Integrated omics analysis reveals the alteration of gut microbiota and fecal metabolites in Cervus elaphus kansuensis

The gut microbiota is the largest and most complex microecosystem in animals. It is influenced by the host's dietary habits and living environment, and its composition and diversity play irreplaceable roles in animal nutrient metabolism, immunity, and adaptation to the environment. Although the gut microbiota of red deer has been studied, the composition and function of the gut microbiota in Gansu red deer (Cervus elaphus kansuensis), an endemic subspecies of red deer in China, has not been reported. In this study, the composition and diversity of the gut microbiome and fecal metabolomics of C. elaphus kansuensis were identified and compared for the first time by using 16S rDNA sequencing, metagenomic sequencing, and LC-MS/MS. There were significant differences in gut microbiota structure and diversity between wild and farmed C. elaphus kansuensis. The 16S rDNA sequencing results showed that the genus UCRD-005 was dominant in both captive red deer (CRD) and wild red deer (WRD). Metagenomic sequencing showed similar results to those of 16S rDNA sequencing for gut microbiota in CRD and WRD at the phylum and genus levels. 16S rDNA and metagenomics sequencing data suggested that Bacteroides and Bacillus might serve as marker genera for CRD and WRD, respectively. Fecal metabolomics results showed that 520 metabolites with significant differences were detected between CRD and WRD and most differential metabolites were involved in lipid metabolism. The results suggested that large differences in gut microbiota composition and fecal metabolites between CRD and WRD, indicating that different dietary habits and living environments over time have led to the development of stable gut microbiome characteristics for CRD and WRD to meet their respective survival and reproduction needs. KEY POINTS: • Environment and food affected the gut microbiota and fecal metabolites in red deer • Genera Bacteroides and Bacillus may play important roles in CRD and WRD, respectively • Flavonoids and ascorbic acid in fecal metabolites may influence health of red deer.

Mechanisms on the removal of gram-negative/positive antibiotic resistant bacteria and inhibition of horizontal gene transfer by ferrate coupled with peroxydisulfate or peroxymonosulfate

The existence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) has been a global public environment and health issue. Due to the different cell structures, gram-positive/negative ARB exhibit various inactivation mechanisms in water disinfection. In this study, a gram-negative ARB Escherichia coli DH5α (E. coli DH5α) was used as a horizontal gene transfer (HGT) donor, while a gram-positive ARB Bacillus as a recipient. To develop an efficient and engineering applicable method in water disinfection, ARB and ARGs removal efficiency of Fe(VI) coupled peroxydisulfate (PDS) or peroxymonosulfate (PMS) was compared, wherein hydroxylamine (HA) was added as a reducing agent. The results indicated that Fe(VI)/PMS/HA showed higher disinfection efficiency than Fe(VI)/PDS/HA. When the concentration of each Fe(VI), PMS, HA was 0.48 mM, 5.15 log E. coli DH5α and 3.57 log Bacillus lost cultivability, while the proportion of recovered cells was 0.0017 % and 0.0566 %, respectively, and HGT was blocked. Intracellular tetA was reduced by 2.49 log. Fe(IV) and/or Fe(V) were proved to be the decisive reactive species. Due to the superiority of low cost as well as high efficiency and practicality, Fe(VI)/PMS/HA has significant application potential in ARB, ARGs removal and HGT inhibition, offering a new insight for wastewater treatment.

Enhanced sporulation of B. licheniformis BF-002 through automatic co-feeding of carbon and nitrogen sources

Bacillus licheniformis formulations are effective for environmental remediation, gut microbiota modulation, and soil improvement. An adequate spore quantity is crucial for the activity of B. licheniformis formulations. This study investigated the synergistic effects of carbon/nitrogen source consumption and concentration on B. licheniformis BF-002 cultivation, with the aim of developing an automatic co-feeding strategy to enhance spore production. Initial glucose (10 g/L) and amino nitrogen (1.5 g/L) concentrations promote cell growth, followed by reduced glucose (2.0 g/L) and amino nitrogen (0.5 g/L) concentrations for sustained spore generation. The spore quantity reached 2.59 × 1010 CFU/mL. An automatic co-feeding strategy was developed and implemented in 5 and 50 L cultivations, resulting in spore quantities of 2.35 × 1010 and 2.86 × 1010 CFU/mL, respectively, improving by 6.81% and 30.00% compared to that with a fixed glucose concentration (10.0 g/L). The culture broth obtained at both the 5 and 50 L scales was spray-dried, resulting in bacterial powder with cell viability rates of 85.94% and 82.68%, respectively. Even after exposure to harsh conditions involving high temperature and humidity, cell viability remained at 72.80% and 69.89%, respectively. Employing the automatic co-feeding strategy increased the transcription levels of the spore formation-related genes spo0A, spoIIGA, bofA, and spoIV by 7.42%, 8.46%, 8.87%, and 9.79%, respectively. The proposed strategy effectively promoted Bacillus growth and spore formation, thereby enhancing the quality of B. licheniformis formulations.

In silico biotechnological potential of Bacillus sp. strain MHSD_37 bacterial endophyte

BACKGROUND

Endophytic bacteria possess a range of unique characteristics that enable them to successfully interact with their host and survive in adverse environments. This study employed in silico analysis to identify genes, from Bacillus sp. strain MHSD_37, with potential biotechnological applications.

RESULTS

The strain presented several endophytic lifestyle genes which encode for motility, quorum sensing, stress response, desiccation tolerance and root colonisation. The presence of plant growth promoting genes such as those involved in nitrogen fixation, nitrate assimilation, siderophores synthesis, seed germination and promotion of root nodule symbionts, was detected. Strain MHSD_37 also possessed genes involved in insect virulence and evasion of defence system. The genome analysis also identified the presence of genes involved in heavy metal tolerance, xenobiotic resistance, and the synthesis of siderophores involved in heavy metal tolerance. Furthermore, LC-MS analysis of the excretome identified secondary metabolites with biological activities such as anti-cancer, antimicrobial and applications as surfactants.

CONCLUSIONS

Strain MHSD_37 thereby demonstrated potential biotechnological application in bioremediation, biofertilisation and biocontrol. Moreover, the strain presented genes encoding products with potential novel application in bio-nanotechnology and pharmaceuticals.

Genomic analysis reveals genes that encode the synthesis of volatile compounds by a Bacillus velezensis-based biofungicide used in the treatment of grapes to control Aspergillus carbonarius

Fungal control strategies based on the use of Bacillus have emerged in agriculture as eco-friendly alternatives to replace/reduce the use of synthetic pesticides. Bacillus sp. P1 was reported as a new promising strain for control of Aspergillus carbonarius, a known producer of ochratoxin A, categorized as possible human carcinogen with high nephrotoxic potential. Grape quality can be influenced by vineyard management practices, including the use of fungal control agents. The aim of this study was to evaluate, for the first time, the quality parameters of Chardonnay grapes exposed to an antifungal Bacillus-based strategy for control of A. carbonarius, supporting findings by genomic investigations. Furthermore, genomic tools were used to confirm that the strain P1 belongs to the non-pathogenic species Bacillus velezensis and also to certify its biosafety. The genome of B. velezensis P1 harbors genes that are putatively involved in the production of volatiles and hydrolytic enzymes, which are responsible for releasing the free form of aroma compounds. In addition to promote biocontrol of phytopathogenic fungi and ochratoxins, the treatment with B. velezensis P1 did not change the texture (hardness and firmness), color and pH of the grapes. Heat map and hierarchical clustering analysis (HCA) of volatiles evaluated by GC/MS revealed that Bacillus-treated grapes showed higher levels of compounds with a pleasant odor descriptions such as 3-hydroxy-2-butanone, 2,3-butanediol, 3-methyl-1-butanol, 3,4-dihydro-β-ionone, β-ionone, dihydroactinidiolide, linalool oxide, and β-terpineol. The results of this study indicate that B. velezensis P1 presents desirable properties to be used as a biocontrol agent.

The biocontrol potentials of rhizospheric bacterium Bacillus velezensis K0T24 against mulberry bacterial wilt disease

Mulberry bacterial wilt disease, caused by Ralstonia pseudosolanacearum, is a devastating soil-borne disease in the silk-mulberry-related industry. In this study, through high-throughput sequencing, we compared the rhizosphere bacterial composition of the mulberry-resistant cultivar (K10) and susceptible cultivar (G12), confirming Bacillus as a genus-level biomarker for K10. Next, twelve Bacillus spp. isolates, derived from the rhizosphere of K10, were screened for their antagonistic activity against R. pseudosolanacearum. The isolate showing strong antagonism was identified as B. velezensis K0T24 and selected for further analysis. The fermentation supernatant of B. velezensis K0T24 significantly inhibited the growth of R. pseudosolanacearum (82.47%) and the expression of its pathogenic genes. Using B. velezensis K0T24 in mulberry seedlings also increased defense enzyme activities and achieved a control efficacy of up to 55.17% against mulberry bacterial wilt disease. Collectively, our findings demonstrate the potential of B. velezensis K0T24 in suppressing mulberry bacterial wilt disease.

