Search Results (3,767)

Odontogenic sinusitis (ODS) is a common cause of unilateral maxillary sinusitis arising from periapical lesions (PALs) or other dental sources. The infection is typically polymicrobial and dominated by anaerobic bacteria, which are often under detected by routine culture. Molecular approaches such as quantitative polymerase chain reaction (QPCR) and next-generation sequencing (NGS) may provide improved characterization of the microbial burden and community structure. This study aimed to compare culture-based methods, targeted quantitative PCR, and 16S rRNA sequencing in paired samples to characterize microbial composition of ODS and evaluate diagnostic performance. Paired sinus mucosal biopsy (SIN) and periapical lesion (PAL) samples were collected from 28 patients with clinically confirmed ODS. Bacterial detection was performed using conventional culture and targeted QPCR assays for ten clinically relevant taxa. In three randomly selected patients, paired samples were additionally analyzed by 16S rRNA gene amplicon sequencing. Microbial load, taxa richness, and similarity between the two anatomically connected sites were assessed using Wilcoxon signed-rank, McNemar, Jaccard distance, and Bray–Curtis dissimilarity analyses. Results: Culture showed low sensitivity, identifying a limited number of pathogens, primarily Staphylococcus aureus, Streptococcus anginosus, and Fusobacterium nucleatum, in a minority of samples. In contrast, QPCR demonstrated substantially higher detection rates, particularly in PAL samples. Porphyromonas gingivalis (96.8%), Fusobacterium spp. (100.0%), and the S. anginosus group (90.3%) were highly prevalent in PAL specimens, with overlapping but lower detection in SIN samples. PAL samples exhibited significantly higher bacterial loads and taxa richness than paired SIN samples (Wilcoxon p = 0.0004). 16S rRNA sequencing confirmed polymicrobial communities at both sites and identified additional taxa not included in the QPCR panel. Similarity analyses revealed pronounced interindividual variability, ranging from near-identical to highly divergent paired microbiota. Periapical lesions act as reservoirs of predominantly anaerobic bacteria that may seed the maxillary sinus in ODS. Although microbial overlap exists, sinus communities display lower burden and site-specific compositional shifts. Culture-based diagnostics underestimate ODS microbial complexity, whereas combined molecular approaches provide a more comprehensive and clinically informative assessment. Full article

West Nile virus (WNV) diagnosis relies on nucleic acid amplifications, but these techniques do not discriminate between infectious and non-infectious viral particles. This limitation can be bypassed by using a genome-binding dye (PMAxx) that is unable to cross membranes and can only bind to the genomes of non-intact (i.e., non-infectious) viral particles. This study evaluated a workflow combining PMAxx treatment with digital PCR to improve the molecular discrimination of intact WNV particles. Fifty-five samples (35 plasma, 20 urine) from 41 patients with WNV fever (WNF) or WNV neuroinvasive disease (WNND) were analyzed. Samples were tested with/without PMAxx treatment. Overall, PMAxx treatment resulted in a significant reduction in detectable viral RNA (median reduction: 1.0 Log copies/mL; p < 0.0001), indicating that a substantial fraction of RNA detected by standard methods originated from non-infectious particles. This reduction was more visible in urine (1.8 Log copies/mL) than in plasma (0.4 Log copies/mL), suggesting a higher proportion of degraded viral particles or free RNA in urine. Stratification by clinical presentation showed significant reductions in both WNF and WNND patients, with no significant differences between groups. This approach may represent a valuable adjunct for improving diagnostic interpretation and epidemiological assessment of WNV infection, particularly in matrices characterized by prolonged RNA persistence. Full article

The Mycobacterium tuberculosis bacterium encodes two active potassium (K⁺)-uptake transport systems, the Trk and the Kdp. The Trk is the low-affinity K⁺ transporter, consisting of two TrkA proteins, while the Kdp consists of the high-affinity K⁺ transporter KdpFABC and the two-component system KdpDE. Both transporters are utilised by the bacteria for growth and survival. During growth, the bacteria utilise the constitutively expressed Trk and suppress the Kdp, but upregulate both transporters during survival. In the current study, we investigated the interactive effects of these systems on bacterial growth and survival. This was achieved by first constructing a M. tuberculosis mutant strain in which both the Trk and Kdp systems were inactivated by homologous recombination. The mutant was evaluated for its growth kinetics in planktonic cultures, as well as survival in biofilm and macrophage cultures. The constructed M. tuberculosis mutant showed faster growth rates in planktonic cultures, but was attenuated for both biofilm formation and intracellular survival in isolated human monocyte-derived macrophages. These results illustrate that both K⁺-uptake systems are essential to sustain slow rates of bacterial growth, as well as for bacterial persistence in hostile environments via optimisation of biofilm formation, and intracellular survival in macrophages. (Words: 194) Full article

