Archives of Microbiology最新文献

Food-borne bacterial pathogens remain a major public health concern, causing extensive illness and economic losses worldwide. Conventional detection methods are often slow and insufficient for identifying viable but non-culturable pathogens. Recent microbiological, biotechnological and bioinformatic advances have markedly improved food safety monitoring. Rapid molecular assays (PCR, qPCR, microarrays), next-generation sequencing, metagenomics, and emerging CRISPR-based diagnostics enable faster and more accurate pathogen detection and outbreak tracing. Bioinformatic tools—including genomic databases, phylogenetics, and machine-learning models—support predictive risk assessment and real-time surveillance. Preventive innovations such as bacteriophages, probiotics, antimicrobial peptides, nanotechnology-based interventions, and engineered microbes provide sustainable alternatives to chemical preservatives. Key challenges include variability across food matrices, biosafety considerations, and limited integration of multi-omics approaches into routine workflows. Overall, these emerging strategies offer improved precision and responsiveness for detecting and preventing food-borne bacterial pathogens.

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The emergence of CRISPR/Cas9 technology has transformed the landscape of gene editing, allowing for precise alterations in DNA that hold great promise for research and potential therapies. However, a significant concern is the occurrence of off-target effects, which can lead to unintended genetic modifications with potentially harmful consequences. This paper explores the nature of off-target effects in CRISPR/Cas9, discussing how they arise and their implications for the reliability of gene editing. We identify the challenges faced in detecting and predicting these off-target interactions, including limitations in current detection techniques and the complexities of cellular biology. We present strategies aimed at minimizing off-target effects, such as careful design of guide RNAs, the use of computational tools for prediction, and improved delivery methods. Through a review of case studies, we highlight successful cases where off-target activity has been significantly reduced, offering insights into best practices for enhancing the accuracy of CRISPR/Cas9 applications. Moreover, we provide a comparative overview of Cas9, Cas12, and Cas13 systems, emphasizing their distinct target specificities, mechanisms of action, and off-target profiles. This comparison offers a broader understanding of how alternative CRISPR effectors may be leveraged to improve genome and transcriptome editing precision. This study underscores the importance of continued research to address the challenges of off-target effects, ultimately supporting the development of safer and more effective gene editing methods for clinical use.

The rise of multidrug-resistant (MDR) bacteria, especially the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), is one of the most significant issues in modern medicine. Berberine, a quaternary ammonium isoquinoline alkaloid derived from a number of plant species, has been shown to be an effective therapeutic agent against resistant pathogens. This review provides a detailed overview of the chemical structure, pharmacology, and mechanism of action for berberine against ESKAPE and other MDR bacteria. The literature suggests that berberine displays antimicrobial activity through several mechanisms, including damaging the membrane, inhibiting DNA gyrase, inhibiting protein synthesis, and inhibiting efflux pumps. Berberine shows considerable synergy when combined with standard antibiotics, which could reverse antibiotic resistance. Notably, berberine demonstrates synergistic effects with β-lactam antibiotics, reducing fractional inhibitory concentration (FIC) indices to 0.25–0.5, thereby enhancing antibacterial efficacy against multidrug-resistant strains. Although berberine exhibits remarkable in vitro antimicrobial activity, its very poor systemic bioavailability (< 1%) results in a more than 1000-fold PK–PD gap between achievable plasma levels and effective MIC values. The clinical and preclinical studies show a good safety profile for use with minimal toxicity at therapeutic concentrations. Therefore, the current clinical use of berberine is limited to adjuvant, topical, or gastrointestinal applications rather than systemic monotherapy. The routes of delivery, pharmacokinetic characteristics, and standardization of treatment remain obstacles for wider application. This review collates the current evidence that supports berberine as an alternative or adjunct therapy to combat the worldwide issue of antibiotic resistance and also indicates areas where further research is required to bring therapies to the clinical level.

