Nanotechnology is rapidly advancing in biomedical, pharmaceutical, environmental and consumer applications, leading to increasing exposure of humans to engineered nanomaterials (ENMs) with a corresponding growing interest in their interactions with the human microbiome. The microbiome, often referred to as the “hidden organ” and plays a critical role in immune regulation, metabolism, tissue homeostasis, and disease processes. Experimental and preclinical studies suggest that nano-sized particles can directly and indirectly affect microbial ecosystems by mechanisms such as generation of reactive oxygen species, disruption of microbial membranes, quorum sensing disruption, and modulation of microbial signaling pathways. These interactions have therapeutic implications as well as potential toxicological implications. Nanomaterials have shown promise in pre- clinical studies for multiple applications such as antimicrobial therapy, disruption of biofilms, modulation of the microbiome, smart wound healing, and precision medicine, particularly by combining hydrogels, probiotics, and stimuli-responsive systems in microbiome-responsive nanoplatforms. However, emerging evidence indicates that long-term exposure to nanoparticles may contribute to dysbiosis, chronic inflammation, the emergence of antimicrobial resistance, immune system dysfunction and ecosystem disruption, although the clinical significance of these effects in humans remains limited. This review provides a comprehensive overview of nano-microbiome interactions, therapeutic applications, toxicological risks, novel advancements in organoid models, multi-omics technologies, artificial intelligence-based prediction, and personalized nanomedicine based on the microbiome for future clinically relevant therapeutic strategies, while highlighting existing knowledge gaps and future research areas that would be useful for clinical translation.
Multidrug-resistant Candida infections represent a critical therapeutic challenge, particularly among immunocompromised patients and in healthcare-associated settings. In this study, the in vitro antifungal and anti-virulence activities of the ethyl acetate extract of Saussurea costus leaves were systematically investigated against clinical Candida isolates. Among 80 clinical specimens examined, 57 Candida isolates were recovered and identified through conventional phenotypic methods, CHROMagar™, and the VITEK® 2 automated identification system. Candida albicans was the predominant species (50.9%), followed by C. tropicalis and C. krusei (24.6% each). Antifungal susceptibility analysis revealed significant variability among tested agents (p < 0.001), with clotrimazole, nystatin, ketoconazole, and amphotericin B showing the highest inhibitory activity, whereas itraconazole and fluconazole exhibited comparatively lower activity and higher resistance rates. Hemolytic profiling demonstrated that the majority of isolates were non-hemolytic (75.42%), while 24.56% exhibited β-hemolytic activity, with significant differences among isolates (p < 0.05).The ethyl acetate extract of S. costus leaves (extraction yield: 1.4% w/w) demonstrated reproducible antifungal activity against multidrug-resistant Candida isolates, with inhibition zones ranging from 14.0 ± 2.1 to 23.0 ± 2.5 mm. The majority of isolates exhibited MIC values of 31.25 mg/mL, whereas isolate 23 showed reduced susceptibility with a higher MIC of 62.5 mg/mL (p < 0.001). The extract significantly inhibited biofilm formation, with MBIC values ranging from 0.488 to 7.813 mg/mL (p < 0.05). In the hyphae-competent isolate 32, extract treatment markedly suppressed filamentation, reducing hyphal formation from 78 ± 4% in untreated controls to 8 ± 2%, accompanied by significant decreases in hyphal length (31.5 ± 2.1 to 4.7 ± 1.3 μm) and hyphal density (120 ± 10 to 15 ± 3 cells/field) (p < 0.001). Scanning electron microscopy further confirmed pronounced disruption of biofilm architecture, characterized by reduced surface coverage (approximately 85% to 48–50%), increased porosity (approximately 10–12% to 32–35%), and significant reductions in biofilm cluster size and density (p < 0.001). GC–MS profiling revealed a chemically diverse composition, with multiple constituents putatively identified by spectral library matching, including eugenol, caryophyllene oxide, myristicin, fatty acid esters, and a major compound tentatively assigned as dehydrocostus lactone. Collectively, these findings demonstrate that the ethyl acetate extract of S. costus exhibits statistically supported in vitro antifungal and anti-virulence activities against multidrug-resistant Candida isolates. However, these findings remain preliminary and restricted to in vitro evaluation; further studies involving bioassay-guided fractionation, compound-level validation, safety assessment, mechanistic investigations, and in vivo evaluation are required to determine its biological significance and translational potential.
