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

Unraveling the ecological interactions between dairy strains Bacillus licheniformis and Bacillus cereus during the dual-species biofilm formation

Bacillus cereus and Bacillus licheniformis are widely presented in dairy products. They can form thick biofilms on surfaces of dairy processing equipment, which may pose serious safety issues and spoilage of final dairy products. However, how ecological interactions between B. cereus and B. licheniformis affect the functions and stability of mixed-species biofilm remains uncovered. In this work, the altered profiles of a dual-species biofilm by dairy-derived B. cereus 121 and B. licheniformis 919 were investigated by RNA-sequencing analysis in combined with phenotype validation (bacterial growth, biofilm-forming capacity, biofilm EPS production, and biofilm structures). The results confirmed that the presence of B. cereus 121 reduced the growth of B. licheniformis 919 planktonic cells, and decreased the biofilm cell numbers of B. licheniformis 919 in the dual-species biofilm when compared to that in its single-species biofilm. The bacterial interaction also reduced the amount of proteins and carbohydrates in the biofilm matrix, and decreased the coverage, average thickness, and total biomass of biofilms. In addition, results from RNA-sequencing analysis showed that the bacterial interaction caused a total of 128 (B. licheniformis 919) and 216 (B. cereus 121) differentially expressed genes (DEGs) during the co-culture of planktonic cells. Functional annotation revealed that the DEGs of B. licheniformis 919 were mainly involved in 10 downregulated pathways including citrate cycle, pyruvate metabolism, nonribosomal peptide structures, glycolysis/gluconeogenesis, quorum sensing, alanine, aspartate and glutamate metabolism, oxidative phosphorylation, beta-Lactam resistance, arginine and proline metabolism, and beta-Alanine metabolism when co-cultured with B. cereus 121. On the other hand, the DEGs from B. cereus 121 were significantly enriched for two downregulated pathways (cysteine and methionine metabolism, and inositol phosphate metabolism) and four upregulated pathways (nitrogen metabolism, glyoxylate and dicarboxylate metabolism, glycine, serine and threonine metabolism, and propanoate metabolism). Results of this study facilitate updated knowledge of how bacterial interaction during the biofilm formation shapes the features of the mixed-species biofilm.

Natural peptides and their synthetic congeners acting against Acinetobacter baumannii through the membrane and cell wall: latest progress

Acinetobacter baumannii is one of the deadliest Gram-negative bacteria (GNB), responsible for 2-10% of hospital-acquired infections. Several antibiotics are used to control the growth of A. baumannii. However, in recent decades, the abuse and misuse of antibiotics to treat non-microbial diseases have led to the emergence of multidrug-resistant A. baumannii strains. A. baumannii possesses a complex cell wall structure. Cell wall-targeting agents remain the center of antibiotic drug discovery. Notably, the antibacterial drug discovery intends to target the membrane of the bacteria, offering several advantages over antibiotics targeting intracellular systems, as membrane-targeting agents do not have to travel through the plasma membrane to reach the cytoplasmic targets. Microorganisms, insects, and mammals produce antimicrobial peptides as their first line of defense to protect themselves from pathogens and predators. Importantly, antimicrobial peptides are considered potential alternatives to antibiotics. This communication summarises the recently identified peptides of natural origin and their synthetic congeners acting against the A. baumannii membrane by cell wall disruption.

Bacillus paralicheniformis SYN-191 isolated from ginger rhizosphere soil and its growth-promoting effects in ginger farming

BACKGROUND

The use of chemical fertilizers and pesticides and the farming without crop rotation may negatively impact the microbial community and the quality of the soils in ginger farm. It is important to improve soil properties to promote the healthy growth of ginger in ginger farm.

RESULTS

We isolated and identified the pathogenic Fusarium ramigenum from infected ginger roots. We then isolated a new Bacillus paralicheniformis strain SYN-191 from the rhizosphere soil around healthy ginger roots, and showed B. paralicheniformis SYN-91 could inhibit F. ramigenum growth, degrade proteins, dissolve silicate, and decompose cellulose. SYN-191 treatment significantly improved the agronomic traits of ginger seedlings in healthy soil and continuous cropping soil. Furthermore, SYN-191 treatment restructured the microbial microbiomes in rhizosphere soil, including reducing the number of harmful fungi, such as Fusarium, and increasing the beneficial bacterial populations such as Bacillus and Pseudomonas. Field experiments showed that SYN-191 application increased ginger yield by 26.47% (P < 0.01). Whole-genome sequencing of strain SYN-191 revealed the relevant genes for antibiotic synthesis, potassium dissolution, and cellulose decomposition.