Research advances in the identification of regulatory mechanisms of surfactin production by Bacillus: a review

Surfactin is a cyclic hexalipopeptide compound, nonribosomal synthesized by representatives of the Bacillus subtilis species complex which includes B. subtilis group and its closely related species, such as B. subtilis subsp subtilis, B. subtilis subsp spizizenii, B. subtilis subsp inaquosorum, B. atrophaeus, B. amyloliquefaciens, B. velezensis (Steinke mSystems 6: e00057, 2021) It functions as a biosurfactant and signaling molecule and has antibacterial, antiviral, antitumor, and plant disease resistance properties. The Bacillus lipopeptides play an important role in agriculture, oil recovery, cosmetics, food processing and pharmaceuticals, but the natural yield of surfactin synthesized by Bacillus is low. This paper reviews the regulatory pathways and mechanisms that affect surfactin synthesis and release, highlighting the regulatory genes involved in the transcription of the srfAA-AD operon. The several ways to enhance surfactin production, such as governing expression of the genes involved in synthesis and regulation of surfactin synthesis and transport, removal of competitive pathways, optimization of media, and fermentation conditions were commented. This review will provide a theoretical platform for the systematic genetic modification of high-yielding strains of surfactin.

Revealing the influence of exogenously inoculated Bacillus spp. on the microbiota and metabolic potential of medium-temperature Daqu: A meta-omics analysis

To determine the unique contribution of the bioturbation to the properties of the medium-temperature Daqu, we investigated the differences in microbiota and metabolic composition using the meta-omics approach. Bioturbation increased the amounts of microbial specie and influenced the contribution of the core microbiota to the metabolome. Specifically, inoculated synthetic microbiota (MQB) enhanced the abundance of Bacillus amyloliquefaciens, while Bacillus licheniformis (MQH) increased the abundance of the two Aspergillus species and four species level of lactic acid bacteria. These changes of the microbial profiles significantly increased the potentials of carbohydrate metabolism, amino acid metabolism, and biosynthesis of ester compounds. Consequently, both patterns significantly increased the content of volatile compounds and free amino acids, which were 27.61% and 21.57% (MQB), as well as 15.14% and 17.83% (MQH), respectively. In addition, the contents of lactic acid in MQB and MQH decreased by 65.42% and 42.99%, respectively, closely related to the up- or down-regulation of the expression of their corresponding functional enzyme genes. These results suggested that bioturbation drove the assembly of the core microbiota, rather than becoming critical functional species. Overall, our study provides new insights into the functional role of exogenous isolates in the Daqu microecosystem.

Multidrug-resistant Bacillus species isolated from hospital soil environment is controlled by nanobiotics incorporated nanoformulation

Multidrug resistance is a serious hazard to the environment, it claims a large number of lives every year. Lack of drug options and easy transmission of these organisms remain the biggest threat in treating the relative infections whose causative systems have evolved and become stronger in due course of time. Hospitals serve as one of the largest breeding grounds for harbouring these organisms. This study aims to isolate and characterize multidrug-resistant microorganisms from soil samples collected from hospital waste dumping premises. Polyherbal nanoformulation was synthesized from ethno-medicinal source Triphala (three berries) and characterized using various physico-chemical characterization techniques. The antibacterial efficacy of the polyherbal nanoformulation was evaluated by employing various assays to determine MIC, MBC, and biofilm inhibition potential in isolated strains. Bacterial colonies were isolated and the DNA was sequenced. The isolated organisms were identified as Bacillus cereus, Bacillus licheniformis, and Bacillus pumilus and they were subjected to antibiotic susceptibility by using various antibiotics. It was found that all the microorganisms were multidrug-resistant and possessed resistance to various classes of antibiotics. The various antibacterial assays showed that the polyherbal nanoformulation was highly effective in controlling growth and biofilm formation even at lower concentrations when compared with commercial antibiotics. The novelty of this research work lies in combining the beneficial effects of silver and polyherbal drugs into a single Polyherbal nanoformulation. This is the first novel report to utilize polyherbal nanoformulation to control the multidrug-resistant microorganisms thriving in hospital waste dumping sites. Hence, this nanobiotics incorporated polyherbal nanoformulation can be developed into a commercial product to treat the hospital waste material before dumping it into the environment.

Investigation of non-classical secretion of oxalate decarboxylase in Bacillus mojavensis XH1 mediated by exopeptide YydF: Mechanism and application

Non-classical secretory proteins are widely found in bacteria and have been extensively studied due to their important physiological roles. However, the relevant non-classical secretory mechanisms remain unclear. In this study, we found that oxalate decarboxylase (Bacm OxDC) from Bacillus mojavensis XH1 belongs to non-classical secretory proteins. Its N-terminus showed high hydrophilicity, which was different from the conventional signal peptide. The truncation test revealed that the deletion of the N-terminus affects the structure resulting in its inability to cross the cell membrane. Further studies verified that the exported peptide YydF played an important role in the secretion process of Bacm OxDC. Experimental results on the secretion mechanism indicated that Bacm OxDC bound to the exported peptide YydF and they are translocated to the cell membrane together, after which Bacm OxDC caused cell membrane relaxation for transmembrane secretion. Thereafter, three recombinant proteins were successfully secreted with certain enzymatic activity by fusing Bacm OxDC as a guide protein with various target proteins. To the best of our knowledge, this was the first time that non-classical secretion mechanism in bacteria has been analyzed. The novel discovery may provide a reference and broaden the horizons of the secretion pathway and expression regulation of proteins.

Engineering of IF1 -susceptive bacterial F1 -ATPase

IF1 , an inhibitor protein of mitochondrial ATP synthase, suppresses ATP hydrolytic activity of F1 . One of the unique features of IF1 is the selective inhibition in mitochondrial F1 (MF1 ); it inhibits catalysis of MF1 but does not affect F1 with bacterial origin despite high sequence homology between MF1 and bacterial F1 . Here, we aimed to engineer thermophilic Bacillus F1 (TF1 ) to confer the susceptibility to IF1 for elucidating the molecular mechanism of selective inhibition of IF1 . We first examined the IF1 -susceptibility of hybrid F1 s, composed of each subunit originating from bovine MF1 (bMF1 ) or TF1 . It was clearly shown that only the hybrid with the β subunit of mitochondrial origin has the IF1 -susceptibility. Based on structural analysis and sequence alignment of bMF1 and TF1 , the five non-conserved residues on the C-terminus of the β subunit were identified as the candidate responsible for the IF1 -susceptibility. These residues in TF1 were substituted with the bMF1 residues. The resultant mutant TF1 showed evident IF1 -susceptibility. Reversely, we examined the bMF1 mutant with TF1 residues at the corresponding sites, which showed significant suppression of IF1 -susceptibility, confirming the critical role of these residues. We also tested additional three substitutions with bMF1 residues in α and γ subunits that further enhanced the IF1 -susceptibility, suggesting the additive role of these residues. We discuss the molecular mechanism by which IF1 specifically recognizes F1 with mitochondrial origin, based on the present result and the structure of F1 -IF1 complex. These findings would help the development of the inhibitors targeting bacterial F1 .

Volatile organic compounds of the soil bacterium Bacillus halotolerans suppress pathogens and elicit defense-responsive genes in plants

Volatile organic compounds (VOCs) produced by bacteria play an important, yet relatively unexplored role in interactions between plants and phytopathogens. In this study, the soil bacterium Bacillus halotolerans NYG5 was identified as a potent biocontrol agent against several phytopathogenic fungi (Macrophomina phaseolina, Rhizoctonia solani, Pythium aphanidermatum, and Sclerotinia sclerotiorum) through the production of VOCs. NYG5-emitted VOCs also inhibited the growth of bacterial pathogens (Agrobacterium tumefaciens, Xanthomonas campestris, Clavibacter michiganensis, and Pseudomonas syringae). When cultured in various growth media, NYG5 produced a variety of VOCs. Five distinct VOCs (2-methylbutanoic acid, 5-methyl-2-hexanone, 2,3-hexanedione, 2-ethyl-1-hexanol, and 6-methyl-2-heptanone) were identified using headspace GC-MS. 2,3-Hexanedione exhibited potent lethal effects on the tested phytopathogens and nematicidal activity against Meloidogyne javanica at a concentration of 50 ppm. In addition, 0.05 ppm 2,3-hexanedione stimulated the expression of pathogenesis-related genes 1 and 2 in Arabidopsis thaliana. Interestingly, 2,3-hexanedione is used as a food additive at higher concentrations than those tested in this study. Hence, 2,3-hexanedione is a promising biologically active compound that might serve as a sustainable alternative to common chemical pesticides and an elicitor of plant defense.