Plastic pollution is a global environmental crisis, and microbial degradation represents a promising remediation strategy. While bacteria have been widely studied, yeasts offer unique advantages for plastic degradation due to their metabolic versatility, stress tolerance, and enzymatic capabilities. However, plastic degradative yeasts have not been reviewed comprehensively. Although several yeasts capable of degrading polyethylene terephthalate (PET) or polyethylene (PE) have been reported (e.g., Moesziomyces antarcticus, Candida tropicalis, Yarrowia lipolytica and Rhodotorula mucilaginosa), degraders of other plastic types are less studied. Although some yeasts can assimilate carbon from plastics, the diversity of yeasts capable of participating in plastic mineralization remains vastly underexplored. In recent years, yeast cell surface display systems for bacterial PETase and fungal cutinase have been developed, demonstrating promising PET degradation efficiency. However, PETase is feedback-inhibited by the intermediate product mono(2-hydroxyethyl)terephthalate (MHET). Systems synergizing PETase with MHETase have shown superior stability during long-term PET degradation and enable large-scale depolymerization of PET waste. For high-crystallinity PET, fungal hydrophobins can be used to modify the surface hydrophobicity of PETase-displaying yeast cells, facilitating their attachment to hydrophobic PET surfaces and ultimately enhancing the degradation efficiency of the whole-cell biocatalyst. Limitations of current research and future directions are also discussed. Full article

As a traditional tonic in Chinese herbal medicine, Codonopsis pilosula exerts anti-aging effects, but studies on Codonopsis pilosula polysaccharides (CPPs) in the regulation of gut microbiota dysbiosis and the associated pathways remain limited. This study explored CPP’s anti-aging effects and mechanisms using a D-galactose-induced aging mouse model. In vivo results showed that CPP improved cognitive deficits, alleviated systemic aging, reduced neuroinflammation/oxidative stress, mitigated pathological tissue changes, and inhibited aging markers (p53, p21, and p16). Transcriptomic/metabolomic analyses indicated that CPP regulated inflammation-related genes and metabolites, with anti-inflammatory effects mediated via the MAPK pathway. 16S rRNA sequencing revealed that CPP restored gut microbiota diversity. In vitro experiments confirmed CPP’s anti-aging effects and identified the MAPK/FOXO1 pathway as a potential target. In conclusion, CPP exhibits potential anti-aging effects, possibly through the MAPK pathway and gut microbiota modulation. Full article

Staphylococcus aureus remains a leading cause of morbidity and mortality worldwide, with persistent and relapsing infections posing a major global health threat. Here, we report that baloxavir, an FDA-approved influenza antiviral, exhibits antibacterial activity against S. aureus. Baloxavir demonstrated potent activity against both MSSA and MRSA clinical isolates with MICs of 2–4 μg/mL and exhibited concentration-dependent antibacterial activity in time-kill assays. Notably, baloxavir effectively eliminated intracellular S. aureus in both A549 alveolar epithelial cells and RAW264.7 macrophages at 10 μg/mL and achieved complete eradication in A549 cells at 50 μg/mL. In vivo, baloxavir (20–40 mg/kg) significantly improved survival in MRSA-infected mice from 12.5% to 75–87.5%. Transcriptomic analysis revealed significant downregulation of purine de novo biosynthesis genes, including purF and purK, which was validated by RT-qPCR (r = 0.862, p = 0.027). This study demonstrates for the first time that baloxavir possesses significant antibacterial activity against S. aureus including MRSA, positioning it as a promising repurposed candidate for treating persistent intracellular infections and post-viral superinfections. Full article

Klebsiella pneumoniae, a member of the ESKAPEE group of priority pathogens, has become one of the most challenging bacterial pathogens in modern clinical practice, largely due to its multidrug resistance and the immune-evasive effect of its capsular polysaccharide (CPS). Phage-encoded depolymerases, which selectively degrade the capsular polysaccharide, have emerged as promising antimicrobial agents capable of restoring bacterial susceptibility to both immune clearance and phage infection. The fragment corresponding to the C-terminal region of a putative depolymerase of bacteriophage KlebP_144, namely DepKP144ΔC, was cloned, expressed in E. coli, and purified using immobilized metal affinity chromatography. DepKP144ΔC displays an enzymatic activity against capsular polysaccharides of 100% K1 capsular-type strains and 85% K2 capsular-type strains, including classical and hypervirulent isolates. It was demonstrated that this protein is capable of inhibiting K. pneumoniae biofilm formation, but it is unable to disrupt mature biofilms. In vivo experiments using a murine K. pneumoniae infection model further confirmed its therapeutic potential: treatment with DepKP144ΔC improved survival rate in mice infected with K2-type K. pneumoniae, indicating significant attenuation of bacterial virulence. Therefore, these results demonstrate the potential role of the C-terminal domain of the bacteriophage KP144 tail-fiber protein in phage entry and show that its carbohydrate-recognition motifs possess enzymatic activity against the Klebsiella capsular polysaccharides. Full article

