Archives of Microbiology最新文献

The adhesion of bacterial cells through extracellular matrices plays a critical role in biofilm formation. Disrupting these matrices offers a promising strategy to overcome the persistent challenge of eradicating biofilms associated with chronic infections. CsgA, a major functional amyloid within the extracellular matrix of Escherichia coli (E. coli), adopts a β-sheet-rich conformation that contributes to the structural integrity of biofilms. The stability of these β-sheets is maintained by an extensive hydrogen-bonding network within the protein, and their disruption can compromise biofilm viability. In this study, computational approaches were employed to identify anti-biofilm peptides capable of targeting the β-sheet structures of CsgA amyloid. Among 41 screened peptides, 10 were predicted to be toxic, and the remaining 31 were subjected to molecular docking and reactivity analyses. The HOMO–LUMO energy gap was evaluated before and after docking to assess peptide reactivity, identifying 22 peptides with high reactivity for further dynamic simulations using discrete molecular dynamics. Comparative analyses revealed that Brevinin-1BW, Kassinatuerin-3, Ranateurin-2Awa, Temporin-B, and Magainin-I-KL decreased the β-sheet content of CsgA relative to the untreated protein. Notably, Magainin-I-KL induced a 7% reduction in β-sheet content and substantial structural disruption, as evidenced by decreased hydrogen bonding, increased metastable states in the free-energy landscape, and deformation patterns in cross-correlation analysis. Steered molecular dynamics simulations further demonstrated that Magainin-I-KL exhibited greater resistance to force-induced dissociation, indicating stronger interactions with CsgA. Overall, Magainin-I-KL effectively destabilizes the CsgA amyloid structure of E. coli, suggesting its potential as a lead peptide for disrupting amyloid-based biofilm formation and enhancing antimicrobial strategies.

Antibiotic resistance has significantly constricted the therapeutic efficacy of antibiotics on treating bacterial infections, creating an urgent need for new antimicrobial agents. However, progress in developing these agents is slow, prompting the exploration of innovative strategies such as combination therapy. This study examined the combined effects of Temporin antimicrobial peptides with antibiotics against Escherichia coli and Pseudomonas aeruginosa. We found that Temporin-GHaR (GHaR) and Temporin-GHaK (GHaK) with polymyxin B (PMB) showed synergistic antibacterial activity against P. aeruginosa and E. coli, with a fractional inhibitory concentration index (FICI) below 0.5. Further mechanistic studies revealed that the combination of GHaR/GHaK with PMB significantly enhanced the bactericidal effect by synergistically augmenting the disruption of the outer and inner membranes of P. aeruginosa and E. coli. Meanwhile, this combination regimen demonstrated efficacy in inhibiting the biofilm formation of P. aeruginosa and E. coli at concentrations lower than those required for single-drug treatments, and enhanced the disruption of mature E. coli biofilms. The synergistic use of GHaR/GHaK and PMB augmented the antibacterial efficacy against P. aeruginosa and E. coli without increasing hemolytic toxicity to murine erythrocytes. These findings provide an experimental foundation and theoretical framework for the application of conventional antimicrobial agents.

Agro-industrial processes generate significant lignocellulosic waste, composed mainly of cellulose, hemicellulose, and lignin. Repurposing these residues for lignocellulolytic enzyme production offers an economical, sustainable approach to biomass valorization and the generation of bioproducts such as lactic acid. This study aimed to optimize enzyme production by Aspergillus species grown on various agro-industrial residues and apply these enzymes to hydrolyze barley bagasse for lactic acid production. Four Aspergillus strains (A. brasiliensis, A. clavatus NRRL1, A. flavus, and A. terreus) were cultivated in minimal medium (pH 6.5) with 1% (w/v) Barley Bagasse, Bean Straw or Rice Straw, at 30 °C and 120 rpm for five days. Nine different holocellulolytic activities were screened using natural and synthetic substrates. A. brasiliensis exhibited the highest enzymatic activity when grown on bean straw. Optimization of its cultivation led to 10 g/L of reducing sugars after five days at pH 5.5 and 35 °C. Subsequent optimization of barley bagasse hydrolysis resulted in 49 g/L of fermentable sugars when using 20% (w/v) of this substrate concentration, at pH 3.0, and 50 °C for 24 h. This corresponded to a hydrolysis yield of 44% relative to the total carbohydrate content. The released sugars were fermented by Lactobacillus rhamnosus ATCC 7469, producing 21.1 g/L of L-lactic acid corresponding to a fermentation yield of 47% relative to the available sugars and a volumetric productivity of 0.15 g/L/h. This work demonstrates an integrated bioprocess that couples low-cost enzyme production with effective saccharification and fermentation of barley bagasse. This approach underscores its potential for sustainable lactic acid production. Unlike previous studies that rely on commercial enzymes or neutral-pH hydrolysis, this process uniquely combines acid-tolerant enzymes produced by Aspergillus brasiliensis grown on bean straw, a rarely used substrate, with direct fermentation by Lactobacillus rhamnosus ATCC 7469 at low pH. The integration of these specific microbial species and agro-residues represents a distinctive and effective approach to biomass valorization.