A thermostable xylanase hydrolyzes several polysaccharides from Bacillus altitudinis JYY-02 showing promise for industrial applications

Polysaccharides have attracted immense attention as the largest source of bioactive compounds. Its bioavailability and bioactivity can be improved by utilizing degradation enzymes to reduce their molecular weight and viscosity. In this study, a 654 bp gene encoding xylanase was screened from the genome of Bacillus altitudinis JYY-02 and overexpressed in Escherichia coli Rosetta (DE3). The recombinant xylanase with a molecular weight of 27.98 kDa was purified (11.7-fold) using Ni-NTA affinity chromatography, with a 43.6% final yield. Through molecular docking, Glu, Arg, Tyr, and Trp were found to be the main amino acids involved in the interaction between xylanase and xylobiose. The effects of pH, temperature, metal ions, and substrates on xylanase activity were determined, and the results showed that the highest catalytic activity was displayed at pH 6.5, 50 °C temperature, with Cu2+ as an activator and xylan as the substrate. The Km (substrate concentration that yields a half-maximal velocity) and Vmax (maximum velocity) of recombinant xylanase were 6.876 mg/mL and 10984.183 μmol/mg∙pr/min, respectively. The recombinant xylanase was thermostable, with 85% and 39% of the enzymatic activity retained after 1 h at 60 °C and 1 h at 90 °C, respectively. The recombinant xylanase demonstrated a significant clarifying effect on fruit juices.

The effect of seed germination and Bacillus spp. on the ripening of plant cheese analogs

Consumer demand for plant cheeses is increasing, but challenges of improving both flavor and quality remain. This study investigated the microbiological and physicochemical impact of seed germination and fermentation with Bacillus velezensis and Bacillus amyloliquefaciens on the ripening of plant cheese analogs. Chlorine treatment or addition of Lactiplantibacillus plantarum and Lactococcus lactis controlled microbial growth during seed germination. Lp. plantarum and Lc. lactis also served as starter cultures for the acidification of soy and lupine milk and were subsequently present in the unripened plant cheese as dominant microbes. Acidification also inhibited the growth and metabolic activity of bacilli but Bacillus spores remained viable throughout ripening. During plant cheese ripening, Lc. lactis was inactivated before Lp. plantarum and the presence of bacilli during seed germination delayed Lc. lactis inactivation. Metagenomic sequencing of full-length 16S rRNA gene amplicons confirmed that the relative abundance of the inoculated strains in each ripened cheese sample exceeded 99%. Oligosaccharides including raffinose, stachyose, and verbascose were rapidly depleted in the initial stage of ripening. Both germination and the presence of bacilli during seed germination had impact on polysaccharide hydrolysis during ripening. Bacilli but not seed germination enhanced proteolysis of plant cheese during ripening. In conclusion, the use of germination with lactic acid bacteria in combination with Bacillus spp. exhibited the potential to improve the quality of ripened plant cheeses with a positive effect on the reduction of hygienic risks.

IMPORTANCE

The development of novel plant-based fermented food products for which no traditional templates exist requires the development of starter cultures. Although the principles of microbial flavor formation in plant-based analogs partially overlap with dairy fermentations, the composition of the raw materials and thus likely the selective pressure on the activity of starter cultures differs. Experiments that are described in this study explored the use of seed germination, the use of lactic acid bacteria, and the use of bacilli to reduce hygienic risks, to acidify plant milk, and to generate taste-active compounds through proteolysis and fermentative conversion of carbohydrates. The characterization of fermentation microbiota by culture-dependent and culture-independent methods also confirmed that the starter cultures used were able to control microbial communities throughout 90 d of ripening. Taken together, the results provide novel tools for the development of plant-based analogs of fermented dairy products.

Perception of the Biocontrol Potential and Palmitic Acid Biosynthesis Pathway of Bacillus subtilis H2 through Merging Genome Mining with Chemical Analysis

Bacillus has been widely studied for its potential to protect plants from pathogens. Here, we report the whole genome sequence of Bacillus subtilis H2, which was isolated from the tea garden soil of Guiyang Forest Park. Strain H2 showed a broad spectrum of antagonistic activities against many plant fungal pathogens and bacteria pathogens, including the rice blast fungus Magnaporthe oryzae, and showed a good field control effect against rice blast. The complete genome of B. subtilis H2 contained a 4,160,635-bp circular chromosome, with an average G + C content of 43.78%. Through the genome mining of strain H2, we identified 7 known antimicrobial compound biosynthetic gene clusters (BGCs) including sporulation killing factor, surfactin, bacillaene, fengycin, bacillibactin, subtilosin A, and bacilysin. Palmitic acid (PA), a secondary metabolite, was detected and identified in the H2 strain through genome mining analysis and gas chromatography-mass spectrometry (GC-MS). Additionally, we propose, for the first time, that the type II fatty acid synthesis (FAS) pathway in Bacillus is responsible for PA biosynthesis. This finding was confirmed by studying the antimicrobial activity of PA and conducting reverse transcription-quantitative polymerase chain reaction (RT-qPCR) experiments. We also identified numerous genes associated with plant-bacteria interactions in the H2 genome, including more than 94 colonization-related genes, more than 34 antimicrobial genes, and more than 13 plant growth-promoting genes. These findings contribute to our understanding of the biocontrol mechanisms of B. subtilis H2 and have potential applications in crop disease control.

Probiotic characterization of Bacillus smithii: Research advances, concerns, and prospective trends

Bacillus smithii is a thermophilic Bacillus that can be isolated from white wine, hot spring soil, high-temperature compost, and coffee grounds, with various biofunctions and wide applications. It is resistant to both gastric acid and high temperature, which makes it easier to perform probiotic effects than traditional commercial probiotics, so it can maintain good vitality during food processing and has great application prospects. This paper starts with the taxonomy and genetics and focuses on aspects, including genetic transformation, functional enzyme production, waste utilization, and application in the field of food science as a potential probiotic. According to available studies during the past 30 years, we considered that B. smithii is a novel class of microorganisms with a wide range of functional enzymes such as hydrolytic enzymes and hydrolases, as well as resistance to pathogenic bacteria. It is available in waste degradation, organic fertilizer production, the feed and chemical industries, the pharmaceutical sector, and food fortification. Moreover, B. smithii has great potentials for applications in the food industry, as it presents high resistance to the technological processes that guarantee its health benefits. It is also necessary to systematically evaluate the safety, flavor, and texture of B. smithii and explore its biological mechanism of action, which is of great value for further application in multiple fields, especially in food and medicine.

In vitro and in silico analysis unravelled clinically desirable attributes of Bacillus altitudinis L-asparaginase

AIMS

To identify a marine L-asparaginase with clinically desirable attributes and characterize the shortlisted candidate through in silico tools.

METHODS AND RESULTS

Marine bacterial strains (number = 105) isolated from marine crabs were evaluated through a stepwise strategy incorporating the crucial attributes for therapeutic safety. The results demonstrated the potential of eight bacterial species for extracellular L-asparaginase production. However, only one isolate (Bacillus altitudinis CMFRI/Bal-2) showed clinically desirable attributes, viz. extracellular production, type-II nature, lack of concurrent L-glutaminase and urease activities, and presence of ansZ (functional gene for clinical type). The enzyme production was 22.55 ± 0.5 µM/mg protein/min within 24 h without optimization. The enzyme also showed good activity and stability in pH 7-8 and temperature 37°C, predicting the functioning inside the human body. The Michealis-Menten constant (Km) was 14.75 µM. Detailed in silico analysis based on functional gene authenticating the results of in vitro characterization and predicted the nonallergenic characteristic of the candidate. Docking results proved the higher affinity of the shortlisted candidate to L-asparagine than L-glutamine and urea.

CONCLUSION

Comprehensively, the study highlighted B. altitudinis type II asparaginase as a competent candidate for further research on clinically safe asparaginases.

Application of PHA surface binding proteins of alkali-tolerant Bacillus as surfactants

Amphiphilic protein has lipophilic and hydrophilic domains, displaying the potential for development as a biosurfactant. The polyhydroxyalkanoate (PHA) surface binding protein derived from Bacillus is a type of protein that has not been studied for its emulsifying properties. In this study, PHA granule-associated protein (PhaP), PHA regulatory protein (PhaQ), and PHA synthase subunit (PhaR) derived from an alkali-tolerant PHA-producing Bacillus cereus HBL-AI were found and heterologously expressed in E. coli and purified to investigate their application as biosurfactants. It showed that the emulsification ability and stability of three amphiphilic proteins were higher than those of widely used chemical surfactants in diesel oil, vegetable oil, and lubricating oil. In particular, the PhaQ protein studied for the first time can form a stable emulsion layer in vegetable oil at a lower concentration (50 µg/mL), which greatly reduced the amount of protein used in emulsification. This clearly demonstrated that the PHA-binding protein of HBL-AI can be well applied as an environmentally friendly biosurfactants.

Lipopeptides from Bacillus: unveiling biotechnological prospects-sources, properties, and diverse applications

Bacillus sp. has proven to be a goldmine of diverse bioactive lipopeptides, finding wide-range of industrial applications. This review highlights the importance of three major families of lipopeptides (iturin, fengycin, and surfactin) produced by Bacillus sp. and their diverse activities against plant pathogens. This review also emphasizes the role of non-ribosomal peptide synthetases (NRPS) as significant enzymes responsible for synthesizing these lipopeptides, contributing to their peptide diversity. Literature showed that these lipopeptides exhibit potent antifungal activity against various plant pathogens and highlight their specific mechanisms, such as siderophore activity, pore-forming properties, biofilm inhibition, and dislodging activity. The novelty of this review comes from its comprehensive coverage of Bacillus sp. lipopeptides, their production, classification, mechanisms of action, and potential applications in plant protection. It also emphasizes the importance of ongoing research for developing new and enhanced antimicrobial agents. Furthermore, this review article highlights the need for future research to improve the production efficiency of these lipopeptides for commercial applications. It recognizes the potential for these lipopeptides to expand the field of biological pest management for both existing and emerging plant diseases.