CONCLUSIONS

A new plant-growth-promoting B. paralicheniformis SYN-191 was obtained. This strain could antagonize ginger root rot pathogenic fungus, improve agronomic traits and ginger yield in field, and improve the microbial community structure in the ginger rhizosphere soil. This study provides a valuable bacterial resource for overcoming obstacles in the continuous cropping of ginger.

Overexpressing Endopeptidase Inhibitor IseA Enhances Biomass and Biochemical Production of Bacillus licheniformis

Cell autolysis could lead to a decrease in both cell viability and the production of biochemicals, presenting one of the significant challenges during fermentation. Bacillus licheniformis, a gram-positive bacterium widely used in the production of various biologic products, also confronts the limitation caused by cell autolysis. In this study, we investigated the impact of peptidoglycan hydrolases (LytC, LytD, LytE, CwlC), endopeptidase inhibitor IseA, and prophage gene xpf on cell growth and biochemical synthesis in B. licheniformis DW2. The results showed that the deletion of xpf and overexpression of iseA could significantly increase cell survival. Then, xpf was deleted on iseA overexpressed strain PP43UTR12iseA to construct engineered strain PP43UTR12iseAΔxpf, which further enhanced viable cells. The results of cell autolysis showed that PP43UTR12iseA could reduce cell autolysis significantly compared to the wild-type, but PP43UTR12iseAΔxpf did not further decrease cell autolysis. Furthermore, the production of bacitracin was 792.23 U/mL in the iseA overexpressed strain, which increased by 13.82% compared with the wild-type, but PP43UTR12iseAΔxpf did not further increase bacitracin production. Through detecting intracellular metabolites, we observed that iseA overexpression did not affect intracellular metabolism, but the precursors of bacitracin synthesis in PP43UTR12iseAΔxpf were lower than that of wild-type and PP43UTR12iseA. Finally, we found that the overexpression of iseA could also significantly improve the production of γ-PGA. In general, the overexpression of iseA could enhance the biomass and cell survival by reducing cell lysis without affecting the intracellular metabolites, which provided a potential strategy to improve production of biochemical.

Is Bacillus cytotoxicus from edible insects a threat?

Bacillus cytotoxicus is considered a potential emerging foodborne pathogen that has been under investigation in recent years. Most studies have focused on strains from vegetables, particularly potato products, but there is limited information on strains from other food sources. This study addresses the current research gap by investigating the genomic and phenotypic features of B. cytotoxicus isolated from edible insects. The whole genomes and key phenotypic traits of 20 strains isolated from edible insects were investigated. The comparative genome analysis also included 44 available genomes from other sources to identify possible genetic links and the mosaicism of virulence profiles (VP) and antimicrobial resistance genes (AMR). B. cytotoxicus isolated from edible insects showed marked thermotolerance, when vegetative forms could grow at 50-60 °C and survive at 65 °C and exhibited marked proteolytic activities, even at higher temperatures. The heterogeneous phenotypes observed suggest potential issues with defining suitable protocols for isolation and identification in this food matrix. Despite the limited genomic diversity observed, it was possible to identify links between isolates, demonstrating the co-isolation of different genomes/phenotypes from various insect samples and suggesting trade links between insect companies and the persistence of certain strains. A genomic comparison suggested segregating strains from edible insects with similar VP and AMR profiles. These findings indicate a degree of adaptation to different food niches, with strains from insects or insect-based products differing partially from those isolated from vegetable sources, showing possible associations with their respective food environments. The survival advantage conferred by thermotolerance underscores the need to assess the presence of these spore-forming bacteria carefully and to calibrate treatments and processes, to address the emerging risk posed by this pathogen and its implications for food safety.

Development and validation of a UPLC-MS/MS method for simultaneous quantification of polymyxins and caspofungin in human plasma for therapeutic drug monitoring

OBJECTIVE

To develop a rapid, convenient, accurate, and low-residual-effect ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method for the determination of polymyxin B sulfate and colistin sulfate in the blood of patients with multidrug-resistant bacterial infections, as well as caspofungin acetate in the blood of patients with fungal infections, thus facilitating the rational use of antibiotics in clinical applications.