Background Pseudomonas aeruginosa is a significant opportunistic pathogen responsible for a wide range of infections. The growing prevalence of antimicrobial resistance in clinical settings has led to a greater reliance on last-resort agents such as colistin. Notably, such antibiotics have long been used in veterinary practices, possibly playing a role in the emergence of resistance. However, despite the growing concern over colistin resistance, no previous systematic review and meta-analysis has estimated the global prevalence of colistin-resistant P. aeruginosa in non-clinical samples. This study aimed to assess the global prevalence of colistin resistance in P. aeruginosa isolates from non-clinical sources through a systematic review and meta-analysis. Methods A comprehensive literature search was conducted in PubMed, Web of Science, and Scopus for studies published up to January 2025. Eligible studies reporting colistin resistance in P. aeruginosa from environmental, animal, or food-related samples were included. A random-effects meta-analysis was used to estimate the pooled prevalence of resistance. Subgroup analyses were performed based on publication year, continent, country, testing guidelines, antimicrobial susceptibility testing methods, and sample source. Results A total of 70 studies were included. The pooled global prevalence of colistin resistance in non-clinical P. aeruginosa isolates was 5% (95% CI: 1–10%), with substantial heterogeneity (I2 = 97%). Subgroup analyses revealed significant variations: the highest resistance was observed in milk samples (47%, 95% CI: 3–94%), in North America (18%, 95% CI: 0–69%), and in Turkey (30%, 95% CI: 0–100%). Resistance increased over time from 7% in 2013 to 21% in 2024 (a 14% increase). No significant publication bias was detected (Egger's test p = 0.54). Conclusion The rising prevalence of colistin resistance in non-clinical P. aeruginosa isolates underscores the urgent need for enhanced antimicrobial surveillance. Standardizing susceptibility testing methods and restricting colistin use in veterinary settings are essential steps to preserve its efficacy and limit the spread of resistance.
Acinetobacter baumannii is a clinically significant pathogen due to its rapid acquisition of multidrug resistance (MDR) and its robust biofilm-forming ability, which contributes to treatment failure. Hence, the current study was designed to examine the structural, biochemical, and genomic characteristics, as well as the antibiofilm potential, of the phytochemical flavone in mature biofilms. Structural and biochemical analysis revealed that the tested clinical isolate produced a thick extracellular polymeric substance (EPS) matrix enriched in polysaccharides and proteins. Whole-genome sequencing (WGS) identified virulence factors such as AdeFGH efflux pumps, PNAG biosynthesis systems, which are crucial in biofilm formation, and resistance determinants, including β-lactamases (ADC-76, OXA-68), fluoroquinolone resistance mutations in parC that contribute to its antimicrobial resistance. Further, the antimicrobial assays demonstrated that flavone inhibited planktonic growth, and biofilm inhibition studies revealed concentration-dependent disruption of mature biofilms, with bactericidal and antibiofilm effects observed at 2xMIC levels. Drug-likeness and pharmacokinetic evaluation using SwissADME indicated that flavone meets the major criteria for oral drug-likeness. Overall, these findings provide integrated insights into A. baumannii biofilm biology and support flavone as a promising natural candidate for combating biofilm-mediated survival in drug-resistant A. baumannii.
Background Prosthetic joint infections (PJIs) caused by multidrug-resistant (MDR) bacteria and biofilm formation are often refractory to standard surgical and antibiotic care. Personalized bacteriophage therapy has emerged as a targeted alternative for such cases. Methods We present a descriptive case series of three patients with chronic MDR PJIs after total knee replacement (TKR) who were treated with locally applied high-titer lytic bacteriophage preparations. Clinical isolates were identified and characterized; environmental phages were isolated, purified, titrated, and tested for host specificity before local therapy. Outcomes were assessed clinically and microbiologically during follow-up. Results All three patients (MDR Staphylococcus aureus, extended-spectrum beta-lactamase-producing Klebsiella pneumoniae, and carbapenem-resistant Pseudomonas aeruginosa) achieved complete wound healing and resolution of infection while retaining their prostheses. Healing times were 56, 60, and 45 days, respectively; no recurrences were observed during the reported follow-up period. Phage titers ranged from 106 to 109 PFU/mL; therapy was well tolerated, with no reported adverse events. Conclusion In this series, personalized, locally applied bacteriophage therapy was as safe and effective as a prosthesis-preserving rescue strategy for refractory MDR PJIs. These findings support further clinical evaluation and protocol standardization for the use of phages in the treatment of complex orthopedic infections.