Analysis of antimicrobial biological activity of a marine Bacillus velezensis NDB

A new strain of Bacillus velezensis NDB was isolated from Xiangshan Harbor and antibacterial test revealed antibacterial activity of this strain against 12 major pathogenic bacteria. The whole genome of the bacterium was sequenced and found to consist of a 4,214,838 bp circular chromosome and a 7410 bp circular plasmid. Furthermore, it was predicted by AntiSMASH and BAGEL4 to have 12 clusters of secondary metabolism genes for the synthesis of the inhibitors, fengycin, bacillomycin, macrolactin H, bacillaene, and difficidin, and there were also five clusters encoding potentially novel antimicrobial substances, as well as three bacteriocin biosynthesis gene clusters of amylocyclicin, ComX1, and LCI. qRT-PCR revealed significant up-regulation of antimicrobial secondary metabolite synthesis genes after 24 h of antagonism with pathogenic bacteria. Furthermore, MALDI-TOF mass spectrometry revealed that it can secrete surfactin non-ribosomal peptide synthase and polyketide synthase to exert antibacterial effects. GC-MS was used to analyze methanol extract of B. velezensis NDB, a total of 68 compounds were identified and these metabolites include 16 amino acids, 17 acids, 3 amines, 11 sugars, 11 alcohols, 1 ester, and 9 other compounds which can inhibit pathogenic bacteria by initiating the antibiotic secretion pathway. A comparative genomic analysis of gene families showed that the specificity of B. velezensis NDB was mainly reflected in environmental adaptability. Overall, this research on B. velezensis NDB provides the basis for elucidating its biocontrol effect and promotes its future application as a probiotic.

Biocontrol of Peach Gummosis by Bacillus velezensis KTA01 and Its Antifungal Mechanism

Peach tree gummosis is a botanical anomaly distinguished by the secretion of dark-brown gum from the shoots of peach trees, and Botryosphaeria dothidea has been identified as one of the fungal species responsible for its occurrence. In South Korea, approximately 80% of gummosis cases are linked to infections caused by B. dothidea. In this study, we isolated microbes from the soil surrounding peach trees exhibiting antifungal activity against B. dothidea. Subsequently, we identified several bacterial strains as potential candidates for a biocontrol agent. Among them, Bacillus velezensis KTA01 displayed the most robust antifungal activity and was therefore selected for further analysis. To investigate the antifungal mechanism of B. velezensis KTA01, we performed tests to assess cell wall degradation and siderophore production. Additionally, we conducted reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis based on whole-genome sequencing to confirm the presence of genes responsible for the biosynthesis of lipopeptide compounds, a well-known characteristic of Bacillus spp., and to compare gene expression levels. Moreover, we extracted lipopeptide compounds using methanol and subjected them to both antifungal activity testing and high-performance liquid chromatography (HPLC) analysis. The experimental findings presented in this study unequivocally demonstrate the promising potential of B. velezensis KTA01 as a biocontrol agent against B. dothidea KACC45481, the pathogen responsible for causing peach tree gummosis.

Emergence of multidrug-resistant Bacillus spp. derived from animal feed, food and human diarrhea in South-Eastern Bangladesh

BACKGROUND

Antimicrobial resistance poses a huge risk to human health worldwide, while Bangladesh is confronting the most severe challenge between the food supply and the huge consumption of antibiotics annually. More importantly, probiotics containing Bacillus spp. are claimed to be an alternative to antimicrobial stewardship programs. However, their antibiotic resistance remains elusive. Thus, we employed the antimicrobial susceptibility test and PCR to assess the prevalence of resistance, including multidrug resistance (MDR) and resito-genotyping of isolated Bacillus spp.

RESULTS

The phenotypic profile showed that Bacillus spp. were 100% sensitive to gentamicin (2 µg/mL), whereas lowered sensitivity to levofloxacin (67.8%, 0.5-1 µg/mL), ciprofloxacin (62.3%, 0.5-1 µg/mL), clindamycin (52.2%, 0.25-0.5 µg/mL), amoxicillin-clavulanic acid (37.6%, 0.06 µg/mL), azithromycin (33.4%, 1-2 µg/mL), tetracycline (25.6%, 2-4 µg/mL), nitrofurantoin (21.1%, 16-32 µg/mL), co-trimoxazole (19.2%, 2 µg/mL), and erythromycin (18.8%, 0.25-0.5 µg/mL). The strains were completely resistant to penicillin, amoxicillin-clavulanic acid, cefixime, ceftriaxone, vancomycin, and co-trimoxazole, and a species-specific trend was seen in both phenotypic and genotypic resistance patterns. Genotypic resistance indicated prevalence of the bla1 (71.5%), tetA (33%), erm1 (27%), blaTEM (13.1%), blaCTX-M-1/blaCTX-M-2 /sul1 (10.1%), blaSHV (9.6%), and qnrS (4.1%) genes. The β-lactamase resistance gene bla1 was found in all penicillin-resistant (MIC ≥ 32 µg/mL) Bacillus spp. One hundred ninety-one isolates (89.6%) were MDR, with 100% from diarrhea, 90.3% from food, and 88.7% from animal feed.

CONCLUSION

Based on the MIC value and profile analysis of antibiotic resistance genes, this is the first study that Bacillus spp. antimicrobial susceptibilities have been identified in Bangladesh, and our study will shed light on the adverse effects of feed-borne Bacillus spp. emerging from animal feed to the food chain. A comprehensive investigation is urgently needed by policymakers on tolerance limits and harmful effects in the animal industry.

Assessment of the phenotypic and genotypic diversity of endophytic strains of Bacillus and closely related genera from Carpinus betulus in the Hyrcanian forests of Iran

BACKGROUND

Identification and characterization of the endophytic microorganism, is gaining their underestimated significance in influencing health, performance, and other biological attributions of plants in general and forest tree species in particular. Because of the scarcity of information on the endophytic microbiome of the Hyrcanian forests species, including hornbeam (Carpinus betulus L.) trees, as a major constituent thereof, the present study aimed at the identification and partial characterization of the endophytic Bacillus species of Carpinus betulus as the first step in this context.

METHODS AND RESULTS

Shoot samples were collected from the Hyrcanian forest locations of Mazandaran and Golestan provinces in Iran. Bacterial strains were isolated from the surface-disinfected shoot segments and subjected to phenotypic characterization. Following assessment of the genetic diversity of the isolates by BOX-PCR fingerprinting, the representative isolates of each of the 15 groups were used for further characterization. Analysis of the nucleotide sequences of the 16S rDNA and HSP60 gene of the isolates led to the identification of 10 species. The predominant species was B. cereus followed by B. subtilis. The other species encountered were B. thuringiensis, Priestia filamentosa, B. velezensis, B. mojavensis, B. amyloliquefaciens, B. safensis, P. aryabhattai, and Gottfriedia acidiceleris. Most isolates possessed characteristics which could contribute to the biocontrol potential of the isolates, including formation of biofilm, production of hydrogen cyanide, tolerant to relatively high concentration of sodium chloride, and antibacterial activity.

CONCLUSIONS

Ten Bacillus species were identified as the prevailing endophytic species of C. betulus in the Hyrcanian forest of northern Iran, most turned up to possess biological activities involved in biocontrol capability of the isolates against some plant pathogens. These potentially capable bacteria could be implemented in the promotion of plant growth as well as in the biological control of pathogens. This is the first report on the characterization and elucidation of the diversity of the potentially beneficial endophytic species of Bacillus and the closely related genera living in the internal tissues of hornbeam trees.

Isolation and Characterization of Paenibacillus polymyxa B7 and Inhibition of Aspergillus tubingensis A1 by Its Antifungal Substances

Screening of Bacillus with antagonistic effects on paddy mold pathogens to provide strain resources for biological control of mold in Oryza sativa L. screening of Bacillus isolates antagonistic towards Aspergillus tubingensis from rhizosphere soil of healthy paddy; classification and identification of antagonistic strains by biological characteristics and 16S rDNA sequence analysis; transcriptome sequencing after RNA extraction from Bacillus-treated Aspergillus tubingensis; and extraction of inhibitory crude proteins of Bacillus by ammonium sulfate precipitation; inhibitory crude protein and Bacillus spp. were treated separately for A. tubingensis and observed by scanning electron microscopy (SEM). An antagonistic strain of Bacillus, named B7, was identified as Paenibacillus polymyxa by 16S rDNA identification and phylogenetic evolutionary tree comparison analysis. Analysis of the transcriptome results showed that genes related to secondary metabolite biosynthesis such as antifungal protein were significantly downregulated. SEM results showed that the mycelium of A. tubingensis underwent severe rupture after treatment with P. polymyxa and antifungal proteins, respectively. In addition, the sporocarp changed less after treatment with P. polymyxa, and the sporangium stalks had obvious folds. P. polymyxa B7 has a good antagonistic effect against A. tubingensis and has potential for biocontrol applications of paddy mold pathogens.