METHODS

All analytes were diluted with 0.2 % aqueous formic acid, and plasma proteins were precipitated using acetonitrile. The selected reaction monitoring (SRM) mode was used for measurement. Separation of all analytes was completed on a Hypersil GOLD C18 column (100 × 2.1 mm, 3.0 µm). They were quantitatively analyzed using electrospray ionization on a triple quadrupole mass spectrometer in the positive ion mode. The mobile phase consisted of water (containing 0.1 % formic acid) and acetonitrile, which was delivered by gradient elution at a flow rate of 0.3 ml/min. The internal standard was bacitracin zinc (BcZn), and the column temperature was maintained at 25 °C. The runtime for each analysis was 3.5 min.

RESULTS

The procedure was validated following the recommendations of the U.S. Food and Drug Administration, which included measurements of accuracy (ranging from 83.27 % to 105.86 % for within-run and between-run accuracy), precision (with coefficients of variation from 2.50 % to 16.51 % for within-run precision and between-run precision), and matrix effects (ranging from 88.65 % to 103.94 %). The extraction recoveries ranged from 38.01 % to 42.76 for polymyxin B1 (PMB1), polymyxin B2 (PMB2), polymyxin E1 (PME1), polymyxin E2 (PME2), and 88.65 % to 89.84 % for caspofungin (CPF). Plasma samples were stable under various storage conditions, including three freeze-thaw cycles at -80 °C, 24-hour periods at room temperature and 4 °C, and 30 days of freezing at both -20 °C and -80 °C, with relative standard deviations (RSD) of less than 15 %.

CONCLUSION

In this study, a UPLC-MS/MS method was developed to simultaneously quantify PMB1, PMB2, PME1, PME2, and CPF in human plasma. The method was validated in blood samples from patients with multidrug-resistant bacteria combined with fungal infections and is suitable for therapeutic drug monitoring.

Cyclic peptides: A powerful instrument for advancing biomedical nanotechnologies and drug development

Cyclic peptides have emerged as an essential tool in the advancement of biomedical nanotechnologies, offering unique structural and functional advantages over linear peptides. This review article aims to highlight the roles of cyclic peptides in the development of biomedical fields, with a particular focus on their application in drug discovery and delivery. Cyclic peptides exhibit exceptional stability, bioavailability, and binding specificity, making them ideal candidates for therapeutic and diagnostic applications. We explore the synthesis and design strategies that enable the precise control of cyclic peptide structures, leading to enhanced performance in targeting specific cellular pathways. The article also highlights recent breakthroughs in the use of cyclic peptides for creating innovative drug delivery systems, including nanoparticle conjugates and peptide-drug conjugates, which have shown promise in improving the efficacy and safety profiles of existing traditional treatments. The integration of cyclic peptides into nanotechnological frameworks holds significant promise for addressing unmet medical needs, providing a foundation for future advancements in personalized medicine and targeted drug delivery.

Combating Bacterial Resistance by Polymers and Antibiotic Composites

(1) Background: Since the discovery of antibiotics in the first half of the 20th century, humans have abused this privilege, giving rise to antibiotic-resistant pathogens. Recent research has brought to light the use of antimicrobial peptides in polymers, hydrogels, and nanoparticles (NPs) as a newer and safer alternative to traditional antibiotics. (2) Methods: This review article is a synthesis of the scientific works published in the last 15 years, focusing on the synthesis of polymers with proven antimicrobial properties. (3) Results: After a critical review of the literature was made, information and data about the synthesis and antimicrobial activity of antibacterial polymers and NPs functionalized with antibiotics were extracted. Fluorinated surfactants such as the Quaterfluo® series presented significant antimicrobial effects and could be modulated to contain thioesters to boost this characteristic. Biopolymers like chitosan and starch were also doped with iodine and used as iodophors to deliver iodine atoms directly to pathogens, as well as being antimicrobial on their own. Quaternary phosphonium salts are known for their increased antimicrobial activity compared to ammonium-containing polymers and are more thermally stable. (4) Conclusions: In summary, polymers and polymeric NPs seem like future alternatives to traditional antibiotics. Future research is needed to determine functional doses for clinical use and their toxicity.