Rheumatoid arthritis (RA) is a chronic autoimmune condition that mostly affects the joints. It is believed that microbial infections play a contributing role in the development of RA. Individuals with preclinical and established RA have altered intestinal bacterial compositions, which imply that the gut microbiota plays a crucial part in the immune dysfunction that defines RA. Endotoxemia and a pro-inflammatory condition brought on by decreased gut integrity can exacerbate RA by triggering autoimmunity, which induces migration of autoreactive cells to joints, causing damage to the synovial membrane and joints. However, little is known about the exact pathways via which gut dysbiosis causes RA. A variety of RA treatment methods may change the diversity of the gut microbiota, indicating that RA prevention or treatment may benefit from gut microbiota modulation. This review gives an overview of the pathogenesis of RA due to gut dysbiosis and therapeutic strategies that may help to guide further research in this field.
Conventional antimicrobial treatment is limited by genetically active reservoirs of resistomes in humans that propagate antimicrobial resistance genes regardless of antibiotic dosage. Interconnected microbiomes gather, spread, and protect resistance genes, making antimicrobial resistance a potential global issue. Broad-spectrum antibiotics disrupt microbial ecology, increase selective pressure, and hasten horizontal gene transfer, hence augmenting genetic resistance. Maintaining the health of microbial populations is crucial while managing resistance factors. This unique CRISPR-Cas-based technique for controlling antimicrobial resistance focuses on resistance genes, virulence factors, and mobile genomic elements while keeping bacteria alive. Our current study explores that native CRISPR immunity reduces plasmid acquisition and resistome expansion; yet, many clinically effective infections lack functional CRISPR systems, suggesting an evolutionary trade-off that favors resistance over immune defense. This ecological perspective guides our critical evaluation of engineered CRISPR-based antimicrobials administered by bacteriophages, conjugative plasmids, nanoparticles, and engineered probiotics to eradicate resistance plasmids, resensitize multidrug-resistant infections, and reduce pathogenicity. Mechanistic and in vivo studies have shown that CRISPR lowers the resistance load and escape pressure in Enterobacteriaceae, Pseudomonas aeruginosa, Staphylococcus aureus, and viruses. The hurdles in designing CRISPR include poor microbiome ecology, delivery effectiveness, anti-CRISPR mechanisms, and transmission through mobilome. Our microecological framework employs CRISPR technologies as resistome-modulating adjuvants to maintain antibiotic efficacy, rather than relying solely on antimicrobials. CRISPR-based medicines revolutionize how antibiotic resistance is regulated considering AMR possesses been linked with genetic flow and ecological balance.
The global rise in antibiotic-resistant infections has created an urgent demand for innovative and potent antimicrobial therapies. Antimicrobial peptides such as nisin, alongside metal-based nanostructures like zinc oxide nanoparticles (ZnO NPs), exhibit notable antibacterial efficacy. In this study, we conducted a comparative assessment of the genomic effects of ZnO NPs and nisin-conjugated zinc oxide nanoparticles (Nisin–ZnO NPs) on Escherichia coli. E. coli cultures were treated with ZnO NPs, nisin, and Nisin–ZnO NPs at concentrations of 25, 50, 100, and 150 μg/mL. Bacterial growth was monitored spectrophotometrically at 600 nm after 2, 4, 6, 8, and 24 h. Genomic DNA was extracted from control and treated groups, and genomic alterations were evaluated using Random Amplified Polymorphic DNA–Polymerase Chain Reaction (RAPD–PCR). The data were analyzed with NTSYS–PC software based on the Dice similarity coefficient. Overall, ZnO NPs and Nisin–ZnO NPs at 150 μg/mL demonstrated the highest antimicrobial activity and effectively inhibited E. coli growth at 2 and 24 h post-treatment, whereas nisin alone exhibited negligible antibacterial activity. RAPD–PCR analysis showed that Nisin–ZnO NPs induced fewer genomic alterations compared with ZnO NPs, suggesting that Nisin–ZnO NPs enhance antibacterial efficacy while minimizing genotoxicity, supporting their promise as an effective antimicrobial strategy with a favorable safety profile.
