Biotechnological applications of Bacillus licheniformis

Bacillus paralicheniformis, an acetate-producing probiotic, alleviates ulcerative colitis via protecting the intestinal barrier and regulating the NLRP3 inflammasome

Ulcerative colitis (UC) presents a challenging scenario in digestive health, characterized by recurrent inflammation that is often hard to manage. Bacteria capable of producing short-chain fatty acids (SCFAs) play a pivotal role in mitigating UC symptoms, rendering them promising candidates for probiotic therapy. In this investigation, we assessed the impact of Bacillus paralicheniformis HMPM220325 on dextran sodium sulfate (DSS)-induced UC in mice. Genomic analysis of the strain revealed the presence of protease genes associated with acetate and butyrate synthesis, with acetic acid detected in its fermentation broth. Administration of B. paralicheniformis HMPM220325 to UC mice ameliorated pathological manifestations of the condition and restored intestinal barrier function. Furthermore, B. paralicheniformis HMPM220325 suppressed the activation of the NLRP3 inflammasome signaling pathway and modulated the composition of the intestinal microbiota. These findings shed significant light on the potential of B. paralicheniformis as a probiotic candidate, offering a novel avenue for the prevention and therapeutic intervention of colitis.

Cloning, characterization and functional analysis of lichenase produced by Bacillus licheniformis RB16 isolated from cattle faeces

Lichenan, 1,3-1,4-β-Glucan, a linear polysaccharide exists in the cell walls of various cereals, has garnered attention for its industrial applications due to its enzymatic breakdown by lichenase enzymes. In this study, Bacillus licheniformis strain RB16, isolated from cattle faeces, was identified as a robust lichenase producer. The lichenase gene, licA, was successfully cloned and characterized. The cloned RB16 lichenase (LicA) demonstrated its highest activity level at pH 7.5. It also retained over 50% of its activity within the pH range of 6.0-8.5 but experienced a decline to 40% at pH 9.0. LicA was active at temperatures ranging from 25 to 65 °C with an optimum at 45 °C. LicA exhibited more than 60% of its activity at the temperature range of 35-55 °C. Zymogram analysis confirmed LicA's lichenan-degrading ability and structural analysis revealed a stable enzyme structure primarily composed of random coils and extended strands. Although LicA exhibited low thermostability, consistent with its relatively low α-helix content, it demonstrated promising industrial potential. Evolutionary analysis placed LicA within a cluster of closely related Bacillus lichenases, particularly B. halotolerans, B. atrophaeus, and B. spizizenii. These findings expand our understanding of lichenases of Bacillus and underscore its potential for various industrial applications.

Enhanced saccharification levels of corn starch using as a strategy a novel amylolytic complex (AmyHb) from the thermophilic fungus Humicola brevis var. thermoidea in association with commercial enzyme

Amylases represent a versatile group of catalysts that are used for the saccharification of starch because they can hydrolyze the glycosidic bonds of starch molecules to release glucose, maltose, and short-chain oligosaccharides. The amylolytic complex of the thermophilic filamentous fungus Humicola brevis var. thermoidea (AmyHb) was produced, biochemically characterized, and compared with the commercial amylase Termamyl. In addition, the biotechnological application of AmyHb in starch saccharification was investigated. The highest production was achieved using a wheat bran medium at 50 °C for 5-6 days in solid-state fermentation (849.6 ± 18.2 U·g-1) without the addition of inducers. Optimum amylolytic activity occurred at pH 5.0 at 60 °C, and stability was maintained between pH 5.0 and 6.0, with thermal stability at 50-60 °C, especially in the presence of Ca2+. These results were superior to those found with Termamyl. Both enzymes were strongly inhibited by Hg2+, Cu2+, and Ag+; however, AmyHb displayed increased activity in the presence of Mn2+ and Na+. In addition, AmyHb showed greater tolerance to a wide range of ethanol concentrations. AmyHb appears to be a complex consisting of glucoamylase and α-amylase, based on its substrate specificity and TLC. The hydrolysis tests on cornstarch flour showed that the cocktail of AmyHb50% + Termamyl50% significantly increased the release of glucose and total reducing sugars (36.6%) when compared to the enzymes alone. AmyHb exhibited promising physicochemical properties and good performance with commercial amylase; therefore, this complex is a biotechnological alternative candidate for the bioprocessing of starch sources.

Advancing Bacillus licheniformis as a Superior Expression Platform through Promoter Engineering

Bacillus licheniformis is recognised as an exceptional expression platform in biomanufacturing due to its ability to produce high-value products. Consequently, metabolic engineering of B. licheniformis is increasingly pursued to enhance its utility as a biomanufacturing vehicle. Effective B. licheniformis cell factories require promoters that enable regulated expression of target genes. This review discusses recent advancements in the characterisation, synthesis, and engineering of B. licheniformis promoters. We highlight the application of constitutive promoters, quorum sensing promoters, and inducible promoters in protein and chemical synthesis. Additionally, we summarise efforts to expand the promoter toolbox through hybrid promoter engineering, transcription factor-based inducible promoter engineering, and ribosome binding site (RBS) engineering.

Co-removal and recycling of Ba2+ and Ca2+ in hypersaline wastewater based on the microbially induced carbonate precipitation technique: Overlooked Ba2+ in extracellular and intracellular vaterite

This study investigates the co-precipitation of calcium and barium ions in hypersaline wastewater under the action of Bacillus licheniformis using microbially induced carbonate precipitation (MICP) technology, as well as the bactericidal properties of the biomineralized product vaterite. The changes in carbonic anhydrase activity, pH, carbonate and bicarbonate concentrations in different biomineralization systems were negatively correlated with variations in metal ion concentrations, while the changes in polysaccharides and protein contents in bacterial extracellular polymers were positively correlated with variations in barium concentrations. In the mixed calcium and barium systems, the harvested minerals were vaterite containing barium. The increasing concentrations of calcium promoted the incorporation and adsorption of barium onto vaterite. The presence of barium significantly increased the contents of O-CO, N-CO, and Ba-O in vaterite. Calcium promoted barium precipitation, but barium inhibited calcium precipitation. After being treated by immobilized bacteria, the concentrations of calcium and barium ions decreased from 400 and 274 to 1.72 and 0 mg/L (GB/T15454-2009 and GB8978-1996). Intracellular minerals were also vaterite containing barium. Extracellular vaterite exhibited bactericidal properties. This research presents a promising technique for simultaneously removing and recycling hazardous heavy metals and calcium in hypersaline wastewater.

BsuMI regulates DNA transformation in Bacillus subtilis besides the defense system and the constructed strain with BsuMI-absence is applicable as a universal transformation platform for wild-type Bacillus

BACKGROUND

To effectively introduce plasmids into Bacillus species and conduct genetic manipulations in Bacillus chassis strains, it is essential to optimize transformation methods. These methods aim to extend the period of competence and enhance the permeability of the cell membrane to facilitate the entry of exogenous DNA. Although various strategies have been explored, few studies have delved into identifying metabolites and pathways associated with enhanced competence. Additionally, derivative Bacillus strains with non-functional restriction-modification systems have demonstrated superior efficiency in transforming exogenous DNA, lacking more explorations in the regulation conducted by the restriction-modification system to transformation process.

RESULTS

Transcriptomic comparisons were performed to discover the competence forming mechanism and the regulation pathway conducted by the BsuMI methylation modification group in Bacillus. subtilis 168 under the Spizizen transformation condition, which were speculated to be the preferential selection of carbon sources by the cells and the preference for specific metabolic pathway when utilizing the carbon source. The cells were found to utilize the glycolysis pathway to exploit environmental glucose while reducing the demand for other phosphorylated precursors in this pathway. The weakening of these ATP-substrate competitive metabolic pathways allowed more ATP substrates to be distributed into the auto-phosphorylation of the signal transduction factor ComP during competence formation, thereby increasing the expression level of the key regulatory protein ComK. The expression of ComK upregulated the expression of the negative regulator SacX of starch and sucrose in host cells, reinforcing the preference for glucose as the primary carbon source. The methylation modification group of the primary protein BsuMI in the restriction-modification system was associated with the functional modification of key enzymes in the oxidative phosphorylation pathway. The absence of the BsuMI methylation modification group resulted in a decrease in the expression of subunits of cytochrome oxidase, leading to a weakening of the oxidative phosphorylation pathway, which promoted the glycolytic rate of cells and subsequently improved the distribution of ATP molecules into competence formation. A genetic transformation platform for wild-type Bacillus strains was successfully established based on the constructed strain B. subtilis 168-R-M- without its native restriction-modification system. With this platform, high plasmids transformation efficiencies were achieved with a remarkable 63-fold improvement compared to the control group and an increased universality in Bacillus species was also obtained.

CONCLUSIONS

The enhanced competence formation mechanism and the regulation pathway conducted by the functional protein BsuMI of the restriction-modification system were concluded, providing a reference for further investigation. An effective transformation platform was established to overcome the obstacles in DNA transformations in wild-type Bacillus strains.