Recent Trends in Therapeutic Drug Monitoring of Peptide Antibiotics

Antimicrobial peptides take a specific position in the field of antibiotics (ATBs), however, from a large number of available molecules only a few of them were approved and are used in clinics. These therapeutic modalities play a crucial role in the management of diseases caused by multidrug-resistant bacterial pathogens and represent the last-line therapy for bacterial infections. Therefore, there is a demand for a rationale use of such ATBs based on optimization of the dosing strategy to minimize the risk of resistance and ensure the sustainable efficacy of the drug in real clinical practice. Therapeutic drug monitoring, as a measurement of drug concentration in the body fluids or tissues, results in the optimization of the patient´s medication and therapy outcome. This strategy is beneficial and could result in tailored therapy for different types of infection and the prolongation of the use and efficacy of ATBs in hospitals. This review paper provides an actual overview of approved antimicrobial peptides used in clinical practice and covers current trends in their analysis by convenient and advanced methodologies used for their identification and/or quantitation in biological matrices for therapeutic drug monitoring purposes. Special emphasis is given to the methods with perspective clinical outcomes.

Bacillus subtilis as a host for natural product discovery and engineering of biosynthetic gene clusters

Covering: up to October 2023Many bioactive natural products are synthesized by microorganisms that are either difficult or impossible to cultivate under laboratory conditions, or that produce only small amounts of the desired compound. By transferring biosynthetic gene clusters (BGCs) into alternative host organisms that are more easily cultured and engineered, larger quantities can be obtained and new analogues with potentially improved biological activity or other desirable properties can be generated. Moreover, expression of cryptic BGCs in a suitable host can facilitate the identification and characterization of novel natural products. Heterologous expression therefore represents a valuable tool for natural product discovery and engineering as it allows the study and manipulation of their biosynthetic pathways in a controlled setting, enabling innovative applications. Bacillus is a genus of Gram-positive bacteria that is widely used in industrial biotechnology as a host for the production of proteins from diverse origins, including enzymes and vaccines. However, despite numerous successful examples, Bacillus species remain underexploited as heterologous hosts for the expression of natural product BGCs. Here, we review important advantages that Bacillus species offer as expression hosts, such as high secretion capacity, natural competence for DNA uptake, and the increasing availability of a wide range of genetic tools for gene expression and strain engineering. We evaluate different strain optimization strategies and other critical factors that have improved the success and efficiency of heterologous natural product biosynthesis in B. subtilis. Finally, future perspectives for using B. subtilis as a heterologous host are discussed, identifying research gaps and promising areas that require further exploration.

Unearthing naturally-occurring cyclic antibacterial peptides and their structural optimization strategies

Natural products with antibacterial activity are highly desired globally to combat against multidrug-resistant (MDR) bacteria. Antibacterial peptide (ABP), especially cyclic ABP (CABP), is one of the abundant classes. Most of them were isolated from microbes, demonstrating excellent bactericidal effects. With the improved proteolytic stability, CABPs are normally considered to have better druggability than linear peptides. However, most clinically-used CABP-based antibiotics, such as colistin, also face the challenges of drug resistance soon after they reached the market, urgently requiring the development of next-generation succedaneums. We present here a detail review on the novel naturally-occurring CABPs discovered in the past decade and some of them are under clinical trials, exhibiting anticipated application potential. According to their chemical structures, they were broadly classified into five groups, including (i) lactam/lactone-based CABPs, (ii) cyclic lipopeptides, (iii) glycopeptides, (iv) cyclic sulfur-rich peptides and (v) multiple-modified CABPs. Their chemical structures, antibacterial spectrums and proposed mechanisms are discussed. Moreover, engineered analogs of these novel CABPs are also summarized to preliminarily analyze their structure-activity relationship. This review aims to provide a global perspective on research and development of novel CABPs to highlight the effectiveness of derivatives design in identifying promising antibacterial agents. Further research efforts in this area are believed to play important roles in fighting against the multidrug-resistance crisis.