Background Schizophrenia is a debilitating psychiatric disorder affecting about 1% of the global population. It is typically characterized by symptoms like hallucinations, delusions, cognitive impairments, and emotional dysregulation. This study investigates the role of the oral microbiome in schizophrenia, emphasizing how oral microbiota disturbances (dysbiosis) may influence neuroinflammation and immune dysfunction, contributing to the disease. We aim to provide insight into the intricate relationship between the microbiome, genetics, and neuroimmune pathways involved in schizophrenia. Methods A review was conducted to gather articles and research papers from scientific databases such as PubMed, Google Scholar, and Scopus. The search focused on articles published within the last decade, using keywords like “oral microbiome and schizophrenia,” “immune modulation,” “neuroinflammation in schizophrenia,” and “microbiome and neuroimmune pathways.” Studies were selected based on their relevance to the oral microbiome’s role in systemic and central nervous system inflammation, immune gene regulation, and its interactions with neurotransmitter systems in schizophrenia. Results Evidence suggests that disturbances in the oral microbiota can activate pro-inflammatory cytokines, influencing the blood-brain barrier and promoting neuroinflammation, which is central to schizophrenia. Genetic predispositions and immune system variations also play a significant role in modulating the microbiome, exacerbating neuroimmune dysfunction. Dysbiosis affects neurotransmitter regulation, including dopamine and glutamate, which are critical to schizophrenia pathophysiology. Conclusion The oral microbiome significantly impacts immune regulation and neuroinflammatory processes in schizophrenia. This integrated approach, combining genetics, microbiome science, and neuroimmune pathways, opens new avenues for microbiome-based therapeutic interventions. By targeting the oral microbiome, it may be possible to reduce inflammation and improve schizophrenia symptoms, paving the way for more personalized treatment strategies.
The gut microbiota is a diverse and dynamic microbial ecosystem playing a pivotal role in nutrient metabolism, immune regulation, and overall host physiology. Disruption of this microbial balance, or dysbiosis, has been implicated in a range of diseases. Among environmental toxicants, organophosphate pesticides such as malathion are recognized for their potential to alter gut microbial communities; however, the specific effects on probiotic strains have not been fully elucidated. In this study, the influence of malathion on selected probiotic strains — Lactobacillus rhamnosus (L. rhamnosus), Lactobacillus plantarum (L. plantarum), L. rhamnosus LB21, L. plantarum 299v, and Bacillus coagulans (B. coagulans)— were evaluated using 2,3,5-triphenyltetrazolium chloride (TTC) assay to assess metabolic activity and colony-forming unit (CFU) assay to measure viability. The malathion exposure resulted in a concentration-dependent decline in both parameters, with L. rhamnosus being the most susceptible. To counteract the observed toxicity, nanocurcumin was synthesized via sonication-assisted process, yielding particles averaging 29 nm in size and exhibiting a zeta potential of −75.8 mV. The antioxidant assays confirmed high radical scavenging activity (IC50 = 19.91 μg/ml) and ferric reducing capacity of nanocurcumin comparable to that of ascorbic acid. The co-treatment with nanocurcumin significantly improved the viability and metabolic activity of malathion-stressed probiotic strains, particularly L. rhamnosus LB21, which demonstrated substantial recovery. These findings suggest that malathion exerts harmful effects on beneficial gut microbes, and nanocurcumin may serve as a protective and restorative agent to mitigate pesticide-induced microbial dysbiosis.
Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide. Emerging evidence suggests that gut microbiota plays a crucial role in the development and progression of CRC, with dysbiosis being strongly associated with increased CRC risk. Certain bacteria, such as Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin producing Escherichia coli, are enriched in CRC patients and are known to produce genotoxins that induce DNA damage and promote carcinogenesis. Specific strains of Escherichia coli (E.coli) are strongly linked to CRC development. With this insight, this study investigates the potential role of E.coli K12, a common commensal strain, as a catalyst in colorectal carcinogenesis through a comprehensive in silico workflow combining subtractive proteomics, host-microbe interaction prediction, molecular docking, and molecular dynamics (MD) simulations. We employed a subtractive proteomics approach to identify E.coli K12 proteins that are non-homologous with human proteins, aiming to pinpoint potential targets involved in CRC. The analysis identified unique E.coli K12 outer membrane proteins that interact with human colon proteome. Subsequent molecular docking studies and MD simulations revealed specific host-microbe interactions that may disrupt normal cellular functions, thereby contributing to a tumorigenic microenvironment. Key E.coli K12 proteins interacting with human colon proteins implicated in carcinogenesis were identified. Complexes such as SLC16A1–UgpA, FLNC–GspO, ADH1A–YgbN, and KARS–YajC exhibited stable dynamics (RMSD <2.5 Å, consistent hydrogen bonding), suggesting potential disruption of host metabolism and cytoskeletal integrity. The findings provide new insights into how commensal E.coli may contribute to CRC under dysbiotic or immunocompromised conditions.