UV-ARTP compound mutagenesis breeding improves macrolactins production of Bacillus siamensis and reveals metabolism changes by proteomic

Macrolactins are a type of compound with complex macrolide structure which mainly be obtained through microbiological fermentation now. They have excellent antifungal, antibacterial and antitumor activity. In order to improve macrolactins production, Bacillus siamensis YB304 was used as the research object, and a mutant Mut-K53 with stable genetic characters was selected by UV-ARTP compound mutagenesis. The yield of macrolactins was 156.46 mg/L, 3.95 times higher than original strain. The metabolic pathway changes and regulatory mechanism of macrolactins were analyzed by quantitative proteomics combined with parallel reaction monitoring. This study revealed that 1794 proteins were extracted from strain YB304 and strain Mut-K53, most of them were related to metabolism. After UV-ARTP compound mutagenesis treatment, the expression of 628 proteins were significantly changed, of which 299 proteins were significantly up-regulated. KEGG pathway analysis showed that differentially expression proteins mainly distributed in biological process, cellular component, and molecular function processing pathways. Such as utilization of carbon sources, glycolysis pathway, and amino acid metabolism pathway. Furthermore, key precursor substances such as acyl-CoA and amino acids of macrolactin biosynthesis are mostly up-regulated, which are one of the main reasons for increased production of macrolactin.This study will provide a new way to increase the yield of macrolactins through mutagenesis breeding and proteomics.

How to identify and quantify the members of the Bacillus genus?

Members of the Bacillus genus are widely distributed throughout natural environments and have been studied for decades among others for their physiology, genetics, ecological functions, and applications. However, despite its prevalence in nature, the characterization and classification of Bacillus remain challenging due to its complex and ever-evolving taxonomic framework. This review addresses the current state of the Bacillus taxonomic landscape and summarizes the critical points in the development of Bacillus phylogeny. With a clear view of Bacillus phylogeny as a foundation, we subsequently review the methodologies applied in identifying and quantifying Bacillus, while also discussing their respective advantages and disadvantages.

Complete genome sequence analysis of Bacillus velezensis A5, a promising biocontrol agent from the Pacific Ocean

Tobacco bacterial wilt (TBW) caused by Ralstonia solanacearum is a serious soil-borne disease, which seriously damages the growth of tobacco crops. Bacillus velezensis A5 was isolated from 3000 m deep-sea sediments of the Pacific Ocean, and was found to be antagonistic to TBW. Here, we report the complete genome sequence of strain A5, which has a 4,000,699-bp single circular chromosome with 3827 genes and a G + C content of 46.44%, 87 tRNAs, and 27 rRNAs. A total of 12 gene clusters were identified in the genome of strain A5, which were responsible for the biosynthesis of antibacterial compounds, including surfactin, bacillaene, fengycin, difficidin, bacillibactin, and bacilysin. Additionally, strain A5 was found to contain a series of genes related to the biosynthesis of carbohydrate-active enzymes and secreted proteins. Our results indicate that strain A5 can be considered a promising biocontrol agent against TBW in agricultural fields.

Environmental factors drive microbial community succession in biofortified wheat Qu and its improvement on the quality of Chinese huangjiu

Wheat Qu plays the role of saccharification fermentation, providing microorganisms and flavor in the fermentation of huangjiu, and the use of functional microorganisms to fortify wheat Qu is becoming increasingly popular. Yet, the mechanisms promoting microbial successions of wheat Qu remain unclear. In this study, we first correlated microbial community succession with physicochemical factors (moisture, temperature, acidity, glucoamylase and amylase) in inoculated raw wheat Qu (IRWQ) with Saccharopolyspora rosea. The Mantel test was performed to investigate the significance and found that temperature (r = 0.759, P = 0.001), moisture (r = 0.732, P = 0.006), and acidity (r = 0.712, P = 0.017) correlated significantly with the bacterial community in phase 1 (0-40 h). Meanwhile, temperature correlated significantly with the fungal community in phases 1 and 2 (40-120 h). To confirm the effect of temperature on microbial communities, the artificial reduction of bio-heat (37°C) in IRWQ also reduced the relative abundance of heat-resistant microorganisms including Bacillus and Saccharopolyspora. A higher abundance of Saccharopolyspora (87%) in IRWQ was observed following biofortified inoculation of S. rosea, in which glucoamylase activity increased by 40% compared to non-inoculated raw wheat Qu (NIRWQ) (1086 U/g vs 776 U/g). Finally, the IRWQ was employed to mechanized huangjiu fermentation and it was found to reduce the bitter amino acid and higher alcohol content by 27% and 8%, respectively, improving the drinking comfort and quality of huangjiu.

Comparative metagenomics and microbial dynamics of jute retting environment

Jute, eco-friendly natural fiber, depends on conventional water-based microbial retting process that suffers from the production of low-quality fiber, restricting its diversified applications. The efficiency of water retting of jute depends on plant polysaccharide fermenting pectinolytic microorganisms. Understanding the phase difference in retting microbial community composition is crucial to provide knowledge on the functions of each member of microbiota for the improvement of retting and fiber quality. The retting microbiota profiling of jute was commonly performed previously using only one retting phase with culture-dependent methods which has limited coverage and accuracy. Here, for the first we have analyzed jute retting water through WGS metagenome approach in three phases (pre-retting, aerobic retting, and anaerobic retting phases) and characterized the microbial communities both culturable and non-culturable along with their dynamics with the fluctuation of oxygen availability. Our analysis revealed a total of 25.99 × 104 unknown proteins (13.75%), 16.18 × 105 annotated proteins (86.08%), and 32.68 × 102 ribosomal RNA (0.17%) in the pre-retting phase, 15.12 × 104 unknown proteins (8.53%), 16.18 × 105 annotated proteins (91.25%), and 38.62 × 102 ribosomal RNA (0.22%) in the aerobic retting phase, and 22.68 × 102 ribosomal RNA and 80.14 × 104 (99.72%) annotated protein in the anaerobic retting phase. Taxonomically, we identified 53 different phylotypes in the retting environment, with Proteobacteria being the dominant taxa comprising over 60% of the population. We have identified 915 genera from Archaea, Viruses, Bacteria, and Eukaryota in the retting habitat, with anaerobic or facultative anaerobic pectinolytic microflora being enriched in the anoxic, nutrient-rich retting niche, such as Aeromonas (7%), Bacteroides (3%), Clostridium (6%), Desulfovibrio (4%), Acinetobacter (4%), Enterobacter (1%), Prevotella (2%), Acidovorax (3%), Bacillus (1%), Burkholderia (1%), Dechloromonas (2%), Caulobacter (1%) and Pseudomonas (7%). We observed an increase in the expression of 30 different KO functional level 3 pathways in the final retting stage compared to the middle and pre-retting stages. The main functional differences among the retting phases were found to be related to nutrient absorption and bacterial colonization. These findings reveal the bacterial groups that are involved in fiber retting different phases and will facilitate to develop future phase-specific microbial consortia for the improvement of jute retting process.

Characterisation of meropenem-resistant Bacillus sp. FW 1 isolated from biogas digestate

Recently a Bacillus sp. strain FW 1 was isolated from biogas digestate and shown to have novel resistance to meropenem (MEM), of critical importance in human medicine. MEM-resistance has so far only been described for one species within the genus Bacillus, that is, Bacillus cereus. Bacillus is an abundant representative of the microbial community in biogas digesters and consequently, the finding indicates a risk of spreading such resistance when using the digestate as fertiliser. In this study, the Bacillus strain was characterised and classified as Heyndrickxia oleronia (previous Bacillus oleronius), previously not described to harbour MEM-resistance. The mechanism of resistance was explored by metallo-β-lactamase (MBL) production, mapping of carbapenemase genes and genome analysis. The transferability of MEM-resistance in strain FW 1 was investigated by plasmid transformation/conjugation, combined with genome analysis. The results confirmed MBL production for both strain FW 1 and the type strain H. oleronia DSM 9356T . However, elevated MEM resistance was found for strain FW 1, which was suggested to be caused by the production of unclassified carbapenemase, or overexpression of MBL. Moreover, the results suggest that the MEM-resistance of strain FW 1 is not transferable, thus representing a limited risk of MEM-resistance spread to the environment when using digestate on arable land.

Low-intensity ultrasound-assisted adaptive laboratory evolution of Bacillus velezensis for enhanced production of peptides

This work aimed to explore low-intensity ultrasound-assisted adaptive laboratory evolution (US-ALE) of Bacillus velezensis and fermentation performance of mutant strains were investigated by nitrogen transformation metabolism. Results showed ultrasound accelerated the process of adaptive evolution and enhanced cell dry weight, amylase and protease activity of mutant strains, accompanied with the improved transformation abilities of NO-3-N to NH4+-N. Compared with original strain, the total peptide-N, peptide-N (<3 kDa) and autolytic peptide-N of mutant strains increased by the maximum 23.17%, 66.07% and 30.30%, respectively, based on ideal fermentation medium. According to the actual liquid-state fermentation of soybean meal and corn gluten meal with mutant strains, the highest peptide yields of 50.63% and 23.67% were noticed in mutant strain US-ALE-BV3, accompanied with the improved amino acid composition by bacterial autolysis technology. Thus, this study showed that low-intensity ultrasound could accelerate the process of adaptive evolution and US-ALE will provide more possibilities for modifying fermentation strains.