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Leptospirosis is a globally significant zoonotic disease caused by the pathogenic Leptospira spp. This study aimed to develop a recombinant Loa22 based lateral flow assay for detecting leptospirosis in dogs and cattle. The loa22 gene from Leptospira interrogans was cloned, expressed in E. coli, and purified using Ni–NTA affinity chromatography. The immunoreactivity of the recombinant protein was confirmed by western blotting, and hyperimmune sera against the protein was raised in mice. Gold nanoparticles (AuNP) were conjugated with rLoa22 under optimized conditions and characterized by UV–Vis spectrophotometry, agarose gel electrophoresis, and transmission electron microscopy. The lateral flow assay (LFA) strips were assembled with AuNP–rLoa22 on the conjugate pad and rLoa22 and hyperimmune sera on the test and control lines, respectively. Diagnostic performance of the assay was evaluated using sera from 100 dogs and 102 cattle suspected for leptospirosis and compared to the reference standard microscopic agglutination test (MAT). Six dog and cattle samples each were tested positive by MAT. The developed LFA further tested 06 dog and 07 cattle samples as positive in addition to the MAT positive samples, representing false positives. In dogs, the LFA showed 100% sensitivity and 93.62% specificity, while in cattle, it showed 100% sensitivity (Se) and 92.71% specificity (Sp) with respect to MAT. The n/N for Se and Sp were, Se_dogs= 6/6; Sp_dogs= 88/94; Se_cattle= 6/6; Sp_cattle= 89/96. The high observed sensitivity could be attributed to the smaller number of MAT+/LFA + samples that resulted in a wide 95% confidence interval (CI). The test was further validated on another 300 canine and 98 cattle serum samples suspected for leptospirosis (prevalence screens, not a part of the accuracy cohorts). The results underscore the potential of the rLoa22–based LFA as a reliable, rapid diagnostic tool for leptospirosis screening in veterinary settings. Further validation of the study is warranted using samples pre-screened for leptospirosis through other commercially available techniques, including qPCR and ELISA.

Emerging contaminants are molecules, either novel or previously recognized, that persist in the environment and may pose risks to ecosystems and human health. Their increasing occurrence, particularly in pharmaceuticals, personal care products, and industrial processes, has intensified research on their detection, monitoring, and ecological impact. Advances in analytical technologies now enable the identification of these compounds at trace concentrations, yet their long-term effects remain uncertain. This review compiles recent findings on microbial ecotoxicology, focusing on representative contaminants of high concern such as penicillin, parabens, caffeine, and microplastics. Microorganisms (bacteria or fungi) are highlighted both as sensitive bioindicators of environmental pollution and as active agents in biodegradation processes. Their ability to metabolize, transform, or neutralize contaminants underscores their potential as sustainable tools for remediation. By integrating evidence from multiple studies, we emphasize microbial-based strategies as promising tools for environmental monitoring and mitigation.

This study investigates the interactions between Pestalotiopsis diospyri and three phytopathogenic fungi—Fusarium guttiforme, Colletotrichum horii, and C. gloeosporioides—isolated from papaya and pineapple. A comparative analysis of metabolite production using ¹H NMR was conducted under axenic and co-culture conditions with rice and potato dextrose broth (PDB) media. Principal Component Analysis (PCA) and Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) of the ¹H NMR data revealed metabolic trends between axenic and co-culture conditions, while compound-specific PCA demonstrated distinct species-based metabolite clustering, supporting the observed metabolic changes during interspecies interactions. The results revealed various classes of metabolites in the axenic cultures; however, in the tri-cultures, α-pyrones synthesized exclusively by P. diospyri were differentially expressed, with compounds 11 and 12 showing up to 2-fold increases in yield. The diverse survival strategies exhibited by these fungi, including antagonistic and parasitic behaviors, notably influenced their interactions, leading to the up-regulation and down-regulation of specific metabolites, particularly α-pyrones. Comparative ¹H NMR profiling indicated that the metabolic response to co-culture was dominated by known α-pyrones, with no detectable emergence of uncharacterized metabolites that might signal the production of potent toxins. Furthermore, our findings indicate that the rice medium enhances substrate-fungi interactions, thereby increasing both chemo-diversity and metabolite yield. Preliminary antifungal assays revealed that the α-pyrones exhibited weak to moderate, strain-specific activity against the phytopathogenic fungi, suggesting their ecological role in interspecies competition rather than as potent antimicrobial agents.