Intestinal dysbiosis is closely related to the progression of Parkinson's disease (PD), affecting gut barrier integrity, immune responses, and hormonal regulation. This microbial imbalance is believed to modulate PD pathogenesis via the brain–gut axis, suggesting that gut microbiome complexity could have a substantial impact on disease progression. To systematically characterize microbial diversity patterns in PD, we reanalyzed 2,102 gut microbiome samples from eight independent studies using a multi-scale diversity framework: Hill numbers for alpha diversity, the Anna Karenina Principle (AKP) for beta diversity, and diversity–area relationships for gamma diversity. Alpha diversity showed statistically significant differences between Parkinson's disease (PD) patients and healthy controls in 25–38% of comparisons, while the remaining 62–75% demonstrated no significant differences. This distribution aligns with the 1/3 diversity–disease relationship conjecture—a pattern initially observed across different diseases (Ma et al. 2019, The ISME Journal), but which our findings now extend to multiple independent studies of the same disease (PD). Beta diversity analysis showed increasing AKP adherence with diversity order: at q = 0 (species richness), 38% of datasets followed AKP, rising to 63% at q = 1 (common species) and q = 2 (dominant species), indicating stronger dysbiosis signals among dominant community members. Gamma diversity analysis showed PD patients harbored 863 total, 64 common, and 28 dominant species versus 894, 57, and 26 in controls, with only common species differing significantly. Overall, PD gut microbiomes exhibit scale-dependent diversity alterations, underscoring the value of integrated diversity frameworks for understanding Parkinson's pathogenesis.
Disruption of the gut microbiome has been implicated in several human disorders, including fibromyalgia, a musculoskeletal disorder characterized by widespread chronic pain and significant impairment of quality of life. Although it has been extensively studied, the results have been inconclusive. This systematic review aimed to analyze the available clinical evidence on the relationship between the altered gut bacterial microbiome and fibromyalgia, considering the microbiota gut brain axis and the use of omics. We searched Medline (Ovid), Scopus, Embase, Web of Science and Google Scholar, including observational studies in adults diagnosed with fibromyalgia, applying molecular, genetic, genomic and metabolomic techniques. The methodological quality was evaluated with tools from the Joanna Briggs Institute and the results were integrated into a narrative synthesis.Of the 732 studies initially identified, 11 fit the inclusion criteria, including a total of 455 patients with fibromyalgia and 385 controls, aged between 30 and 60 years. The overall certainty of the evidence is low to moderate, with greater strength for β-diversity, SCFAs, and the clinical manifestations of pain, fatigue, mood disturbances, and cognitive dysfunction supported by high-resolution techniques. Findings based solely on 16S have low certainty, supporting plausible associations between bacterial gut dysbiosis and fibromyalgia. Challenges such as methodological standardization and control of confounding factors, multi-omics, interdisciplinary and collaborative research are necessary to overcome the gaps in basic research and move towards translational research.