The increasing demand for functional foods has stimulated research on probiotic strains with health-promoting properties. This study investigated the biofunctional traits of the putative exopolysaccharide (EPS)-producing strain Lactiplantibacillus plantarum Lbio1 and evaluated its survival, both free and encapsulated, under simulated gastrointestinal conditions. Safety assessment indicated the absence of haemolytic and gelatinase activities and susceptibility to most tested antibiotics. The strain tolerated acidic pH (2.0) and bile salts (0.3% w/v) with survival rates of 72 and 83%, respectively, and exhibited bile salt hydrolase activity. The strain also grew in 0.1% (v/v) phenol. Adhesion-related properties included high auto-aggregation (92%) and co-aggregation with pathogenic strains (Escherichia coli ATCC 25522, Staphylococcus aureus ATCC 43300, and Micrococcus luteus ATCC 49732), ranging from 43.9 to 71.5%, as well as a biofilm formation capacity, despite exhibiting low hydrophobicity (16%). Cholesterol assimilation reached 82%. The EPS produced by Lbp. plantarum Lbio1 was a high molecular weight heteropolymer composed of glucose and galactose. The encapsulation of Lbp. plantarum Lbio1 in alginate beads (≈ 3 mm, 91% efficiency) efficiently loaded cells, as observed by scanning electron microscopy, and enhanced their survival under simulated gastrointestinal stress. Encapsulated cells retained viability above 10⁶ CFU/g for 34 days at refrigeration temperature, despite a viability loss of approximately 1 log CFU per week. These findings highlight the probiotic potential of Lbp. plantarum Lbio1 and the efficiency of encapsulation in improving bacterial cell survival.

The central challenge in brucellosis prevention and control stems from the marked heterogeneity among Brucella species. This review establishes a “Virulence-Metabolism-Temporal and Spatial” (VMT) model and proposes a Virulence Index (VI) formula to systematically compare the biological characteristics and host interaction mechanisms of four pathogenic Brucella species: B. melitensis, B. abortus, B. suis, and B. canis. Our analysis reveals that these species represent an evolutionary continuum from high virulence with acute dissemination to low virulence with tissue localization. B. melitensis achieves deep immune stealth and triggers systemic spread through its ultra-efficient Type IV Secretion System (T4SS), specific lipid A modifications, and potent apoptosis inhibition. B. suis specifically targets bone marrow and induces bone destruction via acid-inducible T4SS activation and iron metabolic hijacking. B. abortus elicits partial autophagic clearance due to insufficient T4SS efficiency, resulting in self-limiting infections. B. canis provokes intense inflammatory responses through its rough lipopolysaccharide (LPS) and exhibits defective T4SS function, precluding persistent infection establishment. The VMT model elucidates the causal chain linking molecular characteristics to cellular interactions and clinical phenotypes, demonstrating that virulence depends on the precise balance between immune evasion efficiency and host cell fate regulation. These findings provide a theoretical foundation for species-specific diagnosis, stratified therapeutics, and One Health-based precision prevention and control of brucellosis.

Biofilm-associated infections pose a major global health threat due to their inherent resistance to conventional antibiotics, mediated by quorum sensing (QS), extracellular polymeric substances (EPS), persister cells, and immune evasion mechanisms. In this review, we propose the “Triad Warfare” strategy, integrating quorum-sensing inhibition (QSI), nanotechnology-enabled targeted drug delivery, and host-directed immunomodulation to synergistically disrupt biofilms while minimizing the risk of antimicrobial resistance (AMR). Specifically, QSI-mediated EPS disruption enhances nanoparticle penetration, facilitating controlled release of antimicrobial agents, while immunomodulators potentiate macrophage and neutrophil activity to clear residual bacterial populations, including metabolically dormant persisters. We provide a comparative analysis of natural and synthetic QS inhibitors, surface-modified nanoparticles (e.g., PEGylated AgNPs), and immunotherapeutic approaches (macrophage polarization, NET modulation, cytokine delivery), highlighting their efficacy, translational challenges, and clinical trial updates (Phase 1–2). Recent metabolic stimulation strategies (e.g., mannitol with aminoglycosides) and CRISPR-guided antimicrobials are also discussed for persister eradication. Furthermore, AI-driven anti-biofilm drug discovery using datasets such as AntiBiofilmDB, ChEMBL, and PubChem is evaluated for predictive design of combinatorial therapeutics. Collectively, this review emphasizes the mechanistic synergy, translational feasibility, and adaptive optimization of the triad approach, providing a roadmap for the development of next-generation anti-biofilm therapies with minimized resistance potential.