Establishment of the CRISPR-Cpf1 gene editing system in Bacillus licheniformis and multiplexed gene knockout

Bacillus licheniformis is a significant industrial microorganism. Traditional gene editing techniques relying on homologous recombination often exhibit low efficiency due to their reliance on resistance genes. Additionally, the established CRISPR gene editing technology, utilizing Cas9 endonuclease, faces challenges in achieving simultaneous knockout of multiple genes. To address this limitation, the CRISPR-Cpf1 system has been developed, enabling multiplexed gene editing across various microorganisms. Key to the efficient gene editing capability of this system is the rigorous screening of highly effective expression elements to achieve conditional expression of protein Cpf1. In this study, we employed mCherry as a reporter gene and harnessed P mal for regulating the expression of Cpf1 to establish the CRISPR-Cpf1 gene editing system in Bacillus licheniformis. Our system achieved a 100 % knockout efficiency for the single gene vpr and up to 80 % for simultaneous knockout of the double genes epr and mpr. Furthermore, the culture of a series of protease-deficient strains revealed that the protease encoded by aprE contributed significantly to extracellular enzyme activity (approximately 80 %), whereas proteases encoded by vpr, epr, and mpr genes contributed to a smaller proportion of extracellular enzyme activity. These findings provide support for effective molecular modification and metabolic regulation in industrial organisms.

Antioxidant and Emulsifying Activity of the Exopolymer Produced by Bacillus licheniformis

The exopolymer (ESPp) was obtained from Bacillus licheniformis IDN-EC, composed of a polyglutamic acid and polyglycerol phosphate chain O-substituted with αGal moieties (αGal/αGlcNH2 3:1 molar ratio) and with a 5000 Da molecular weight. The cytotoxicity activity of EPSp was determined by reducing the MTT (3-[4,5-dimethyl-thiazol-2-yl]-2,5-diphenyltetrazolium bromide) to formazan on HeLa cells. This EPS did not show cytotoxicity against the tested cell line. The ESPp presented great advantages as an antioxidant with free radical scavenging activities (1,1-diphenyl-2-picryl-hydrazyl radical (DPPH),hydroxyl radical (OH), and superoxide anion (O2-)) (65 ± 1.2%, 98.7 ± 1.9%, and 97 ± 1.7%), respectively. Moreover, EPSp increased the enzyme activity for catalase (CAT) and glutathione peroxidase (GSH-Px) in HeLa cells (CAT, 2.6 ± 0.24 U/mL; and GSH-Px, 0.75 ± 0.3 U/L). The presence of ESPp showed a significant protective effect against H2O2 in the cell line studied, showing great viability (91.8 ± 2.8, 89.9 ± 2.9, and 93.5 ± 3.6%). The EPSp presented good emulsifying activity, only for vegetable oils, olive oil (50 ± 2.1%) and sesame (72 ± 3%). Sesame was effective compared to commercials products, Triton X-100 (52.38 ± 1.6%), Tween 20 (14.29 ± 1.1%), and sodium dodecyl sulphate (SDS) (52.63 ± 1.6%). Furthermore, the EPS produced at 0.6 M has potential for environmental applications, such as the removal of hazardous materials by emulsification whilst resulting in positive health effects such as antioxidant activity and non-toxicity. EPSp is presented as a good exopolysaccharide for various applications.

LC-MS/MS profiling and analysis of Bacillus licheniformis extracellular proteins for antifungal potential against Candida albicans

Candida albicans, a significant human pathogenic fungus, employs hydrolytic proteases for host invasion. Conventional antifungal agents are reported with resistance issues from around the world. This study investigates the role of Bacillus licheniformis extracellular proteins (ECP) as effective antifungal peptides (AFPs). The aim was to identify and characterize the ECP of B. licheniformis through LC-MS/MS and bioinformatics analysis. LC-MS/MS analysis identified 326 proteins with 69 putative ECP, further analyzed in silico. Of these, 21 peptides exhibited antifungal properties revealed by classAMP tool and are predominantly anionic. Peptide-protein docking revealed interactions between AFPs like Peptide chain release factor 1 (Q65DV1_Seq1: SASEQLSDAK) and Putative carboxy peptidase (Q65IF0_Seq7: SDSSLEDQDFILESK) with C. albicans virulent SAP5 proteins (PDB ID 2QZX), forming hydrogen bonds and significant Pi-Pi interactions. The identification of B. licheniformis ECP is the novelty of the study that sheds light on their antifungal potential. The identified AFPs, particularly those interacting with bonafide pharmaceutical targets SAP5 of C. albicans represent promising avenues for the development of antifungal treatments with AFPs that could be the pursuit of a novel therapeutic strategy against C. albicans. SIGNIFICANCE OF STUDY: The purpose of this work was to carry out proteomic profiling of the secretome of B. licheniformis. Previously, the efficacy of Bacillus licheniformis extracellular proteins against Candida albicans was investigated and documented in a recently communicated manuscript, showcasing the antifungal activity of these proteins. In order to achieve high-throughput identification of ES (Excretory-secretory) proteins, the utilization of liquid chromatography tandem mass spectrometry (LC-MS) was utilized. There was a lack of comprehensive research on AFPs in B. licheniformis, nevertheless. The proteins secreted by B. licheniformis in liquid medium were initially discovered using liquid chromatography-tandem mass spectrometry (LC-MS) analysis and identification in order to immediately characterize the unidentified active metabolites in fermentation broth.

Effects of Feather Hydrolysates Generated by Probiotic Bacillus licheniformis WHU on Gut Microbiota of Broiler and Common carp

Due to the ever-increasing demand for meat, it has become necessary to identify cheap and sustainable sources of protein for animal feed. Feathers are the major byproduct of poultry industry, which are rich in hard-to-degrade keratin protein. Previously we found that intact feathers can be digested into free amino acids, short peptides, and nano-/micro-keratin particles by the strain Bacillus licheniformis WHU in water, and the resulting feather hydrolysates exhibit prebiotic effects on mice. To explore the potential utilization of feather hydrolysate in the feed industry, we investigated its effects on the gut microbiota of broilers and fish. Our results suggest that feather hydrolysates significantly decrease and increase the diversity of gut microbial communities in broilers and fish, respectively. The composition of the gut microbiota was markedly altered in both of the animals. The abundance of bacteria with potentially pathogenic phenotypes in the gut microbial community of the fish significantly decreased. Staphylococcus spp., Pseudomonas spp., Neisseria spp., Achromobacter spp. were significantly inhibited by the feather hydrolysates. In addition, feather hydrolysates significantly improved proteolytic activity in the guts of broilers and fish. In fish, the expression levels of ZO-1 and TGF-α significantly improved after administration of feather hydrolysates. The results presented here suggest that feather hydrolysates generated by B. licheniformis WHU could be an alternative protein source in aquaculture and could exert beneficial effects on fish.

Exploring Bacillus subtilis: Ecology, biotechnological applications, and future prospects

From its early identification by Christian Gottfried Ehrenberg to its current prominence in scientific research, Bacillus subtilis (B. subtilis) has emerged as a foundational model organism in microbiology. This comprehensive review delves deep into its genetic, physiological, and biochemical intricacies, revealing a sophisticated cellular blueprint. With the incorporation of advanced techniques such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 and integrative computational methodologies, the potential applications of B. subtilis span diverse sectors. These encompass its significant contributions to biotechnology, agriculture, and medical fields and its potential for aiding environmental cleanup efforts. Yet, as we move forward, we must grapple with concerns related to safety, ethics, and the practical implementation of our lab findings in everyday scenarios. As our understanding of B. subtilis deepens, it is evident that its contributions will be central to pioneering sustainable solutions for global challenges in the years to come.

Modulation of Gut Microbial Community and Metabolism by Bacillus licheniformis HD173 Promotes the Growth of Nursery Piglets Model

Maintaining the balance and stability of the gut microbiota is crucial for the gut health and growth development of humans and animals. Bacillus licheniformis (B. licheniformis) has been reported to be beneficial to the gut health of humans and animals, whereas the probiotic effects of a new strain, B. licheniformis HD173, remain uncertain. In this study, nursery piglets were utilized as animal models to investigate the extensive impact of B. licheniformis HD173 on gut microbiota, metabolites, and host health. The major findings were that this probiotic enhanced the growth performance and improved the health status of the nursery piglets. Specifically, it reduced the level of pro-inflammatory cytokines IL-1β and TNF-α in the serum while increasing the level of IL-10 and SOD. In the gut, B. licheniformis HD173 reduced the abundance of pathogenic bacteria such as Mycoplasma, Vibrio, and Vibrio metschnikovii, while it increased the abundance of butyrate-producing bacteria, including Oscillospira, Coprococcus, and Roseburia faecis, leading to an enhanced production of butyric acid. Furthermore, B. licheniformis HD173 effectively improved the gut metabolic status, enabling the gut microbiota to provide the host with stronger metabolic abilities for nutrients. In summary, these findings provide scientific evidence for the utilization of B. licheniformis HD173 in the development and production of probiotic products for maintaining gut health in humans and animals.