Fungi represent a prolific source of structurally diverse secondary metabolites, yet the extent to which culture conditions reshape the metabolic profile and functional bioactivity remains incompletely understood. In this exploratory study, ten fungal strains belonging to genera Penicillium and Aspergillus were cultivated in Yeast Extract Sucrose (YES) and Czapek Yeast Autolysate (CYA) media and analysed using untargeted LC-HRMS metabolomics. The objective of this study was to evaluate how culture medium influences metabolic profiles and to investigate medium-dependent metabolic variation and its relation to cytotoxic, antibacterial, and antifungal activities. Global metabolic profiling revealed moderate but statistically significant medium-associated metabolite variation, with discriminant metabolites predominantly enriched under CYA conditions. Putative structural annotation suggested patterns consistent with differential regulation of isoprenoid-derived sterols, terpenoids, alkaloid-like metabolites, and aromatic polyketides. While antimicrobial activities displayed a heterogeneous, strain-dependent pattern with limited correlation to individual metabolites, cytotoxic activity co-varied with metabolite composition in OPLS regression modelling. Sterols and terpenoid-related features emerged as major contributors to cytotoxicity. Given the absence of biological replication and the limited sample size inherent to this pilot study, all findings should be considered hypothesis-generating and interpreted within an exploratory framework. These results suggest that nutrient composition influences biosynthetic pathway activation while functional outcomes remain strongly dependent on strain-specific metabolic capacity. This work provides a systematic framework and targeted hypothesis for future investigations into condition-dependent fungal chemical diversity in natural product discovery. Full article

The gut microbiota plays a multifaceted role in calcium homeostasis and bone metabolism —acting through metabolic, immunological, and hormonal pathways that collectively constitute the gut–bone axis. The microbiota influences calcium bioavailability through several overlapping mechanisms that act in the intestine. Moreover, microbial fermentation products may directly impact the osteoblast–osteoclast interplay and, by modulating immune and endocrine functions, are crucial for bone metabolism. A healthy microbiota supports bone formation; however, intestinal dysbiosis may impair bone structure and function. This narrative review aims to present pathways linking the gut microbiota to bone metabolism, both in health and disease. First, we will discuss the influence of gut microbiota on calcium absorption. We will then outline the role that microbial metabolites, such as bile acids and short-chain fatty acids (SCFAs), play in regulating bone structure and function. In the following section, we will discuss the role of the microbiota in the immunological and hormonal modulation of bone metabolism. Finally, we will discuss how dysbiosis affects bone and how therapeutic interventions, such as probiotics, prebiotics, and postbiotics, may influence bone tissue quality. Full article

HIV-1 protease (PR) is an essential enzyme in the viral life cycle and a primary target of antiretroviral therapies, particularly protease inhibitors (PIs). Understanding the dynamics of viral evolution and the factors governing the emergence or loss of resistance-associated mutations is critical for improving PI efficacy and managing drug resistance in HIV/AIDS treatment. In this study, we investigated the impact of three natural HIV-1 polymorphisms (T12A, L63Q, and H69N), whose prevalence varies depending on treatment status and viral subtype, on the structural stability and conformational dynamics of PR using molecular dynamics (MD) simulations. Three independent 500 ns MD simulations were performed for the native protease and each mutant system. Although none of the mutations disrupts the overall structural integrity of HIV-1 PR, they induce mutation-specific alterations in flexibility and residue interactions. In particular, T12A and H69N exhibit increased structural deviations, especially in the flap regions, along with enhanced conformational fluctuations. In contrast, the L63Q mutation shows a slight reduction in flap flexibility compared to both the native protease and the other mutants. Consistently, the fraction of time spent in open-flap conformations is higher for T12A and H69N and lower for L63Q relative to the native system. Moreover, mutations in the Fulcrum (T12A) and Cantilever (L63Q and H69N) regions do not disrupt the long-range network of correlated motions observed in the native protease, both inter- and intra-monomer, but instead increase the extent of correlated and anti-correlated motions in other regions of PR. Full article