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We report the first complete genome sequence of cucumber mosaic virus (CMV) and its associated satellite RNA (satRNA) from naturally infected zucchini (Cucurbita pepo) in Iraq. The tripartite CMV-Iq genome (RNA1: 3,358 nt, RNA2: 3,051 nt, RNA3: 2,220 nt) and a 335-nt satRNA were determined by RNA-seq and validated via Sanger sequencing. Genome annotation revealed ORFs encoding replicase (1a), RNA-dependent RNA polymerase (2a), silencing suppressor (2b), movement protein (3a), and coat protein (3b) with conserved domains. Phylogenetic analysis placed CMV-Iq in subgroup I, forming a distinct clade closely related to isolates from East Asia, Europe, the USA and the Middle East, with reassortment detected in RNA2 and RNA3. Viral coding regions showed high haplotype and nucleotide diversity under differential selective pressures, with purifying selection strongest in 1a and weakest in 2b, and episodic positive selection detected at a few sites. Mutations, selection, gene flow, and reassortment shape the genetic structure of CMV populations. The Iraqi satRNA clustered within the necrogenic B subgroup, forming a distinct sublineage with Syrian isolates and retaining the conserved necrogenic motif. Transcriptomic profiling revealed RNA3 as the most abundant segment, followed by RNA2 and RNA1, with satRNA surpassing RNA1 and RNA2 in abundance. At the gene level, 3b and 2a were most expressed, 3a and 1a intermediate, and 2b lowest, consistent with its regulatory function. High 3b expression reflects translation from subgenomic RNA4, enabling coat protein synthesis for virion assembly and systemic movement, while abundant satRNA suggests a modulatory role in viral replication and host interactions.

Fungi serve as pivotal industrial platforms to produce essential compounds from pharmaceuticals like antibiotics and statins to diverse enzymes, organic acids and nutraceuticals. Fungi drive innovation across the medical, food and biofuel sectors through the synthesis of specialized pigments, flavors and bioactive molecules. Despite this potential, the development of efficient genetic toolkits has historically been slowed by low homologous recombination rates and biological complexity of diverse fungal taxa. The adaptation of CRISPR/Cas technologies including Cas9, Cas12a (Cpf1), and base editing has recently bypassed these bottlenecks and offers record precision in fungal genome engineering. This review provides a detailed analysis of current mechanistic approaches such as the use of ribonucleoprotein (RNP) complexes and specialized promoters for guide RNA expression. We have explored how these tools enable the multiplexed editing of genes and the fine-tuning of transcriptional modulation (i.e. CRISPR inactivation/activation) to redirect target metabolites for high industrial output by optimizing fungal physiology. Furthermore, the integration of CRISPR-based biosensors for the rapid, high-sensitivity detection of fungal pathogens, highlighting the dual role of these technologies in both production and food security has also been discussed.

Biological synthesis of nanoparticles has been widely explored as a sustainable alternative to physical and chemical routes. Nevertheless, the majority of current methods are based on intact microbial cells or crude plant extracts, which leads to lack of reproducibility, biomolecular interference, and difficulties in mechanistic interpretation and scale-up. We present microbial secretome-mediated nanotechnology as a new and under researched paradigm in this review, which separates nanoparticle synthesis from cellular complexity and preserves biological precision. We quantitatively analyze the composition of microbial secretomes, redox enzymes, extracellular proteins, peptides, polysaccharides, and membrane-derived vesicles and map their respective functions in nanoparticle nucleation, growth, stabilization, and functionalization. Emerging biochemical and mechanistic evidence is creating a direct understanding of how the composition of the secretome relates to the nanoparticle morphology, surface chemistry, and bioactivity, moving beyond organism-specific reports. Notably, we critically assess secretome-mediated synthesis by comparing and contrasting it with whole-cell and plant-extract techniques, highlighting specific benefits including; enhanced batch-to-batch reproducibility, minimized polysaccharide and biomass contamination, better control over particle size and shape, reduced toxicity hazards, and increased feasibility of downstream processing and scale-up. Emerging approaches, such as secretome fractionation, omics-inspired secretome engineering, and vesicle-mediated nano-delivery, are mentioned as directions for developing tunable and application-specific nanomaterials. Altogether, the given review offers a mechanistic and translational roadmap of the microbial secretome-mediated nanotechnology, which cannot be regarded as the extension of green synthesis, but rather as a controllable bio-nanoengineering platform with significant potential in medical, agrarian, and environmental cleanup fields.

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Bacterial wilt caused by Ralstonia solanacearum seriously threatens tomato production. At present, tomato bacterial wilt control mainly relies on chemical agents, but long-term use can lead to environmental problems and resistance. Bacillus velezensis is a potential biocontrol bacterium; however, studies on its extracellular proteins related to antibacterial activity remain limited. In this study, B. velezensis TR-1 was used to identify key extracellular protein components with antagonistic activity against R. solanacearum and to evaluate their biocontrol potential. Crude extracellular proteins were obtained from the TR-1 culture supernatant by ammonium sulfate precipitation. Active components were separated using Sephadex G-75 and identified by LC–MS/MS. The results showed that serine protease was the major component of the active fraction. Meanwhile, pot experiments showed that the crude protein solution achieved a control effect of approximately 60% against tomato bacterial wilt. This study is the first to identify multiple serine proteases in the active components of the B. velezensis supernatant. Based on SEM and TEM observations and protein structure prediction, serine proteases are inferred to be involved in the inhibition of R. solanacearum, providing a new perspective for the green control of tomato bacterial wilt.