Comparative Genomics Unveils Functional Diversity, Pangenome Openness, and Underlying Biological Drivers among Bacillus subtilis Group

The Bacillus subtilis group (Bs group), with Bacillus subtilis as its core species, holds significant research and economic value in various fields, including science, industrial production, food, and pharmaceuticals. However, most studies have been confined to comparative genomics analyses and exploration within individual genomes at the level of species, with few conducted within groups across different species. This study focused on Bacillus subtilis, the model of Gram-positive bacteria, and 14 other species with significant research value, employing comparative pangenomics as well as population enrichment analysis to ascertain the functional enrichment and diversity. Through the quantification of pangenome openness, this work revealed the underlying biological drivers and significant correlation between pangenome openness and various factors, including the distribution of toxin-antitoxin- and integrase-related genes, as well as the number of endonucleases, recombinases, repair system-related genes, prophages, integrases, and transfer mobile elements. Furthermore, the functional enrichment results indicated the potential for secondary metabolite, probiotic, and antibiotic exploration in Bacillus licheniformis, Bacillus paralicheniformis, and Bacillus spizizenii, respectively. In general, this work systematically exposed the quantification of pangenome openness, biological drivers, the pivotal role of genomic instability factors, and mobile elements, providing targeted exploration guidance for the Bs group.

Effect of Ba2+ on the biomineralization of Ca2+ and Mg2+ ions induced by Bacillus licheniformis

The effect of barium ions on the biomineralization of calcium and magnesium ions is often overlooked when utilizing microbial-induced carbonate precipitation technology for removing barium, calcium, and magnesium ions from oilfield wastewater. In this study, Bacillus licheniformis was used to bio-precipitate calcium, magnesium, and barium ions. The effects of barium ions on the physiological and biochemical characteristics of bacteria, as well as the components of extracellular polymers and mineral characteristics, were also studied in systems containing coexisting barium, calcium, and magnesium ions. The results show that the increasing concentrations of barium ions decreased pH, carbonic anhydrase activity, and concentrations of bicarbonate and carbonate ions, while it increased the contents of humic acids, proteins, polysaccharides, and DNA in extracellular polymers in the systems containing all three types of ions. With increasing concentrations of barium ions, the content of magnesium within magnesium-rich calcite and the size of minerals precipitated decreased, while the full width at half maximum of magnesium-rich calcite, the content of O-C=O and N-C=O, and the diversity of protein secondary structures in the minerals increased in systems containing all three coexisting ions. Barium ions does inhibit the precipitation of calcium and magnesium ions, but the immobilized bacteria can mitigate the inhibitory effect. The precipitation ratios of calcium, magnesium, and barium ions reached 81-94%, 68-82%, and 90-97%. This research provides insights into the formation of barium-enriched carbonate minerals and offers improvements for treating oilfield wastewater.

Bacillus licheniformis ameliorates Aflatoxin B1-induced testicular damage by improving the gut-metabolism-testis axis

Global aflatoxin B1 (AFB1) contamination is inevitable, and it can significantly damage testicular development. However, the current mechanism is confusing. Here, by integrating the transcriptome, microbiome, and serum metabolome, we comprehensively explain the impact of AFB1 on testis from the gut-metabolism-testis axis. Transcriptome analysis suggested that AFB1 exposure directly causes abnormalities in testicular inflammation-related signalling, such as tumor necrosis factor (TNF) pathway, and proliferation-related signalling pathways, such as phosphatidylinositide 3-kinases-protein kinase B (PI3K-AKT) pathway, which was verified by immunofluorescence. On the other hand, we found that upregulated inflammatory factors in the intestine after AFB1 exposure were associated with intestinal microbial dysbiosis, especially the enrichment of Bacilli, and enrichment analysis showed that this may be related to NLR family pyrin domain containing 3 (NLRP3)-mediated NOD-like receptor signalling. Also, AFB1 exposure caused blood metabolic disturbances, manifested as decreased hormone levels and increased oxidative stress. Significantly, B. licheniformis has remarkable AFB1 degradation efficiency (> 90%). B. licheniformis treatment is effective in attenuating gut-testis axis damage caused by AFB1 exposure through the above-mentioned signalling pathways. In conclusion, our findings indicate that AFB1 exposure disrupts testicular development through the gut-metabolism-testis axis, and B. licheniformis can effectively degrade AFB1.

Molecular mechanism of cellulose depolymerization by the two-domain BlCel9A enzyme from the glycoside hydrolase family 9

Carbohydrate-active enzymes from the glycoside hydrolase family 9 (GH9) play a key role in processing lignocellulosic biomass. Although the structural features of some GH9 enzymes are known, the molecular mechanisms that drive their interactions with cellulosic substrates remain unclear. To investigate the molecular mechanisms that the two-domain Bacillus licheniformis BlCel9A enzyme utilizes to depolymerize cellulosic substrates, we used a combination of biochemical assays, X-ray crystallography, small-angle X-ray scattering, and molecular dynamics simulations. The results reveal that BlCel9A breaks down cellulosic substrates, releasing cellobiose and glucose as the major products, but is highly inefficient in cleaving oligosaccharides shorter than cellotetraose. In addition, fungal lytic polysaccharide oxygenase (LPMO) TtLPMO9H enhances depolymerization of crystalline cellulose by BlCel9A, while exhibiting minimal impact on amorphous cellulose. The crystal structures of BlCel9A in both apo form and bound to cellotriose and cellohexaose were elucidated, unveiling the interactions of BlCel9A with the ligands and their contribution to substrate binding and products release. MD simulation analysis reveals that BlCel9A exhibits higher interdomain flexibility under acidic conditions, and SAXS experiments indicate that the enzyme flexibility is induced by pH and/or temperature. Our findings provide new insights into BlCel9A substrate specificity and binding, and synergy with the LPMOs.

Draft genome sequences of Bacillus licheniformis strains MEZBL63 and MEZBL64 harboring the lichenysin toxin operon isolated from livestock in South Africa

Here, we report the draft genome sequences of two Bacillus licheniformis strains harboring the lichenysin operon that were isolated from healthy goat and horse in South Africa. The genomes were sequenced using Illumina MiSeq and had a length of 4,152,826 and 4,110,075 bp, respectively, with a G + C content of 46%.

Development of Biological Coating from Novel Halophilic Exopolysaccharide Exerting Shelf-Life-Prolonging and Biocontrol Actions for Post-Harvest Applications

The literature presents the preserving effect of biological coatings developed from various microbial sources. However, the presented work exhibits its uniqueness in the utilization of halophilic exopolysaccharides as food coating material. Moreover, such extremophilic exopolysaccharides are more stable and economical production is possible. Consequently, the aim of the presented research was to develop a coating material from marine exopolysaccharide (EPS). The significant EPS producers having antagonistic attributes against selected phytopathogens were screened from different marine water and soil samples. TSIS01 isolate revealed the maximum antagonism well and EPS production was selected further and characterized as Bacillus tequilensis MS01 by 16S rRNA analysis. EPS production was optimized and deproteinized EPS was assessed for biophysical properties. High performance thin layer chromatography (HPTLC) analysis revealed that EPS was a heteropolymer of glucose, galactose, mannose, and glucuronic acid. Fourier transform infrared spectroscopy, X-ray diffraction, and UV-visible spectra validated the presence of determined sugars. It showed high stability at a wide range of temperatures, pH and incubation time, ≈1.63 × 106 Da molecular weight, intermediate solubility index (48.2 ± 3.12%), low water holding capacity (12.4 ± 1.93%), and pseudoplastic rheologic shear-thinning comparable to xanthan gum. It revealed antimicrobial potential against human pathogens and antioxidants as well as anti-inflammatory potential. The biocontrol assay of EPS against phytopathogens revealed the highest activity against Alternaria solani. The EPS-coated and control tomato fruits were treated with A. solani suspension to check the % disease incidence, which revealed a significant (p < 0.001) decline compared to uncoated controls. Moreover, it revealed shelf-life prolonging action on tomatoes comparable to xanthan gum and higher than chitosan. Consequently, the presented marine EPS was elucidated as a potent coating material to mitigate post-harvest losses.

Genome sequence and assembly of the amylolytic Bacillus licheniformis T5 strain isolated from Kazakhstan soil

OBJECTIVES

The data presented in this study were collected with the aim of obtaining the complete genomes of specific strains of Bacillus bacteria, namely, Bacillus licheniformis T5. This strain was chosen based on its enzymatic activities, particularly amylolytic activity. In this study, nanopore sequencing technology was employed to obtain the genome sequences of this strain. It is important to note that these data represent a focused objective within a larger research context, which involves exploring the biochemical features of promising Bacilli strains and investigating the relationship between enzymatic activity, phenotypic features, and the microorganism's genome.