Lincomycin is a clinically important lincosamide antibiotic. Its biosynthetic efficiency is limited by the presence of the rare UUA codon in the key positive regulators LmbU and AdpA. In this study, we developed a universal metabolic optimization strategy based on tRNA modification engineering. Co-overexpression of the UUA-decoding tRNA gene bldA and its post-transcriptional modification enzyme gene miaA markedly increased lincomycin production. Further optimization was achieved by expressing miaA under the phase-dependent promoter PlmbU. Mechanistic analysis showed that this strategy enhances the decoding efficiency of the UUA codon, thereby improving translation of LmbU and AdpA. Because bldA and miaA are highly conserved among species of Streptomyces, this approach may be broadly applicable to other rare-codon-dependent secondary metabolites. Our work provides a new and rational strategy for microbial secondary metabolic engineering through precise control of tRNA modification.

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Reactive oxygen species (ROS) are key mediators of plasma-induced microbial inactivation. This study investigated the influence of pulsed plasma parameters, specifically duty ratio and unit time, on the inactivation of Listeria monocytogenes and Staphylococcus aureus. Pulsed plasma-activated water PAW was generated under controlled discharge conditions, where the unit time, defined as the duration of a single plasma discharge cycle, and the duty ratio, the fraction of the unit time during which the plasma is actively on, were systematically varied to optimize bactericidal efficacy. Optimization of the parameters significantly enhanced inactivation, achieving reductions of 5.88 ± 0.10 log CFU for L. monocytogenes and 5.89 ± 0.09 log CFU for S. aureus. The optimal treatment condition (duty ratio 0.5 and unit time 2 min) resulted in a 2.7-fold increase in intracellular ROS compared with continuous plasma exposure. Fluorescence- and spectrophotometry-based analyses confirmed substantial ROS accumulation, accompanied by a reduction in bacterial viability as determined by plate counts. In situ evaluation using fresh-cut lettuce demonstrated 5.25 ± 0.15 and 5.18 ± 0.19 log CFU reductions for L. monocytogenes and S. aureus, respectively, without adversely affecting physicochemical quality. These findings demonstrate that ROS-mediated oxidative stress is the primary mechanism of pulsed plasma–driven microbial inactivation and highlight that both duty ratio and unit time critically regulate ROS dynamics and bacterial susceptibility. This study provides mechanistic insight into plasma–microbe interactions and supports the practical implementation of pulsed plasma technology for microbial control in food systems.

Microbial fuel cells (MFCs) are bioelectrochemical systems that harness electrogenic bacteria (EB) to catalyze electrochemical reactions at electrodes for electricity generation. Despite their promise for clean energy, challenges such as low efficiency, high cost and secondary pollutant formation limit their widespread application. Geobacter sulfurreducens, a model electrogenic bacterium, plays a central role in MFC research due to its robust extracellular electron transfer (EET) capabilities and ability to form stable, conductive biofilms. Understanding and engineering its metabolic pathways, gene expression and synergistic interactions with other microorganisms can significantly enhance MFC performance. This review highlights advances in the metabolic and genetic modification of G. sulfurreducens, its syntrophic interactions with other bacteria and approaches for improving MFC performance. Through bibliometric analysis, we identify publication trends, research hotspots and emerging approaches in MFCs. Collectively, this work provides a roadmap for leveraging G. sulfurreducens and microbial consortia to improve bioelectrochemical system efficiency and advance sustainable energy technologies.

This study compares the physiological and biochemical effects of 3-ring polycyclic aromatic hydrocarbons (PAHs), Anthracene (ANT, linear arrangement) and Phenanthrene (PHE, angular arrangement), on microalgae Chlorella vulgaris and Scenedesmus acutus. The findings revealed that PHE exerted significant toxic effects on algal growth and photosynthetic parameters, including electron transport rate of PSII [ETR(II)] and quantum yield of PSII [Y(II)], in both species. Additionally, it significantly influenced the regulation of the non-photochemical quenching mechanism [Y(NPQ) and Y(NO)], which was responsible for the energy distribution. Moreover, it altered the photosynthetic pigments content, biomolecules profile, and non-enzymatic antioxidants in both microalgae. On the other hand, ANT exposure showed noticeable positive changes in the measured parameters. Both microalgae exhibited a slight increase in chlorophyll content, biochemical compounds, and PSII activity, with the more pronounced effects observed in S. acutus, indicating its higher resistance to ANT. Furthermore, our findings also reveal that both species effectively removed ANT and PHE from the medium within 7 days of cultivation. These findings suggest that PAH toxicity is not only influenced by molecular weight and the number of benzene rings but also by the structural arrangement of their rings. Importantly, this study highlights that both microalgae can tolerate ANT and are suitable candidates for ANT bioremediation, but not for PHE.

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