The emergence of multidrug-resistant Pseudomonas strains poses a serious threat to public health. Essential oil components, such as thymol (TH), exhibit potent antibacterial activity. However, the effects of continuous sublethal TH exposure and resulting changes to antibiotic susceptibility remain poorly understood. Here, we investigated a multi-resistant Pseudomonas psychrophila strain after TH adaptation using an integrated transcriptomic and metabolomic approach. Treatment with TH caused a significant decrease in MIC values for aminoglycosides (streptomycin, gentamicin, kanamycin) and tetracycline and increased susceptibility to five other antibiotics. Multi-omics analyses revealed coordinated changes in fatty acid metabolism (FabI downregulation and accumulation of unsaturated fatty acids), lipid A biosynthesis (LpxC downregulation), peptidoglycan synthesis (Mur genes downregulated, accompanied by increased spermine levels), and stress response pathways (such as GABA, GadA, maltose, and MalK). These results suggest that metabolic alterations and envelope remodeling potentially affect cell wall integrity and growth, which could, in turn, contribute to increased antibiotic susceptibility and re-sensitization. Overall, our findings highlight the potential of TH-mediated sensitization as a complementary strategy to restore antibiotic efficacy. Full article

Genetically modified (GM) lactic acid bacteria (LAB) are gaining attention as tools for innovation in the food sector, health applications, and industrial processes. LAB have long been used safely due to their GRAS/QPS status, making them suitable for improving fermentation and synthesizing specific and beneficial metabolites. Advances in genomics and gene editing have significantly expanded the available tools, ranging from classical mutagenesis to site-specific recombination, homologous recombination in non-coding regions, CRISPR-based systems, and food-grade chromosomal integration. These approaches enable the insertion of desired genes and the development of engineered strains with tailored functionalities. GM-LAB are also being studied as live delivery systems for therapeutic molecules, including cytokines, hormones, antimicrobial peptides, and vaccine antigens. Engineered strains of Lactococcus lactis and Lactobacillus spp. have yielded promising outcomes in applications such as mucosal immunization, modulation of inflammatory and metabolic responses, and inhibition of pathogenic microorganisms, including multidrug-resistant bacteria. From an industrial perspective, several studies highlight their potential for cost-effective recombinant protein production and the synthesis of high-value metabolites through fermentation. However, within the European Union, their use is subject to stringent regulatory oversight, requiring comprehensive molecular and environmental risk assessments, careful evaluation of horizontal gene transfer, and a preference for markerless chromosomal integrations. Despite these constraints, GM-LAB offer significant potential to improve food quality, sustainability, and human health. Full article

Staphylococcus aureus is a high-priority pathogen causing skin and soft tissue infections (SSTIs). The frequent resistance to anti-staphylococcal agents exhibited by this underscores the need for accurate diagnostics to guide effective therapy. Therefore, this study aimed to compare phenotypic and genotypic resistance in S. aureus isolates from nasal carriers and SSTIs and to elucidate gene-silencing mechanisms. In total, 355 S. aureus isolates (256 isolated from carriers and 79 from SSTIs) were studied for their phenotypic and genotypic resistance to β-lactams, macrolides, tetracyclines, aminoglycosides, and mupirocin. The silenced mupA gene (low prevalence: 0.6%; 2/335), linked to mupirocin resistance, was sequenced, and expression was assessed via reverse transcription qualitative PCR (RT-qPCR) in all mupA-positive isolates. SSTI isolates showed significantly higher resistance to erythromycin, gentamicin, and mupirocin, along with a higher prevalence of multidrug-resistant strains and ermC and tetM genes. Sequencing revealed multiple mutations in silent mupA, including a critical frameshift (c.372 delA) in a poly(A) tract that brings about premature truncation. RT-qPCR indicated upregulation of silent mupA variants and high variability in functional strains, suggesting that frameshift alone prevents resistance. These findings highlight silent resistance genes as key targets for advancing S. aureus surveillance and for combating emerging threats. Full article

Microbial lipids have emerged as a promising sustainable alternative to plant- and petroleum-derived oils, with applications spanning biofuels, oleochemicals, nutraceuticals, and specialty materials. Significant advances in metabolic engineering and strain development have increased lipid production capacity across diverse microorganisms. Numerous reviews have summarized the biological and metabolic advances in this field, highlighting significant progress in metabolic engineering and strain development that has increased lipid production capacity across diverse microorganisms. However, translating these gains into economically viable industrial processes remains a major challenge. This review examines process engineering strategies for microbial lipid production across the full bioprocessing pipeline, from laboratory-scale strain evolution to industrial-scale operation. We discuss recent developments in adaptive laboratory evolution, systems-guided strain optimization, and robustness engineering, emphasizing their implications for process performance. Key bioprocess parameters—including substrate selection, nutrient limitation strategies, reactor design, oxygen transfer, and process control—are critically evaluated for their impact on lipid yield, productivity, and scalability. Furthermore, downstream processing considerations and techno-economic constraints are analyzed in the context of large-scale implementation. By integrating strain-level innovations with process engineering principles, this review highlights current bottlenecks, emerging solutions, and future directions for achieving efficient and scalable microbial lipid biomanufacturing. Full article