DATA DESCRIPTION

In this study, the whole-genome sequence was obtained from one Bacillus strain, Bacillus licheniformis T5, isolated from soil samples in Kazakhstan. Sample preparation and genomic DNA library construction were performed according to the Ligation sequencing gDNA kit (SQK-LSK109) protocol and NEBNext module. The prepared library was sequenced on a MinION instrument (Oxford Nanopore Technologies nanopore sequencer with a maximum throughput of up to 30 billion nucleotides per run and no limit on read length), using a flow cell for nanopore sequencing FLO-MIN106D. The genome de novo assembly was performed using the long sequencing reads generated by MinION Oxford Nanopore platform. Finally, one circular contig was obtained harboring a length of 4,247,430 bp with 46.16% G + C content and the mean contig 428X coverage. B. licheniformis T5 genome assembly annotation revealed 5391 protein-coding sequences, 81 tRNAs, 51 repeat regions, 24 rRNAs, 3 virulence factors and 53 antibiotic resistance genes. This sequence encompasses the complete genetic information of the strain, including genes, regulatory elements, and noncoding regions. The data reveal important insights into the genetic characteristics, phenotypic traits, and enzymatic activity of this Bacillus strain. The findings of this study have particular value to researchers interested in microbial biology, biotechnology, and antimicrobial studies. The genomic sequence offers a foundation for understanding the genetic basis of traits such as endospore formation, alkaline tolerance, temperature range for growth, nutrient utilization, and enzymatic activities. These insights can contribute to the development of novel biotechnological applications, such as the production of enzymes for industrial purposes. Overall, this study provides valuable insights into the genetic characteristics, phenotypic traits, and enzymatic activities of the Bacillus licheniformis T5 strain. The acquired genomic sequences contribute to a better understanding of this strain and have implications for various research fields, such as microbiology, biotechnology, and antimicrobial studies.

Let There Be Light: Genome Reduction Enables Bacillus subtilis to Produce Disulfide-Bonded Gaussia Luciferase

Bacillus subtilis is a major workhorse for enzyme production in industrially relevant quantities. Compared to mammalian-based expression systems, B. subtilis presents intrinsic advantages, such as high growth rates, high space-time yield, unique protein secretion capabilities, and low maintenance costs. However, B. subtilis shows clear limitations in the production of biopharmaceuticals, especially proteins from eukaryotic origin that contain multiple disulfide bonds. In the present study, we deployed genome minimization, signal peptide screening, and coexpression of recombinant thiol oxidases as strategies to improve the ability of B. subtilis to secrete proteins with multiple disulfide bonds. Different genome-reduced strains served as the chassis for expressing the model protein Gaussia Luciferase (GLuc), which contains five disulfide bonds. These chassis lack extracellular proteases, prophages, and key sporulation genes. Importantly, compared to the reference strain with a full-size genome, the best-performing genome-minimized strain achieved over 3000-fold increased secretion of active GLuc while growing to lower cell densities. Our results show that high-level GLuc secretion relates, at least in part, to the absence of major extracellular proteases. In addition, we show that the thiol-disulfide oxidoreductase requirements for disulfide bonding have changed upon genome reduction. Altogether, our results highlight genome-engineered Bacillus strains as promising expression platforms for proteins with multiple disulfide bonds.

Effect of lipopeptide extracted from Bacillus licheniformis on the expression of bap and luxI genes in multi-drug-resistant Acinetobacter baumannii and Pseudomonas aeruginosa

Recently, opportunistic pathogens like Acinetobacter baumannii and Pseudomonas aeruginosa have caused concern due to their ability to cause antibiotic resistance in weakened immune systems. As a result, researchers are always seeking efficient antimicrobial agents to tackle this issue. The hypothesis of the recent study was that probiotic products derived from bacteria would be effective in reducing drug resistance in other bacteria. This research aimed to investigate the antimicrobial properties of probiotic products from various bacterial strains, including Lactobacillus rhamnosus, Pediococcus acidilactisi, Bacillus coagulans, Bacillus subtilis, and Bacillus licheniformis. These were tested against multi-drug-resistant (MDR) standard strains A. baumannii and P. aeruginosa. B. licheniformis was found to be the most effective probiotic strain, possessing the LanA and LanM lantibiotic genes. The lipopeptide nature of the probiotic product was confirmed through high-performance liquid chromatography (HPLC) and Fourier-transform infrared spectroscopy (FTIR) techniques. The anti-biofilm and antimicrobial properties of this probiotic were measured using an SEM electron microscope and minimum inhibitory concentration (MIC) test. Real-time PCR (qPCR) was used to compare the expression of bap and luxI genes, which are considered virulence factors of drug-resistant bacteria, before and after treatment with antimicrobial agents. The MIC results showed that the probiotic product prevented the growth of bacteria at lower concentrations compared to antibiotics. In addition, the ΔΔCqs indicated that gene expression was significantly down-regulated following treatment with the obtained probiotic product. It was found that B. licheniformis probiotic products could reduce drug resistance in other bacteria, making it a potential solution to antibiotic resistance.

Bioconversion of feather waste into bioactive nutrients in water by Bacillus licheniformis WHU

Feathers become hazardous pollutants when deposited directly into the environment. The rapid expansion of the poultry industry has significantly increased feather waste, necessitating the development of new ways to degrade and utilize feathers. This study investigated the ability of Bacillus licheniformis WHU to digest intact chicken feathers in water. The results indicated that yields of free amino acids, bioactive peptides, and keratin-derived nano-/micro-particles were improved in bacteria- versus purified keratinase-derived feather hydrolysate. Bacteria-derived feather hydrolysate supplementation induced health benefits in mice, including significantly increased intestinal villus height and zonula occludens-1 protein expression, as well as increased secretory immunoglobulin A levels in the intestinal mucosa and superoxide dismutase activity in serum. Additionally, feather hydrolysate supplementation modulated the mouse gut microbiota, reflected by increased relative abundance of probiotics such as Lactobacillus spp., decreased relative abundance of Proteobacteria at the phylum level and pathogens such as Staphylococcus spp., and increased Bacteroidota/Firmicutes ratio. This study developed a simple, cost-effective method to degrade feathers by B. licheniformis WHU digestion, yielding a hydrolysate that can be directly used as a bioactive nutrient resource. The study findings have applications in the livestock, poultry, and aquaculture industries, which have high demands for cheap protein. KEY POINTS: • Bacillus licheniformis could degrade intact feather in water. • The resulting feather hydrolysate shows prebiotic effects on mouse.

Bacillus subtilis RBT-7/32 and Bacillus licheniformis RBT-11/17 as New Promising Strains for Use in Probiotic Feed Additives

The normal functioning of a gastrointestinal microflora in poultry and livestock is of significant importance, since its imbalance negatively influences an organism's functions. In this study, the UV mutagenesis and selection were used to obtain two Bacillus strains possessing antagonistic activity towards Escherichia coli and Staphylococcus aureus, and their potential as a probiotic feed additive was evaluated. Compared to the parental strains, the ability of B. subtilis RBT-7/32 and B. licheniformis RBT-11/17 strains to suppress E. coli increased by 77 and 63%, respectively; the corresponding ability of these strains to suppress S. aureus increased by 80 and 79%, respectively. RBT-11/17 could not utilize microcrystalline cellulose and carboxymethyl cellulose, whereas cellulolytic activity of RBT-7/32 was doubled compared to the initial strain. The amylolytic activity of new strains was increased by 40%. Cultivation of strains on media containing soybean, pea, and corn meal did not provide any difference in the biomass production compared to the control. The heating of a water suspension of a dried biomass of the strains for 10-20 min at 80 and 100 °C or incubation in water solutions of citric, ascorbic, acetic, and formic acids (pH 3.0) for 3 and 24 h at 40 °C did not provide any negative influence on the spore survivability. Both strains were evaluated for their resistance to a number of veterinary antibiotics. Thus, RBT-7/32 and RBT-11/17 strains have good prospects for use in feed additives.

Response of a new rumen-derived Bacillus licheniformis to different carbon sources

Introduction

Bacillus licheniformis (B. licheniformis) is a microorganism with a wide range of probiotic properties and applications. Isolation and identification of novel strains is a major aspect of microbial research. Besides, different carbon sources have varying effects on B. licheniformis in regulating the microenvironment, and these mechanisms need to be investigated further.

Methods

In this study, we isolated and identified a new strain of B. licheniformis from bovine rumen fluid and named it B. licheniformis NXU98. The strain was treated with two distinct carbon sources-microcrystalline cellulose (MC) and cellobiose (CB). A combination of transcriptome and proteome analyses was used to investigate different carbon source effects.

Results

The results showed that B. licheniformis NXU98 ABC transporter proteins, antibiotic synthesis, flagellar assembly, cellulase-related pathways, and proteins were significantly upregulated in the MC treatment compared to the CB treatment, and lactate metabolism was inhibited. In addition, we used MC as a distinct carbon source to enhance the antibacterial ability of B. licheniformis NXU98, to improve its disease resistance, and to regulate the rumen microenvironment.

Discussion

Our research provides a potential new probiotic for feed research and a theoretical basis for investigating the mechanisms by which bacteria respond to different carbon sources.

The protective effects of Bacillus licheniformis against inflammatory responses and intestinal barrier damage in broilers with necrotic enteritis induced by Clostridium perfringens

BACKGROUND

Bacillus licheniformis is a gram-positive bacterium that has strong environmental adaptability and can improve the growth performance, immunity, and antioxidant function of broilers. The current study aimed to elucidate the protective capability of B. licheniformis against inflammatory responses and intestinal barrier damage in broilers with necrotic enteritis (NE) induced by Clostridium perfringens (CP).

