a regulatory maximum allowable limit for grape products. The purpose of this study was to assess the ability of four Amazonian strains of Bacillus (P1, P7, P11, and P45) to biocontrol A. carbonarius and various forms of ochratoxins in grapes. Berries treated with strain P1 presented no fungal colonies (100% reduction), while P7, P11 and P45 strains caused a reduction of 95, 95 and 61% on fungal counts, respectively. Six forms of ochratoxin were found in the grapes inoculated with A. carbonarius, including ochratoxin α, ochratoxin β, ochratoxin α methyl-ester, ochratoxin α amide, N-formyl-ochratoxin α amide, and OTA. Four of these ochratoxin forms (ochratoxin β, ochratoxin α methyl-ester, ochratoxin α amide, N-formyl-ochratoxin α amide) are reported for the first time in grapes. These ochratoxins were identified using liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC-QToF-MS). All Bacillus strains inhibited the synthesis of OTA, which is the most toxic form of ochratoxin. No ochratoxin form was found when P1 and P7 were used. Although some forms of ochratoxin were detected in grapes treated with Bacillus spp. P11 and P45, the levels decreased by 97%. To our knowledge, this is the first report on the inhibition of Aspergillus carbonarius-derived ochratoxin by Bacillus species. P1 strain, identified as Bacillus velezensis, was found to be the most promising for completely inhibiting fungal growth and production of all ochratoxins.