The Bacillus subtilis cell envelope stress-inducible ytpAB operon modulates membrane properties and contributes to bacitracin resistance

Antibiotics that inhibit peptidoglycan synthesis trigger the activation of both specific and general protective responses. σM responds to diverse antibiotics that inhibit cell wall synthesis. Here, we demonstrate that cell wall-inhibiting drugs, such as bacitracin and cefuroxime, induce the σM-dependent ytpAB operon. YtpA is a predicted hydrolase previously proposed to generate the putative lysophospholipid antibiotic bacilysocin (lysophosphatidylglycerol), and YtpB is the branchpoint enzyme for the synthesis of membrane-localized C35 terpenoids. Using targeted lipidomics, we reveal that YtpA is not required for the production of lysophosphatidylglycerol. Nevertheless, ytpA was critical for growth in a mutant strain defective for homeoviscous adaptation due to a lack of genes for the synthesis of branched chain fatty acids and the Des phospholipid desaturase. Consistently, overexpression of ytpA increased membrane fluidity as monitored by fluorescence anisotropy. The ytpA gene contributes to bacitracin resistance in mutants additionally lacking the bceAB or bcrC genes, which directly mediate bacitracin resistance. These epistatic interactions support a model in which σM-dependent induction of the ytpAB operon helps cells tolerate bacitracin stress, either by facilitating the flipping of the undecaprenyl phosphate carrier lipid or by impacting the assembly or function of membrane-associated complexes involved in cell wall homeostasis.IMPORTANCEPeptidoglycan synthesis inhibitors include some of our most important antibiotics. In Bacillus subtilis, peptidoglycan synthesis inhibitors induce the σM regulon, which is critical for intrinsic antibiotic resistance. The σM-dependent ytpAB operon encodes a predicted hydrolase (YtpA) and the enzyme that initiates the synthesis of C35 terpenoids (YtpB). Our results suggest that YtpA is critical in cells defective in homeoviscous adaptation. Furthermore, we find that YtpA functions cooperatively with the BceAB and BcrC proteins in conferring intrinsic resistance to bacitracin, a peptide antibiotic that binds tightly to the undecaprenyl-pyrophosphate lipid carrier that sustains peptidoglycan synthesis.

Hydrolysis of Antimicrobial Peptides by Extracellular Peptidases in Wastewater

Several antimicrobial peptides (AMPs) are emerging as promising novel antibiotics. When released into wastewater streams after use, AMPs might be hydrolyzed and inactivated by wastewater peptidases─resulting in a reduced release of active antimicrobials into wastewater-receiving environments. A key step towards a better understanding of the fate of AMPs in wastewater systems is to investigate the activity and specificity of wastewater peptidases. Here, we quantified peptidase activity in extracellular extracts from different stages throughout the wastewater treatment process. For all four tested municipal wastewater treatment plants, we detected highest activity in raw wastewater. Complementarily, we assessed the potential of enzymes in raw wastewater extracts to biotransform 10 selected AMPs. We found large variations in the susceptibility of AMPs to enzymatic transformation, indicating substantial substrate specificity of extracted enzymes. To obtain insights into peptidase specificities, we searched for hydrolysis products of rapidly biotransformed AMPs and quantified selected products using synthetic standards. We found that hydrolysis occurred at specific sites and that these sites were remarkably conserved across the four tested wastewaters. Together, these findings provide insights into the fate of AMPs in wastewater systems and can inform the selection and design of peptide-based antibiotics that are hydrolyzable by wastewater peptidases.

Nanosilver: An Old Antibacterial Agent with Great Promise in the Fight against Antibiotic Resistance

Antibiotic resistance in bacteria is a major problem worldwide that costs 55 billion USD annually for extended hospitalization, resource utilization, and additional treatment expenditures in the United States. This review examines the roles and forms of silver (e.g., bulk Ag, silver salts (AgNO3), and colloidal Ag) from antiquity to the present, and its eventual incorporation as silver nanoparticles (AgNPs) in numerous antibacterial consumer products and biomedical applications. The AgNP fabrication methods, physicochemical properties, and antibacterial mechanisms in Gram-positive and Gram-negative bacterial models are covered. The emphasis is on the problematic ESKAPE pathogens and the antibiotic-resistant pathogens of the greatest human health concern according to the World Health Organization. This review delineates the differences between each bacterial model, the role of the physicochemical properties of AgNPs in the interaction with pathogens, and the subsequent damage of AgNPs and Ag+ released by AgNPs on structural cellular components. In closing, the processes of antibiotic resistance attainment and how novel AgNP-antibiotic conjugates may synergistically reduce the growth of antibiotic-resistant pathogens are presented in light of promising examples, where antibiotic efficacy alone is decreased.