RESULTS

The results showed that B. licheniformis enhanced the final body weight in broilers compared with that of broilers in the CP group after the stress of infection (P < 0.05). Bacillus licheniformis reversed the decreased levels of serum and jejunum mucosa immunoglobulins and anti-inflammatory cytokines, reduced the values of villus height and the ratio of villus height to crypt depth, and mitigated the increased levels of serum d-lactic acid and diamine oxidase in CP-challenged broilers (P < 0.05). Moreover, B. licheniformis modulated the expression levels of genes involved in the TLR4/NF-κB signalling pathway, the NLRP3 inflammasome activation pathway, and the sirt 1/Parkin signalling pathway in CP-challenged broilers. Compared with the CP challenge group, the B. licheniformis-treated group exhibited reduced abundance values of Shuttleworthia and Alistipes and enhanced abundance values of Parabacteroides in the caecal contents (P < 0.05).

CONCLUSION

Bacillus licheniformis improved the final body weight and alleviated the inflammatory response and intestinal barrier function damage in birds with NE induced by CP by maintaining intestinal physiological function, enhancing immunity, regulating inflammatory cytokine secretion, modulating the mitophagy response, and increasing the abundance of beneficial intestinal flora. © 2023 Society of Chemical Industry.

Bacillus licheniformis reduces mortality, improves symptoms, and controls residual pathogenicity in juvenile sea cucumbers Apostichopus japonicus infected with skin ulceration syndrome

Mass mortality caused by skin ulceration syndrome (SUS) is the bottle-neck for the sustainable aquaculture of the sea cucumber Apostichopus japonicus. In the present study, probiotic Bacillus licheniformis (0.25 × 109 CFU/g) was used as the treatment for A. japonicus infected with the SUS that caused by Vibrio harveyi. We found that B. licheniformis significantly reduced the number of infected sea cucumbers 5 days and 7 days after the treatment (group B), compared to those without B. licheniformis treatment (group C) (P < 0.001; P < 0.001). Further, the sea cucumbers fed B. licheniformis had significantly lower mortality at the end of the experiment (<10%) than that of those without the B. licheniformis treatment (>60%) (P < 0.001). These results suggest that the treatment of B. licheniformis is an effective method to reduce the mass mortality resulted from SUS in sea cucumber aquaculture. Further, 3-5 days of treatment significantly improved the adverse symptoms of SUS on the physiology and behavior of sea cucumbers, including the righting behavior, adhesion behavior, food consumption, fecal output and mobility. This indicates B. licheniformis treatment has the advantage in the recovery of sea cucumbers after SUS. Moreover, there was no significant difference observed in the physiology and behavior of sea cucumbers between the SUS infected sea cucumbers after the 7-day treatment of B. licheniformis and the healthy individuals. SUS infected sea cucumbers effectively returned to a stage of normalcy. Further, we found a significantly lower infected rate in sea cucumbers exposed to the culture water of group B (∼5%) than that of those in exposure to the culture water of group C (∼60%). This indicates that the treatment of B. licheniformis efficiently controls the residual pathogenicity of SUS in culture water. The present study demonstrated the effectiveness of B. licheniformis treatment as an environmentally friendly approach to reducing mortality, improving symptoms, and controlling residual pathogenicity in sea cucumber aquaculture.

Evaluating the potential of Bacillus licheniformis YZCUO202005 isolated from lichens in maize growth promotion and biocontrol

Lichens exist in an organismal organization of mycobiont, photobiont, and non-photoautotrophic bacteria. These organisms contribute to the growth of lichens even in poor nutrition substrates. However, studies on the isolation and application of non-photoautotrophic bacteria in plant growth and biocontrol are scanty. Therefore, a study was conducted to isolate and evaluate the potential of non-photoautotrophic bacteria from lichen tissues in maize plant growth promotion and biocontrol of plant pathogens (fungi and bacteria). Five bacterial strains were isolated and tested for their ability to produce indole-3-Acetic Acid (IAA). One bacterium named YZCUO202005 produced IAA, siderophores and biofilms, solubilized phosphate and potassium and exhibited extracellular enzymes (cellulases, proteases, amylase, and β -1,3-Glucanase). Based on the 16S rRNA sequence analysis results, YZCUO202005 was identified as Bacillus licheniformis. The strain inhibited the growth of five pathogenic fungi with an inhibition percent of between 58.7% and 71.7% and two pathogenic bacteria. Under greenhouse conditions, YZCUO202005 was tested for its abilities to enhance maize seed germination, and vegetative growth. Compared with the control treatment, the strain significantly enhanced the growth of stem length (i.e. 18 ± 0.64 cm, 78 ± 0.92 cm), leaf length (i.e. 10 ± 0.36 cm, 57 ± 1.42 cm), leaf chlorophyll levels (i.e., 13 ± 0.40, 40 ± 0.43 SPAD), and root length (i.e, 9.8 ± 2.25 cm, 22.5 ± 6.59 cm). Our results demonstrated that B. licheniformis YZCUO202005 from lichens has the potential to promote plant growth and reduce fungal and bacterial pathogens' growth. Furthermore, the results suggest that lichens are naturally rich sources of plant growth promotion and biocontrol agents that would be used in agriculture.

A New Mechanism of Carbon Metabolism and Acetic Acid Balance Regulated by CcpA

Catabolite control protein A (CcpA) is a critical regulator in Gram-positive bacteria that orchestrates carbon metabolism by coordinating the utilization of different carbon sources. Although it has been widely proved that CcpA helps prioritize the utilization of glucose over other carbon sources, this global regulator's precise mechanism of action remains unclear. In this study, a mutant Bacillus licheniformis deleted for CcpA was constructed. Cell growth, carbon utilization, metabolites and the transcription of key enzymes of the mutant strain were compared with that of the wild-type one. It was found that CcpA is involved in the regulation of glucose concentration metabolism in Bacillus. At the same time, CcpA regulates glucose metabolism by inhibiting acetic acid synthesis and pentose phosphate pathway key gene zwF. The conversion rate of acetic acid is increased by about 3.5 times after ccpA is deleted. The present study provides a new mechanism of carbon metabolism and acetic acid balance regulated by CcpA. On the one hand, this work deepens the understanding of the regulatory function of CcpA and provides a new view on the regulation of glucose metabolism. On the other hand, it is helpful to the transformation of B. licheniformis chassis microorganisms.

Molecular dynamics and simulation analysis against superoxide dismutase (SOD) target of Micrococcus luteus with secondary metabolites from Bacillus licheniformis recognized by genome mining approach

Micrococcus luteus, also known as M. luteus, is a bacterium that inhabits mucous membranes, human skin, and various environmental sources. It is commonly linked to infections, especially among individuals who have compromised immune systems. M. luteus is capable of synthesizing the enzyme superoxide dismutase (SOD) as a component of its protective response to reactive oxygen species (ROS). This enzyme serves as a promising target for drug development in various diseases. The current study utilized a subtractive genomics approach to identify potential therapeutic targets from M. luteus. Additionally, genome mining was employed to identify and characterize the biosynthetic gene clusters (BGCs) responsible for the production of secondary metabolites in Bacillus licheniformis (B. licheniformis), a bacterium known for its production of therapeutically relevant secondary metabolites. Subtractive genomics resulted in identification of important extracellular protein SOD as a drug target that plays a crucial role in shielding cells from damage caused by ROS. Genome mining resulted in identification of five potential ligands (secondary metabolites) from B. licheniformis such as, Bacillibactin (BAC), Paenibactin (PAE), Fengycin (FEN), Surfactin (SUR) and Lichenysin (LIC). Molecular docking was used to predict and analyze the binding interactions between these five ligands and target protein SOD. The resulting protein-ligand complexes were further analyzed for their motions and interactions of atoms and molecules over 250 ns using molecular dynamics (MD) simulation analysis. The analysis of MD simulations suggests, Bacillibactin as the probable candidate to arrest the activities of SOD. All the five compounds reported in this study were found to act by directly/indirectly interacting with ROS molecules, such as superoxide radicals (O2-) and hydrogen peroxide (H2O2), and transforming them into less reactive species. This antioxidant activity contributes to its protective effects against oxidative stress-induced damage in cells making them likely candidate for various applications, including in the development of antioxidant-based therapies, nutraceuticals, and functional foods.

Transcriptome analysis of Cryptocaryon irritans tomont responding to Bacillus licheniformis treatment

Cryptocaryon irritans is a ciliated obligate parasite that causes cryptocaryonosis (white spot disease) and poses great threat to marine fish farming. In recent years, the use of probiotics protects fish from pathogens, which has been identified as the sustainable and environmentally friendly tool to maintain the health and well-being of the host. Accordingly, Cryptocaryon irritans tomont and probiotic Bacillus strain (B.licheniformis, previously isolated from aquaculture water) were co-cultured to detect whether B. licheniformis has anti-C. irritants effect. The result showed that during 4-day incubation, B. licheniformi with 1 × 107 CFU/mL and 1 × 108 CFU/mL concentration effectively inhibited the incubation of C. irritans tomont, indicating that B. licheniformi could inhibit the transformation from reproductive tomont to infective theront of C. irritans. Later, C. irritans samples in the control (without B. licheniformi supplementation) and 1 × 107 CFU/mL B. licheniformi treatment group were sent for transcriptome analysis. Compare with the control group, a total of 3237 differentially expressed genes were identified, among which 626 genes were up-regulated and 2611 genes were down-regulated in 1 × 107 CFU/mL B. licheniformi group. Further Kyoto Encyclopedia of Genes and Genomes pathways analysis showed that anti-C. irritans mechanism of B. licheniformi was mainly involved in the energy metabolism (carbon metabolism, oxidative phosphorylation, biosynthesis of amino acids), transcription and translation (Ribosomes, spliceosomes, RNA transport, etc), lysosome-based degradation (lysosome, phagosome, protein processing in endoplasmic reticulum) and PI3K-Akt pathways. Our study findings raised the possibility of using marine microorganism B. licheniformi in handling aquaculture associated pathogen C. irritans, and preliminarily clarified the molecular mechanism.