Biodegradation of low-density polyethylene by plasma-activated Bacillus strain

Plastic biodegradation by microorganisms is an eco-friendly and sustainable method without any ramifications. Herein, we used a cultivation method and 16S rRNA sequencing to screen bacteria that can efficiently colonize and degrade low-density polyethylene (LDPE) from various plastic wastes. We identified Bacillus safensis BS-10L through whole-genome sequencing analysis and verified its LDPE-degradation ability. However, the decomposition mechanism of the isolated bacteria was unclear and the decomposition efficiency was insufficient, so low-temperature plasma was used to increase the decomposition efficiency of the bacteria. The population and viability of bacteria treated with cold plasma increased. Plasma-activated bacteria could induce cracks, holes, and roughness on the surface of LDPE films over 90 days, and over 30 days; the LDPE film lost 13.40 ± 0.013% and 27.78 ± 0.014% of its mass by BS-10L and plasma-treated BS-10L, respectively. Fourier-transform infrared spectroscopic analysis identified new peaks of the C=O and C-O groups in the plasma-treated LDPE film, exhibiting high transmittance in the LDPE film that was inoculated with bacteria. X-ray photoelectron spectroscopic analysis showed that C-O bonds were generated by BS-10L strain, and relatively strong C=O bonds were generated in the film inoculated with plasma-treated BS-10L strain. Plasma treatment increased the colonization of the BS-10L strain and changed the chemical bonding of the LDPE film, suggesting that plasma-activated BS-10L could accelerate decomposition by oxidation by increasing the carbonyl group of the PE film. Therefore, plasma technology may be effective for enhancing the plastic-degrading ability of microorganisms.

Tartrate Dehydrogenase in Bacillus Species: Deciphering Unique Catalytic Diversity Through Kinetic, Structural and Molecular Docking Analysis

Divergently evolved Tartrate dehydrogenase (TDH) exhibits multiple catalytic activities at a single active site; the enzyme from P. putida (pTDH) being structurally and biochemically well-characterized. Occurrence of TDH-associated ability to aerobically metabolize L-tartrate in Bacillus isolates and limited resemblance of ycsA-encoded protein sequences with pTDH rendered Bacillus TDH as an intriguing enzyme with possible catalytic diversity as well as evolutionary significance. The present study explores substrate interactions of TDHs from B. subtilis 168 (168bTDH) and B. licheniformis DSM-13 (429bTDH) through kinetic, structural and molecular docking-based analysis. Heterologously expressed bTDHs, purified from insoluble fractions of E. coli BL21(DE3) cells, could significantly catalyze L-tartrate and meso-tartrate as substrates in forward reaction. Unlike pTDH, bTDHs distinctly and more efficiently catalyzed the reverse reaction using dihydroxyfumarate substrate following sigmoidal kinetics; the ability being ~ 4 fold higher in 168bTDH. Their binding energies predicted from molecular docking, further substantiated the relative substrate specificities, while revealing major residues involved in protein-ligand interactions at active site. The kinetic analysis and homology modelling validated using Ramachandran Plot analysis predicted a dimeric nature for bTDH. Collectively, the results highlight unique catalytic potential of phylogenetically recent bTDHs, offering an important protein engineering target to mediate efficient enantioselective enzymatic biotransformations.

Enhancing the efficiency and functionality of xylanase from Bacillus sp. RTS11: Optimization, purification, characterization, and prospects in kraft pulp bleaching

Bacillus sp. RTS11, a xylanolytic strain, was isolated from the Algerian desert rocks. Genetic analysis revealed a remarkable 98.69% similarity to Bacillus pumilus. We harnessed optimization techniques, including Plackett-Burman screening and Box-Behnken optimization design, to amplify xylanase production and activity. The outcome of these efforts was an optimized medium that yielded an impressive xylanase production titer of 448.89 U, a threefold increase compared to the non-optimized medium (146 U). The Purification of xylanase was achieved through the three-phase partitioning technique, employing t-butanol and various chromatographic methods. Notably, anion exchange chromatography led to isolating a highly pure enzyme with a molecular weight of 60 kDa. The xylanase exhibited its peak activity at a temperature of 60°C and a pH of 9.0. When applied to pulp pretreatment, 20 U/g of xylanase demonstrated a substantial increase in the release of phenolic and chromophore compounds while reducing sugar content in the pulp. Furthermore, this versatile xylanase shows its ability to efficiently hydrolyze a variety of agro-industrial residues, including wheat bran, corn and grape waste, wheat straw, and sugarcane bagasse. These findings underscore the significant potential of this xylanase enzyme in biobleaching processes and the utilization of agro-industrial waste, opening up exciting avenues for sustainable and environmentally friendly industrial applications.

Bacillus and Streptomyces spp. as hosts for production of industrially relevant enzymes

The application of enzymes is expanding across diverse industries due to their nontoxic and biodegradable characteristics. Another advantage is their cost-effectiveness, reflected in reduced processing time, water, and energy consumption. Although Gram-positive bacteria, Bacillus, and Streptomyces spp. are successfully used for production of industrially relevant enzymes, they still lag far behind Escherichia coli as hosts for recombinant protein production. Generally, proteins secreted by Bacillus and Streptomyces hosts are released into the culture medium; their native conformation is preserved and easier recovery process enabled. Given the resilience of both hosts in harsh environmental conditions and their spore-forming capability, a deeper understanding and broader use of Bacillus and Streptomyces as expression hosts could significantly enhance the robustness of industrial bioprocesses. This mini-review aims to compare two expression hosts, emphasizing their specific advantages in industrial surroundings such are chemical, detergent, textile, food, animal feed, leather, and paper industries. The homologous sources, heterologous hosts, and molecular tools used for the production of recombinant proteins in these hosts are discussed. The potential to use both hosts as biocatalysts is also evaluated. Undoubtedly, Bacillus and Streptomyces spp. as production hosts possess the potential to take on a more substantial role, providing superior (bio-based) process robustness and flexibility. KEY POINTS: • Bacillus and Streptomyces spp. as robust hosts for enzyme production. • Industrially relevant enzyme groups for production in alternative hosts highlighted. • Molecular biology techniques are enabling easier utilization of both hosts.

Molecular identification and safety assessment of the potential probiotic strain Bacillus paralicheniformis HMPM220325 isolated from artisanal fruit dairy products

Bacillus probiotics exhibit considerable economic potential owing to their heightened resilience to external stressors and relatively lower costs related to production and preservation. Although Bacillus paralicheniformis has been acknowledged as a plant-promoting bacterium for a long time, understanding its potential as a probiotic is still in its nascent stages. In this study, the safety and probiotic characteristics of a strain of HMPM220325, isolated from artisanal fruit dairy products, were examined through whole-genome sequencing and phenotypic analysis. The whole genome of HMPM220325 was analyzed for antimicrobial resistance genes, pathogenicity factors, and genes associated with probiotic traits including stress resistance, spore formation, gut adhesion, competitive exclusion of pathogens, bacteriocin expression, and carbohydrate metabolism related to prebiotic utilization. Also, wet lab experiments were conducted for the characterization of probiotics. The identification of the organism as B. paralicheniformis was verified. Its safety was assessed through in silico analysis, the haemolytic activity test, and the acute oral toxicity test. B. paralicheniformis HMPM220325 demonstrated its ability to survive in the pH range of 4-10 and bile salt concentrations of 0-0.9% (w/v), tolerate temperatures between 20 and 60 °C, and exhibit a robust antioxidant capacity. Moreover, B. paralicheniformis HMPM220325 demonstrated a moderate level of hydrophobicity, had the ability to form biofilms, achieved a self-aggregation rate of 51.77 ± 1.01% within 6 hours, and successfully colonized the mouse intestine for a duration of up to 17 days. Additionally, the genome of B. paralicheniformis HMPM220325 contains three gene clusters associated with the biosynthesis of bacteriocins and exhibits co-aggregation with Staphylococcus aureus, Pseudomonas aeruginosa, and Salmonella enterica serovar Typhimurium. The findings of the genomic analysis align with those obtained from the experimental investigation, thereby substantiating the potential of B. paralicheniformis HMPM220325 as a probiotic suitable for incorporation in dairy functional foods and feed applications.