Bacillus licheniformis: A Producer of Antimicrobial Substances, including Antimycobacterials, Which Are Feasible for Medical Applications

Bacillus licheniformis produces several classes of antimicrobial substances, including bacteriocins, which are peptides or proteins with different structural composition and molecular mass: ribosomally synthesized by bacteria (1.4-20 kDa), non-ribosomally synthesized peptides and cyclic lipopeptides (0.8-42 kDa) and exopolysaccharides (>1000 kDa). Different bacteriocins act against Gram-positive or Gram-negative bacteria, fungal pathogens and amoeba cells. The main mechanisms of bacteriocin lytic activity include interaction of peptides with membranes of target cells resulting in structural alterations, pore-forming, and inhibition of cell wall biosynthesis. DNase and RNase activity for some bacteriocines are also postulated. Non-ribosomal peptides are synthesized by special non-ribosomal multimodular peptide synthetases and contain unnatural amino acids or fatty acids. Their harmful effect is due to their ability to form pores in biological membranes, destabilize lipid packaging, and disrupt the peptidoglycan layer. Lipopeptides, as biosurfactants, are able to destroy bacterial biofilms. Secreted polysaccharides are high molecular weight compounds, composed of repeated units of sugar moieties attached to a carrier lipid. Their antagonistic action was revealed in relation to bacteria, viruses, and fungi. Exopolysaccharides also inhibit the formation of biofilms by pathogenic bacteria and prevent their colonization on various surfaces. However, mechanism of the harmful effect for many secreted antibacterial substances remains unknown. The antimicrobial activity for most substances has been studied in vitro only, but some substances have been characterized in vivo and they have found practical applications in medicine and veterinary. The cyclic lipopeptides that have surfactant properties are used in some industries. In this review, special attention is paid to the antimycobacterials produced by B. licheniformis as a possible approach to combat multidrug-resistant and latent tuberculosis. In particular, licheniformins and bacitracins have shown strong antimycobacterial activity. However, the medical application of some antibacterials with promising in vitro antimycobacterial activity has been limited by their toxicity to animals and humans. As such, similar to the enhancement in the antimycobacterial activity of natural bacteriocins achieved using genetic engineering, the reduction in toxicity using the same approach appears feasible. The unique capability of B. licheniformis to synthesize and produce a range of different antibacterial compounds means that this organism can act as a natural universal vehicle for antibiotic substances in the form of probiotic cultures and strains to combat various types of pathogens, including mycobacteria.

Enhancing Protease and Amylase Activities in Bacillus licheniformis XS-4 for Traditional Soy Sauce Fermentation Using ARTP Mutagenesis

This study was conducted to increase the enzymatic activity of Bacillus licheniformis XS-4, which was isolated from the traditional fermented mash of Xianshi soy sauce. The mutation was induced by atmospheric and room-temperature plasma (ARTP), and a mutant strain, mut80, was obtained. mut80 exhibited significant increases in protease and amylase activity by 90.54% and 143.10%, respectively, and the enhanced enzymatic activities were stably maintained after 20 consecutive incubations. Re-sequencing analysis of mut80 revealed that the mutation sites were located in 1518447(AT-T) and 4253106(G-A) in its genome, which was involved in the metabolic pathways of amino acids. The expression of the protease synthetic gene (aprX) increased 1.54 times, while that of the amylase gene (amyA) increased 11.26 times, as confirmed via RT-qPCR. Using ARTP mutagenesis, the present study proposes a highly efficient microbial resource with enhanced protease and amylase activity provided by B. licheniformis, which can potentially be used to improve the efficiency of traditional soy sauce fermentation.

Microbial synthesis of bacitracin: Recent progress, challenges, and prospects

Microorganisms are important sources of various natural products that have been commercialized for human medicine and animal healthcare. Bacitracin is an important antibacterial natural product predominantly produced by Bacillus licheniformis and Bacillus subtilis, and it is characterized by a broad antimicrobial spectrum, strong activity and low resistance, thus bacitracin is extensively applied in animal feed and veterinary medicine industries. In recent years, various strategies have been proposed to improve bacitracin production. Herein, we systematically describe the regulation of bacitracin biosynthesis in genus Bacillus and its associated mechanism, to provide a theoretical basis for bacitracin overproduction. The metabolic engineering strategies applied for bacitracin production are explored, including improving substrate utilization, using an enlarged precursor amino acid pool, increasing ATP supply and NADPH generation, and engineering transcription regulators. We also present several approaches of fermentation process optimization to facilitate the industrial large-scale production of bacitracin. Finally, the challenges and prospects associated with microbial bacitracin synthesis are discussed to facilitate the establishment of high-yield and low-cost biological factories.

Understanding the ADHD-Gut Axis by Metabolic Network Analysis

Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder diagnosed with hyperactivity, impulsivity, and a lack of attention inconsistent with the patient's development level. The fact that people with ADHD frequently experience gastrointestinal (GI) dysfunction highlights the possibility that the gut microbiome may play a role in this condition. The proposed research aims to determine a biomarker for ADHD by reconstructing a model of the gut-microbial community. Genome-scale metabolic models (GEM) considering the relationship between gene-protein-reaction associations are used to simulate metabolic activities in organisms of gut. The production rates of dopamine and serotonin precursors and the key short chain fatty acids which affect the health status are determined under three diets (Western, Atkins', Vegan) and compared with those of healthy people. Elasticities are calculated to understand the sensitivity of exchange fluxes to changes in diet and bacterial abundance at the species level. The presence of Bacillota (genus Coprococcus and Subdoligranulum), Actinobacteria (genus Collinsella), Bacteroidetes (genus Bacteroides), and Bacteroidota (genus Alistipes) may be possible gut microbiota indicators of ADHD. This type of modeling approach taking microbial genome-environment interactions into account helps us understand the gastrointestinal mechanisms behind ADHD, and establish a path to improve the quality of life of ADHD patients.

Bacillus licheniformis reverses the environmental ceftriaxone sodium-induced gut microbial dysbiosis and intestinal inflammation in mice

Antibiotics used as a common clinical treatment have saved many lives. Widespread use of antibiotic therapy has been known to disrupt the balance of pathogenic bacteria, host-associated microorganisms and environment. However, our understanding of Bacillus licheniformis for health benefits and ability to restore the ceftriaxone sodium-induced gut microbial dysbiosis is severely limited. We used Caco-2 cell, H&E (hematoxylin-eosin staining), RT-PCR and 16S rRNA sequencing techniques to investigate the influence of Bacillus licheniformis on gut microbial dysbiosis and inflammation following ceftriaxone sodium treatment. The results showed that treatment of ceftriaxone sodium in 7 days suppressed the expression of Nf-κB pathway mRNA levels, which caused cytoplasmic vacuolization in intestinal tissues, afterward, the administration of Bacillus licheniformis could effectively restore intestinal morphology and inflammation levels. Moreover, the ceftriaxone sodium treatment entirely affected the intestinal microbial ecology, leading to a decrease in microbial abundance. Firmicutes, Proteobacteria, and Epsilonbacteraeota were the most predominant phyla in each of the four groups. Specifically, the MA group (ceftriaxone sodium treatment) resulted in a significant decrease in the relative abundance of 2 bacterial phyla and 20 bacterial genera compared to the administration of Bacillus licheniformis after ceftriaxone sodium treatment. The supplementation of Bacillus licheniformis could increase the growth of Firmicutes and Lactobacillus and encourage the construction of a more mature and stable microbiome. Furthermore, Bacillus licheniformis could restore the intestinal microbiome disorders and inflammation levels following ceftriaxone sodium treatment.

Promoting cell growth for bio-chemicals production via boosting the synthesis of L/D-alanine and D-alanyl-D-alanine in Bacillus licheniformis

Metabolic engineering is a substantial approach for escalating the production of biochemical products. Cell biomass is lowered by system constraints and toxication carried on by the aggregation of metabolites that serve as inhibitors of product synthesis. In order to increase the production of biochemical products, it is important to trace the relationship between alanine metabolism and biomass. According to our investigation, the appropriate concentration of additional L/D-alanine (0.1 g/L) raised the cell biomass (OD₆₀₀) in Bacillus licheniformis in contrast to the control strain. Remarkably, it was also determined that high levels of intracellular L/D-alanine and D-alanyl-D-alanine were induced by the overexpression of the ald, dal, and ddl genes to accelerate cell proliferation. Our findings clearly revealed that 0.2 g/L of L-alanine and D-alanine substantially elevated the titer of poly-γ-glutamic acid (γ-PGA) by 14.89% and 6.19%, correspondingly. And the levels of γ-PGA titer were hastened by the overexpression of the ald, dal, and ddl genes by 19.72%, 15.91%, and 16.64%, respectively. Furthermore, overexpression of ald, dal, and ddl genes decreased the by-products (acetoin, 2,3-butanediol, acetic acid and lactic acid) formation by about 14.10%, 8.77%, and 8.84% for augmenting the γ-PGA production. Our results also demonstrated that overexpression of ald gene amplified the production of lichenysin, pulcherrimin and nattokinase by about 18.71%, 19.82% and 21.49%, respectively. This work delineated the importance of the L/D-alanine and D-alanyl-D-alanine synthesis to the cell growth and the high production of bio-products, and provided an effective strategy for producing bio-products.