Biocontrol potential of Bacillus velezensis wr8 secondary metabolites against Penicillium sp

The aim of this study was to isolate and identify native Bacillus from citrus fruits, with inhibition phenotypes to Penicillium sp. We investigated the antifungal effect of Bacillus velezensis wr8 on the postharvest pathogens Penicillium sp. inoculated on fruits, as well as on the growth of these fungi on Petri dishes with defined media. MALDI-TOF MS was conducted to enlighten the underlying mechanism. Results showed that Bacillus velezensis wr8 significantly inhibited Penicillium sp. growth in vitro. Moreover, secondary metabolites suppressed the disease development of citrus fruits artificially inoculated with Penicillium sp. in 25 °C. Furthermore, MALDI-TOF MS indicated that lipoprotein with the molecular mass of 30.2 kDa was a key component about against Penicillium sp. In addition, the secondary metabolites with antibacterial activity against Escherichia coli showed antimicrobial peptide with the molecular weight of 9.8 kDa. These results demonstrated that Bacillus velezensis wr8 could produce lipoprotein and antimicrobial peptide to inhibit Penicillium sp. and Escherichia coli which has broad application prospect in the future development. Finally, Bacillus velezensis wr8 is to provide data support for the development and utilization of high activity bacteriocin at room temperature and its application in the field of food safety.

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

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

Cellulase with Bacillus velezensis improves physicochemical characteristics, microbiota and metabolites of corn germ meal during two-stage co-fermentation

Corn germ meal (CGM) is one of the major byproducts of corn starch extraction. Although CGM has rich fiber content, it lacks good protein content and amino acid balance, and therefore cannot be fully utilized as animal feed. In this study, we investigated the processing effect of cellulase synergized with Bacillus velezensis on the nutritional value of pretreated CGM (PCGM) in two-stage solid-state fermentation (SSF). High-throughput sequencing technology was used to explore the dynamic changes in microbial diversity. The results showed that compared with four combinations of B. velezensis + Lactiplantibacillus plantarum (PCGM-BL), cellulase + L. plantarum (PCGM-CL),control group (PCGM-CK), and cellulase + B. velezensis + L. plantarum (PCGM-BCL), the fourth combination of PCGM-BCL significantly improved the nutritional characteristics of PCGM. After two-stage SSF (48 h), viable bacterial count and contents of crude protein (CP) and trichloroacetic acid-soluble protein (TCA-SP) all were increased in PCGM-BCL (p < 0.05), while the pH was reduced to 4.38 ± 0.02. In addition, compared with PCGM-BL, the cellulose degradation rate increased from 5.02 to 50.74%, increasing the amounts of short-chain fatty acids (216.61 ± 2.74 to 1727.55 ± 23.00 µg/g) and total amino acids (18.60 to 21.02%) in PCGM-BCL. Furthermore, high-throughput sequencing analysis revealed significant dynamic changes in microbial diversity. In the first stage of PCGM-BCL fermentation, Bacillus was the dominant genus (99.87%), which after 24 h of anaerobic fermentation changed to lactobacillus (37.45%). Kyoto Encylopaedia of Genes and Genomes (KEGG) metabolic pathway analysis revealed that the pathways related to the metabolism of carbohydrates, amino acids, cofactors, and vitamins accounted for more than 10% of the enriched pathways throughout the fermentation period. Concisely, we show that cellulase can effectively improve the nutritional value of PCGM when synergized with B. velezensis in two-stage SSF.

In-silico analysis of probiotic attributes and safety assessment of probiotic strain Bacillus coagulans BCP92 for human application

The whole genome sequence (WGS) of Bacillus coagulans BCP92 is reported along with its genomic analysis of probiotics and safety features. The identification of bacterial strain was carried out using the 16S rDNA sequencing method. Furthermore, gene-related probiotic features, safety assessment (by in vitro and in silico), and genome stability were also studied using the WGS analysis for the possible use of the bacterial strain as a probiotic. From the BLAST analysis, bacterial strain was identified as Bacillus (Heyndrickxia) coagulans. WGS analysis indicated that the genome consists of a 3 475 658 bp and a GC-content of 46.35%. Genome mining of BCP92 revealed that the strain is consist of coding sequences for d-lactate dehydrogenase and l-lactate dehydrogenases, 36 genes involved in fermentation activities, 29 stress-responsive as well as many adhesions related genes. The genome, also possessing genes, is encoded for the synthesis of novel circular bacteriocin. Using an in-silico approach for the bacterial genome study, it was possible to determine that the Bacillus (Heyndrickxia) coagulans strain BCP92 contains genes that are encoded for the probiotic abilities and did not harbour genes that are risk associated, thus confirming the strain's safety and suitability as a probiotic to be used for human application.

Establishment and application of quantitative detection of Bacillus velezensis HMB26553, a biocontrol agent against cotton damping-off caused by Rhizoctonia

A highly sensitive quantitative PCR (qPCR) method was developed for detection and quantification of Bacillus velezensis HMB26553 in cotton rhizosphere. The study aimed to develop a quantitative detection method for the strain HMB26553, and explore the relationship between its colonization of the cotton rhizosphere and its control effect. The whole genome sequence of strain HMB26553 was obtained by genome sequencing and a unique specific sequence pB-gene0026 on plasmid plaBV2 was identified by using high-throughput alignment against NCBI. Plasmid plaBV2 could be stably genetically inherited. Based on this sequence, specific primers for amplifying 106 bp and a minor groove binder (MGB) TaqMan probe for enhancing sensitivity were designed. The copy number of plaBV2 in strain HMB26553, which was 2, was confirmed by internal reference primers and the MGB TaqMan probe based on housekeeping gene gyrB. The established detection technique based on these primers and probes had high specificity and sensitivity compared to traditional plate counting method, with a detection limit of 1.5 copy genome. Using this method, the study discovered a likely correlation between the quantity of colonization in cotton rhizosphere and efficacy against cotton damping-off caused by Rhizoctonia after seed soaking and irrigation with strain HMB26553. Thus, this method provides scientific support for the rational application of strain HMB26553 in the future.

A smart RBS library and its prediction model for robust and accurate fine-tuning of gene expression in Bacillus species

Bacillus species, such as Bacillus subtilis and Bacillus licheniformis, are important industrial bacteria. However, there is a lack of standardized and predictable genetic tools for convenient and reproducible assembly of genetic modules in Bacillus species to realize their full potential. In this study, we constructed a Ribosome Binding Site (RBS) library in B. licheniformis, which provides incremental regulation of expression levels over a 104-fold range. Additionally, we developed a model to quantify the resulting translation rates. We successfully demonstrated the robust expression of various target genes using the RBS library and showed that the model accurately predicts the translation rates of arbitrary coding genes. Importantly, we also extended the use of the RBS library and prediction model to B. subtilis, B. thuringiensis, and B. amyloliquefacie. The versatility of the RBS library and its prediction model enables quantification of biological behavior, facilitating reliable forward engineering of gene expression.

Production and characterization of novel thermostable CotA-laccase from Bacillus altitudinis SL7 and its application for lignin degradation

Laccases are multi-copper oxidases and found in ligninolytic bacteria catalyzing the oxidation of both phenolic and non-phenolic compounds, however its application in lignin degradation suffers due to low oxidation rate, which have intensified the search for new laccases. In the present study, spore coat A protein (CotA) encoding gene having laccase like activity from Bacillus altitudinis SL7 (CotA-SL7) was cloned and expressed in Escherichia coli. The purified CotA-SL7 was active at wide range of temperature and pH with optimum activity at 55 °C and pH 5.0. The kinetic parameters of CotA-SL7 was determined with Km, Vmax, and kcat values 0.4 mM, 2777 μmol/min/mg, and 5194 s-1, respectively. Molecular docking revealed the presence of Pro, Phe, Asp, Asn, His, and Ile residues at the active site taking part in the oxidation of ABTS. The purified CotA-SL7 reduced lignin contents by 31 % and changes in lignin structure were analyzed through fourier transformed infrared spectroscopy (FTIR), scanning electron microsscopy (SEM) and gas chromatography mass-spectrometry (GC-MS). The appearance of low molecular size compounds clearly indicates the cleavage of lignin polymer and opening of the benzene ring by purified CotA-SL7. Thus, high catalytic efficiency of CotA-SL7 makes it a suitable bio-catalyst for remediation of lignin contaminated wastewater from pulp and paper industries with clear insights into lignin degradation at molecular level.

Exploring the hemicellulolytic properties and safety of Bacillus paralicheniformis as stepping stone in the use of new fibrolytic beneficial microbes

Bacillus strains from the Moroccan Coordinated Collections of Microorganisms (CCMM) were characterised and tested for fibrolytic function and safety properties that would be beneficial for maintaining intestinal homeostasis, and recommend beneficial microbes in the field of health promotion research. Forty strains were investigated for their fibrolytic activities towards complex purified polysaccharides and natural fibres representative of dietary fibres (DFs) entering the colon for digestion. We demonstrated hemicellulolytic activities for nine strains of Bacillus aerius, re-identified as Bacillus paralicheniformis and Bacillus licheniformis, using xylan, xyloglucan or lichenan as purified polysaccharides, and orange, apple and carrot natural fibres, with strain- and substrate-dependent production of glycoside hydrolases (GHs). Our combined methods, based on enzymatic assays, secretome, and genome analyses, highlighted the hemicellulolytic activities of B. paralicheniformis and the secretion of specific glycoside hydrolases, in particular xylanases, compared to B. licheniformis. Genomic features of these strains revealed a complete set of GH genes dedicated to the degradation of various polysaccharides from DFs, including cellulose, hemicellulose and pectin, which may confer on the strains the ability to digest a variety of DFs. Preliminary experiments on the safety and immunomodulatory properties of B. paralicheniformis fibrolytic strains were evaluated in light of applications as beneficial microbes' candidates for health improvement. B. paralicheniformis CCMM B969 was therefore proposed as a new fibrolytic beneficial microbe candidate.