Quantification of the antagonistic and synergistic effects of Pb2+, Cu2+, and Zn2+ bioaccumulation by living Bacillus subtilis biomass using XGBoost and SHAP

Bioaccumulation and adsorption are efficient methods for removing heavy metal ions (HMIs) from aqueous environments. However, methods to quantifiably characterize the removal selectivity for co-existing HMIs are limited. In this study, we applied Shapley additive explanations (SHAP) following extreme gradient boosting (XGBoost) modeling, to generate SHAP values. We used these values to create an affinity interference index (AII) that quantitatively represented the interference between metal ions in a multi-metal bioaccumulation system. The selectivity for simultaneous bioaccumulation of Pb²⁺, Cu²⁺, and Zn²⁺ by living Bacillus subtilis biomass was then characterized as a proof of concept. The AII indicated that the bioaccumulation of Zn²⁺ was more strongly inhibited by Pb²⁺/Cu²⁺ (AII = 1) than that of Pb²⁺/Cu²⁺ by Zn²⁺. Moreover, the presence of Zn²⁺ promoted the bioaccumulation of Pb²⁺ (AII = 0.39), which was confirmed in further experiments where the bioaccumulation of Pb²⁺ (300 μM) was increased by 38% with Zn²⁺ (300 μM). This study demonstrated that the combination of XGBoost and SHAP is effective in the quantifiable characterization of the antagonistic and synergistic effects in a multi-metal simultaneous bioaccumulation system. This method could also be generalized to similar tasks for analyzing the selectivity effects in a multi-component system.

Biotechnological and food synthetic biology potential of platform strain: Bacillus licheniformis

Bacillus licheniformis is one of the most characteristic Gram-positive bacteria. Its unique genetic background and safety characteristics make it have important biologic applications in the food industry, including, the biosynthesis of high value-added bioproducts, probiotic functions, biological treatment of wastes derived from food production, etc. In this review, these recent advances are summarized and presented systematically for the first time. In addition, we highlight synthetic biology strategies as a potential driver of developing this strain for wider and more efficient application in the food industry. Finally, we present the current challenges faced and provide our unique perspective on relevant future research directions. In summary, this review will provide an illuminating and comprehensive perspective that will allow an in-depth understanding of B. licheniformis and promote its more effective development in the food industry.

Characterization and biodegradation of paracetamol by biomass of Bacillus licheniformis strain PPY-2 isolated from wastewater

Industrialization leads to the entry of diverse xenobiotic compounds into the environment. One such compound is paracetamol (APAP), which is emerging as a pharmaceutical and personal care pollutant (PPCP). In this study, the APAP degrading bacterium was isolated by enrichment culture method from the sewage sample. The microscopy, biochemical, and 16S rRNA gene sequence analyzed the isolate PPY-2, which belongs to Bacillus licheniformis, and GenBank assigned accession number MN744328. Physiological and batch culture degradation studies have indicated that the strain involved in the degradation of APAP. The optimum pH for degradation of the PPY-2 was 7.7, whereas the temperature was 25 °C, agitation speed was 142 rpm, and concentration of APAP was 621 mg/L reported, and the optimum temperatures were 42 °C and 32 °C, respectively. Biomass kinetic was studied at optimal physical conditions, which suggested that the specific growth rate (μ) was 721 mg/L. The GC-MS chromatogram peaks have detected metabolites, viz., oxalic acid, 2-isopropyl-5-methyl cyclohexanone, and phenothiazine. The study confirmed that Bacillus licheniformis strain PPY-2 exhibits metabolic potential to biodegradation APAP and can be further deployed in bioremediation.

Evaluation of wool protein hydrolysate as peptone for production of microbial enzymes

Peptones are one of the most expensive components of microbial culture media. The present study was conducted to test the usability of low-cost sheep wool peptone (SWP) as an organic nitrogen source in the production of six industrially important enzymes (lipase, amylase, tannase, pectinase, cellulase and invertase). SWP was prepared by alkaline hydrolysis and acid neutralization. Bacillus licheniformis and Aspergillus niger were selected as test microorganisms for enzyme production. To evaluate the efficacy of SWP in enzyme production, it was compared with commercial tryptone peptone (TP) in the shaking flask cultures of the test microorganisms. The optimum concentration of both SWP and TP was determined to be 8 g/L for the production of B. licheniformis-derived enzymes, but 6 g/L for the production of A. niger-derived enzymes. It was determined that SWP was superior to TP in the production of four enzymes (lipase, amylase, tannase and pectinase) of both B. licheniformis and A. niger. This is the first study about the usage of sheep wool protein hydrolysate (SWP) as an organic nitrogen source or a peptone in fermentative production of microbial enzymes.

Milk Pathogens in Correlation with Inflammatory, Oxidative and Nitrosative Stress Markers in Goat Subclinical Mastitis

Goat mastitis is still frequently diagnosed in dairy farms, with serious consequences on milk quality and composition. The aim of this study was to establish correlations between milk microorganisms and biochemical parameters in goats with no signs of clinical mastitis. Thus, 76 milk samples were collected from a dairy goat farm, Carpathian breed, followed by microbiological, molecular (16S rRNA sequencing) and somatic cells analysis, determination of lactate dehydrogenase (LDH), β-glucuronidase, catalase (CAT), glutathione peroxidase (GPx) activity, total antioxidant capacity (TAC), nitric oxide (NO) and lipid peroxides (LPO) using spectrophotometry and the ELISA method for 8-hydroxy-deoxyguanosine (8-OHdG) as the oxidative DNA damage indicator. Samples positive for bacterial growth showed a significant (p < 0.05) increase in the number of somatic cells, LDH and β-glucuronidase activity, as well as higher levels of CAT, GPx, NO, LPO and 8-OHdG compared with pathogen-free milk whereas TAC was lower in milk from an infected udder. These findings suggest that subclinical mastitis is associated with increased enzymatic activity and induction of oxidative stress. Nevertheless, changes in biochemical parameters tended to vary depending on the pathogen, the most notable mean values being observed overall in milk positive for Staphylococcus aureus.

Enhanced Thermostability and Molecular Insights for l-Asparaginase from Bacillus licheniformis via Structure- and Computation-Based Rational Design

l-Asparaginase has gained much attention for effectively treating acute lymphoblastic leukemia (ALL) and mitigating carcinogenic acrylamide in fried foods. Due to high-dose dependence for clinical treatment and low mitigation efficiency for thermal food processes caused by poor thermal stability, a method to achieve thermostable l-asparaginase has become a critical bottleneck. In this study, a rational design including free energy combined with structural and conservative analyses was applied to engineer the thermostability of l-asparaginase from Bacillus licheniformis (BlAsnase). Two enhanced thermostability mutants D172W and E207A were screened out by site-directed saturation mutagenesis. The double mutant D172W/E207A exhibited highly remarkable thermostability with a 65.8-fold longer half-life at 55 °C and 5 °C higher optimum reaction temperature and melting temperature (T_m) than those of wild-type BlAsnase. Further, secondary structure, sequence, molecular dynamics (MD), and 3D-structure analysis revealed that the excellent thermostability of the mutant D172W/E207A was on account of increased hydrophobicity and decreased flexibility, highly rigid structure, hydrophobic interactions, and favorable electrostatic potential. As the first report of rationally designing l-asparaginase with improved thermostability from B. licheniformis, this study offers a facile and efficient process to improve the thermostability of l-asparaginase for industrial applications.

Potential application of the probiotic Bacillus licheniformis as an adjuvant in the treatment of diseases in humans and animals: A systematic review

The use of Bacillus licheniformis as a probiotic has increased significantly in recent years. Published reports demonstrate that it provides multiple benefits for health. Although there are already studies in humans and is marketed, it is mostly used in the veterinary industry still. However, its benefits could be extrapolated to humans in future. This review addresses the application of B. licheniformis, its sporulation, mechanisms of action, and its role in the resolution, treatment, and prevention of different conditions and diseases. It focuses on scientific advances from 2016 to mid-2022 and emphasizes the most common diseases in the general population. Most of the 70% of published studies about the health benefits of B. licheniformis have been published from 2016 until now. The intake of B. licheniformis has been related to the effects of modulation of the intestinal microbiota, antimicrobial activity, growth promotion, anti-inflammatory and immunostimulatory effects, promotion of the regulation of the lipid profile, increase of neurotransmitters, and stress reduction, among others. These results provide novel possible applications of this and other probiotics in general. Although many benefits can be reported on a microorganism, the combination with others could provide a better effect. Further studies like this need to be done to understand the specific advantages of each probiotic and its strains and therefore achieve a better selection of them for a specific disease or disorder.

Inhibitory Effect of Bacillus licheniformis Strains Isolated from Canine Oral Cavity

Bacillus licheniformis is used in a broad spectrum of areas, including some probiotic preparations for human and veterinary health. Moreover, B. licheniformis strains are known producers of various bioactive substances with antimicrobial and antibiofilm effects. In searching for new potentially beneficial bacteria for oral health, the inhibitory effect of B. licheniformis strains isolated from canine dental biofilm against pathogenic oral bacteria was evaluated. The antimicrobial effect of neutralized cell-free supernatants (nCFS) was assessed in vitro on polystyrene microtiter plates. Furthermore, molecular and morphological analyses were executed to evaluate the production of bioactive substances. To determine the nature of antimicrobial substance present in nCFS of B. licheniformis A-1-5B-AP, nCFS was exposed to the activity of various enzymes. The nCFS of B. licheniformis A-1-5B-AP significantly (p < 0.0001) reduced the growth of Porphyromonas gulae 3/H, Prevotella intermedia 1/P and Streptococcus mutans ATCC 35668. On the other hand, B. licheniformis A-2-11B-AP only significantly (p < 0.0001) inhibited the growth of P. intermedia 1/P and S. mutans ATCC 35668. However, enzyme-treated nCFS of B. licheniformis A-1-5B-AP did not lose its antimicrobial effect and significantly (p < 0.0001) inhibited the growth of Micrococcus luteus DSM 1790. Further studies are needed for the identification of antimicrobial substances.

Vitamin D3 Nutritional Status Affects Gut Health of Salmonella-Challenged Laying Hens

Salmonella enterica serovar Enteritidis (SE) is one of the most common pathogens associated with poultry health and foodborne Salmonellosis worldwide. The gut plays a pivotal role in inhibiting SE transintestinal transmission and contaminating poultry products. The nutritional status of vitamin D (VD) is involved in gut health apart from bone health. However, the impact of VD₃ nutritional status on the gut health of Salmonella-challenged hens is rarely investigated. This study investigated the impact and possible mechanisms of VD₃ nutritional status on the gut health of hens challenged with SE. Hens were fed basal diets with either 0 (deficient) or 3000 IU (sufficient) VD₃/kg of diet, respectively. After 10 weeks of feeding, half of the hens were orally inoculated with either SE (1 × 10⁹ CFU /bird). Results indicated that VD₃ sufficiency reversed the disruptive effects on the laying performance of hens caused by Salmonella challenge or VD₃ insufficiency by promoting VD₃ metabolism. In addition, VD₃ sufficiency ameliorated gut injury induced by either Salmonella or VD₃ deficiency, shown by reducing Salmonella load and histopathological scores, suppressing TLR4-mediated inflammatory responses, and increasing expression of TJs along with decreasing pro-apoptotic protein expression and the number of TUNEL-positive cells in the jejunum. Besides, VD₃ enriched the abundance of probiotics, such as Lactobacillus and Bacilli, and restored the balance of gut microflora. Collectively, dietary VD₃ sufficient supplementation could alleviate Salmonella or VD₃ deficiency-induced intestinal damage of hens via modulating intestinal immune, barrier function, apoptosis along with gut microbiota composition, revealing that VD₃ could act as a novel nutritional strategy defending Salmonella invasion in hens.

Metagenomic-Metabolomic Mining of Kinema, a Naturally Fermented Soybean Food of the Eastern Himalayas

Kinema is a popular sticky fermented soybean food of the Eastern Himalayan regions of North East India, east Nepal, and south Bhutan. We hypothesized that some dominant bacteria in kinema may contribute to the formation of targeted and non-targeted metabolites for health benefits; hence, we studied the microbiome-metabolite mining of kinema. A total of 1,394,094,912 bp with an average of 464,698,304 ± 120,720,392 bp was generated from kinema metagenome, which resulted in the identification of 47 phyla, 331 families, 709 genera, and 1,560 species. Bacteria (97.78%) were the most abundant domain with the remaining domains of viruses, eukaryote, and archaea. Firmicutes (93.36%) was the most abundant phylum with 280 species of Bacillus, among which Bacillus subtilis was the most dominant species in kinema followed by B. glycinifermentans, B. cereus, B. licheniformis, B. thermoamylovorans, B. coagulans, B. circulans, B. paralicheniformis, and Brevibacillus borstelensis. Predictive metabolic pathways revealed the abundance of genes associated with metabolism (60.66%), resulting in 216 sub-pathways. A total of 361 metabolites were identified by metabolomic analysis (liquid chromatography-mass spectrophotometry, LC-MS). The presence of metabolites, such as chrysin, swainsonine, and 3-hydroxy-L-kynurenine (anticancer activity) and benzimidazole (antimicrobial, anticancer, and anti-HIV activities), and compounds with immunomodulatory effects in kinema supports its therapeutic potential. The correlation between the abundant species of Bacillus and primary and secondary metabolites was constructed with a bivariate result. This study proves that Bacillus spp. contribute to the formation of many targeted and untargeted metabolites in kinema for health-promoting benefits.

CRISPR-Mediated Base Editing: From Precise Point Mutation to Genome-Wide Engineering in Nonmodel Microbes

Nonmodel microbes with unique and diverse metabolisms have become rising stars in synthetic biology; however, the lack of efficient gene engineering techniques still hinders their development. Recently, the use of base editors has emerged as a versatile method for gene engineering in a wide range of organisms including nonmodel microbes. This method is a fusion of impaired CRISPR/Cas9 nuclease and base deaminase, enabling the precise point mutation at the target without inducing homologous recombination. This review updates the latest advancement of base editors in microbes, including the conclusion of all microbes that have been researched by base editors, the introduction of newly developed base editors, and their applications. We provide a list that comprehensively concludes specific applications of BEs in nonmodel microbes, which play important roles in industrial, agricultural, and clinical fields. We also present some microbes in which BEs have not been fully established, in the hope that they are explored further and so that other microbial species can achieve arbitrary base conversions. The current obstacles facing BEs and solutions are put forward. Lastly, the highly efficient BEs and other developed versions for genome-wide reprogramming of cells are discussed, showing great potential for future engineering of nonmodel microbes.

Combining Precursor-Directed Engineering with Modular Designing: An Effective Strategy for De Novo Biosynthesis of l-DOPA in Bacillus licheniformis

3-Hydroxy-l-tyrosine (l-DOPA) is a promising drug for treating Parkinson's disease. Tyrosine hydroxylase catalyzes the microbial synthesis of l-DOPA, which is hindered by the efficiency of catalysis, the supply of cofactor tetrahydrobiopterin, and the regulation of the pathway. In this study, the modular engineering strategy in Bacillus licheniformis was identified to effectively enhance l-DOPA production. First, the catalytic efficiency of biocatalyst tyrosine hydroxylase from Streptosporangium roseum DSM 43021 (SrTH) was improved by 20.3% by strengthening its affinity toward tetrahydrobiopterin. Second, the tetrahydrobiopterin supply pool was increased by bottleneck gene expression, oxygen transport facilitation, budC (encoding meso-2,3-butanediol dehydrogenase) deletion, and tetrahydrobiopterin regeneration using a native YfkO nitroreductase. The strain 45AB^vC successfully produced tetrahydrobiopterin, which was detected as pterin (112.48 mg/L), the oxidation product of tetrahydrobiopterin. Finally, the yield of precursor l-tyrosine reached 148 mg/g_DCW, with an increase of 71%, with the deletion of a novel spliced transcript 41sRNA associated with the regulation of the shikimate pathway. The engineered strain 45AB^vCS::PD produced 167.14 mg/L (2.41 times of wild-type strain) and 1290 mg/L l-DOPA in a shake flask and a 15 L bioreactor, respectively, using a fermentation strategy on a mixture of carbon sources. This study holds great potential for constructing a microbial source of l-DOPA and its high-value downstream pharmaceuticals.

Endophytic Bacteria Colonizing the Petiole of the Desert Plant Zygophyllum dumosum Boiss: Possible Role in Mitigating Stress

Zygophyllum dumosum is a dominant shrub in the Negev Desert whose survival is accomplished by multiple mechanisms including abscission of leaflets to reduce whole plant transpiration while leaving the fleshy, wax-covered petioles alive but dormant during the dry season. Petioles that can survive for two full growing seasons maintain cell component integrity and resume metabolic activity at the beginning of the winter. This remarkable survival prompted us to investigate endophytic bacteria colonizing the internal tissues of the petiole and assess their role in stress tolerance. Twenty-one distinct endophytes were isolated by culturing from surface-sterile petioles and identified by sequencing of the 16S rDNA. Sequence alignments and the phylogenetic tree clustered the isolated endophytes into two phyla, Firmicutes and Actinobacteria. Most isolated endophytes displayed a relatively slow growth on nutrient agar, which was accelerated by adding petiole extracts. Metabolic analysis of selected endophytes showed several common metabolites whose level is affected by petiole extract in a species-dependent manner including phosphoric acid, pyroglutamic acid, and glutamic acid. Other metabolites appear to be endophyte-specific metabolites, such as proline and trehalose, which were implicated in stress tolerance. These results demonstrate the existence of multiple endophytic bacteria colonizing Z. dumosum petioles with the potential role in maintaining cell integrity and functionality via synthesis of multiple beneficial metabolites that mitigate stress and contribute to stress tolerance.