Levels and types of microbial contaminants in different plant-based ingredients used in dairy alternatives

In this study levels and types of microbial contaminants were investigated in 88 different plant-based ingredients including many that are used to manufacture dairy alternatives. Studied ingredients encompassed samples of pulses (pea, faba bean, chickpea, and mung bean), cereals/pseudocereals (oat, rice, amaranth and quinoa) and drupes (coconut, almond and cashew). The microbial analysis included: i) total viable count (TVC), ii) total aerobic mesophilic spore count (TMS), iii) heat resistant aerobic thermophilic spore count (HRTS), iv) anaerobic sulfite reducing Clostridium spore count (SRCS), and v) Bacillus cereus spore count (BCES). Microorganisms isolated from the counting plates with the highest sample dilutions were identified using 16S rRNA and MALDI-TOF MS analyses. Many of the investigated ingredients showed a high proportion of spores as part of their total aerobic mesophilic counts. In 63 % of the samples, the difference between TVC and TMS counts was 1 Log10 unit or less. This was particularly the case for the majority of pea isolates and concentrates, faba bean isolates, oat kernels and flakes, and for single samples of chickpea isolate, almond, amaranth, rice, quinoa, and coconut flours. Concentrations of TVC ranged between <1.0 and 5.3 Log10 CFU/g in different samples, and TMS varied between <1.0 and 4.1 Log10 CFU/g. Levels of HTRS, BCES and SRCS were generally low, typically around or below the LOD of 1.0 Log10 CFU/g. In total, 845 individual bacterial colonies were isolated belonging to 33 different genera. Bacillus licheniformis and B. cereus group strains were most frequently detected among Bacillus isolates, and these species originated primarily from pea and oat samples. Geobacillus stearothermophilus was the main species encountered as part of the HRTS. Among the Clostridium isolates, Clostridum sporogenes/tepidum were predominant species, which were mostly found in pea and almond samples. Strains with potential to cause foodborne infection or intoxication were typed using the PCR-based method for toxin genes detection. In the B. cereus group, 9 % of isolates contained the ces gene, 28 % contained hbl, 42 % cytK, and 69 % were positive for the nhe gene. Absence of the boNT-A and -B genes was confirmed for all isolated C. sporogenes/tepidum strains. Nearly all (98 %) B. licheniformis isolates were positive for the lchAA gene. Insight into the occurrence of microbial contaminants in plant-based ingredients, combined with knowledge of their key inactivation and growth characteristics, can be used for the microbial risk assessment and effective design of plant-based food processing conditions and formulations to ensure food safety and prevent spoilage.

Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis

Bacillus sp. MEP218, a soil bacterium with high potential as a source of bioactive molecules, produces mostly C16-C17 fengycin and other cyclic lipopeptides (CLP) when growing under previously optimized culture conditions. This work addressed the elucidation of the genome sequence of MEP218 and its taxonomic classification. The genome comprises 3,944,892 bp, with a total of 3474 coding sequences and a G + C content of 46.59%. Our phylogenetic analysis to determine the taxonomic position demonstrated that the assignment of the MEP218 strain to Bacillus velezensis species provides insights into its evolutionary context and potential functional attributes. The in silico genome analysis revealed eleven gene clusters involved in the synthesis of secondary metabolites, including non-ribosomal CLP (fengycins and surfactin), polyketides, terpenes, and bacteriocins. Furthermore, genes encoding phytase, involved in the release of phytic phosphate for plant and animal nutrition, or other enzymes such as cellulase, xylanase, and alpha 1-4 glucanase were detected. In vitro antagonistic assays against Salmonella typhimurium, Acinetobacter baumanii, Escherichia coli, among others, demonstrated a broad spectrum of C16-C17 fengycin produced by MEP218. MEP218 genome sequence analysis expanded our understanding of the diversity and genetic relationships within the Bacillus genus and updated the Bacillus databases with its unique trait to produce antibacterial fengycins and its potential as a resource of biotechnologically useful enzymes.

Diamide-based screening method for the isolation of improved oxidative stress tolerance phenotypes in Bacillus mutant libraries

IMPORTANCE

During their life cycle, bacteria are exposed to a range of different stresses that need to be managed appropriately in order to ensure their growth and viability. This applies not only to bacteria in their natural habitats but also to bacteria employed in biotechnological production processes. Oxidative stress is one of these stresses that may originate either from bacterial metabolism or external factors. In biotechnological settings, it is of critical importance that production strains are resistant to oxidative stresses. Accordingly, this also applies to the major industrial cell factory Bacillus subtilis. In the present study, we, therefore, developed a screen for B. subtilis strains with enhanced oxidative stress tolerance. The results show that our approach is feasible and time-, space-, and resource-efficient. We, therefore, anticipate that it will enhance the development of more robust industrial production strains with improved robustness under conditions of oxidative stress.

Identification of bioactive compounds of Bacillus velezensis HNA3 that contribute to its dual effects as plant growth promoter and biocontrol against post-harvested fungi

IMPORTANCE

The current study is an extension to our previous work on the plant growth-promoting rhizobacteria (PGPR) Bacillus velezensis HNA3 strain, which comes to confirm and reveals the huge stock of active secondary metabolites produced by HNA3. HNA3-emitted volatile organic compounds (VOCs) have demonstrated the capacity to impede the growth of phytopathogens affecting some fruits and vegetables, even in the absence of direct contact. Additionally, these volatiles enhanced soybean seed germination by breaking seed dormancy and inducing root system development. Furthermore, they promoted seedling growth, giving it prominence in soybean cultivation. The relevance of active volatiles derives from the fact that they can be developed as natural-safe biocontrol agents and plant promoters. This research validates the remarkable bioactivities exhibited by the Bacillus velezensis HNA3 and their potential applications in agriculture as an inoculant, encompassing biocontrol, plant growth promotion, and seed germination activities, thereby offering a safer alternative to hazardous chemicals.

Genome-wide transformation reveals extensive exchange across closely related Bacillus species

Bacterial transformation is an important mode of horizontal gene transfer that helps spread genetic material across species boundaries. Yet, the factors that pose barriers to genome-wide cross-species gene transfer are poorly characterized. Here, we develop a replacement accumulation assay to study the effects of genomic distance on transfer dynamics. Using Bacillus subtilis as recipient and various species of the genus Bacillus as donors, we find that the rate of orthologous replacement decreases exponentially with the divergence of their core genomes. We reveal that at least 96% of the B. subtilis core genes are accessible to replacement by alleles from Bacillus spizizenii. For the more distantly related Bacillus atrophaeus, gene replacement events cluster at genomic locations with high sequence identity and preferentially replace ribosomal genes. Orthologous replacement also creates mosaic patterns between donor and recipient genomes, rearranges the genome architecture, and governs gain and loss of accessory genes. We conclude that cross-species gene transfer is dominated by orthologous replacement of core genes which occurs nearly unrestricted between closely related species. At a lower rate, the exchange of accessory genes gives rise to more complex genome dynamics.

Biodegradation of furfuryl alcohol by indigenous Bacillus species of industrial effluent-contaminated sites: estimation, biokinetics and toxicity assessment of bio-transformed metabolites

Furfuryl alcohol (FA) and other furanic compounds have garnered considerable attention in the quest for sustainable alternatives. FA-based resins have been used in various sectors that entail the release of FA into the environment. Hence, to ensure sustainability in this scenario, devising a dependable approach to its degradation is imperative. Given the crucial role of bacterial strains in the biodegradation of various organic pollutants, this study investigates the microbial degradation of FA, using bacterial strains isolated from sites that are constantly exposed to industrial waste. Three potential isolates were identified as B. paramycoides, B. cereus, and B. tequilensis by 16S rRNA gene sequencing. At a concentration of 300 µg/ml, these isolates demonstrated efficient FA degradation; 60-70% (at 300 µg/ml FA) and 50-60%, (at 500 µg/ml FA). Fourier-transform infrared (FTIR) spectroscopy and High-Performance Liquid Chromatography (HPLC) analysis further supported the result that the bacterial isolates consumed FA as the carbon source. Liquid chromatography-mass spectrometry (LC-MS) facilitates the detection of the major metabolic intermediate product in which FA gets transformed. The prominent peaks at 113 and 119 m/z obtained in the MS spectra of the degraded FA samples indicated the possibility of the conversion of FA into furoic acid or levulinic acid. The phytotoxicity bioassay findings revealed the non-toxic nature of the bio-transformed products as compared to pure FA. This investigation presents the initial documentation of the FA degradative potential of Bacillus strains, thereby augmenting the understanding of the prospective implementation of Bacillus species in industrial waste treatment projects.