The complex nature of cancer poses significant challenges in deciphering its underlying molecular mechanisms. To facilitate advancements in biological research and therapeutic development, computational models have emerged as powerful tools for elucidating cancer biology. In the present study, in-silico approaches were employed to identify metabolites from Bacillus velezensis strain with anticancer potential by targeting protein molecules associated with malignancies. Genome mining revealed biosynthetic potential of the strain, and target prediction was conducted using BindingDB (p≥0.7). Pathway enrichment analysis was performed using STRING and KEGG databases, which showed involvement of compounds in modulation of multiple pathways involved in cancer. Molecular docking simulations showed that fengycin, a secondary metabolite derived from B. velezensis, exhibited strongest binding affinity toward MAPK9, with a docking energy of −17.1 kcal/mol. This interaction was validated through Molecular Dynamics (MD) simulation. The mean RMSD values for the APO and MAPK9 complexes were 0.29 ± 0.03 nm and 0.32 ± 0.03 nm, respectively, confirming structural stability throughout the simulation. The mean radius of gyration (Rg) values were 2.33 ± 0.02 nm for APO and 2.35 ± 0.02 nm for MAPK9, indicating compactness of the protein-ligand complex. RMSF values were recorded as 0.15 ± 0.09 nm for APO and 0.14 ± 0.07 nm for MAPK9, reflecting minimal residue-level fluctuations. Solvent Accessible Surface Area (SASA) remained stable at 177.63 ± 5.8 nm2 for APO and 179.67 ± 3.4 nm2 for MAPK9, suggesting no significant conformational alterations. Additionally, MAPK9 displayed a van der Waals energy of −493.903 ± 17.608 kJ/mol, electrostatic energy of −118.975 ± 26.098 kJ/mol, polar solvation energy of 480.496 ± 21.551 kJ/mol, and a final binding energy of −189.266 ± 33.873 kJ/mol, indicating a strong and stable interaction with the drug candidate. Overall, metabolites derived from B. velezensis, particularly fengycin, demonstrated potential anticancer attributes and warrant further experimental validation.
Multidrug-resistant tuberculosis (MDR-TB) continues to represent a critical global health challenge due to resistance against first- and second-line anti-TB drugs. Emerging evidence highlights the pivotal role of the human microbiota in TB pathogenesis, immune regulation, and drug response. This review systematically explores the microbiota–MDR-TB axis, with a focus on phytomolecule-based therapeutic interventions. A comprehensive literature search was conducted in PubMed, Scopus, Web of Science, Google Scholar, and Elsevier ScienceDirect following PRISMA guidelines, covering studies from January 2004 to August 2025. Included studies encompassed in vitro, in vivo, and clinical investigations elucidating microbiota alterations during TB infection and therapy, mechanistic insights into microbiota-derived metabolites (short-chain fatty acids, indoles), and their regulation of host immunity through AMPK–mTOR signaling, autophagy, and Treg/Th1 cell balance. Our analysis reveals that TB-associated gut and lung dysbiosis leads to SCFA depletion, epithelial barrier disruption, and systemic inflammation, weakening granuloma integrity and favoring M.tb persistence. Phytomolecules such as curcumin, emodin, resveratrol, and berberine exhibit dual actions by exerting direct antimycobacterial effects while simultaneously restoring the microbiota. These effects help reprogram immune responses through PRR, AHR, and AMPK pathways. Additionally, microbiota-sparing drug formulations, including ridinilazole, cadazolid, and lolamicin, along with probiotics, prebiotics, and synbiotics, demonstrate potential as adjunctive strategies to mitigate dysbiosis and enhance treatment outcomes. This review provides a mechanistic and translational framework for integrating phytomolecules and microbiome-modulating approaches into precision therapy, supporting the development of microbiota-informed host-directed therapies for MDR-TB.
In recent years, the accelerating emergence of antibiotic-resistant bacterial pathogens has posed profound challenges to the therapeutic management, prophylactic strategies, and epidemiological control of infectious diseases caused by these microorganisms. Consequently, identifying resistant bacteria is essential for therapeutic decisions and epidemiological studies. However, conventional approaches for the detection of antibiotic resistance are frequently constrained by lengthy protocols, substantial costs, and operational intricacies, thereby impeding the rapid and precise identification of resistance phenotypes. Raman optical tweezers have proven useful for classifying different bacterial species and isolates. This study establishes a fast, reliable, and cost-effective method to differentiate between Escherichia coli strains with antibiotic resistance (extended spectrum β-lactam resistant, ESBL) and susceptible strains using Raman optical tweezers and deep learning techniques. High-quality single-cell Raman spectra were collected from antibiotic-resistant and susceptible strains without exposure to antibiotics, revealing a higher nucleic acid/protein ratio in resistant strains. We propose a new network, RamanU-Net, for the accurate classification of these Raman spectra. The model achieved 99.5% average accuracy in identifying antibiotic-resistant and sensitive strains of Escherichia coli. Our results demonstrate that combining Raman optical tweezers with deep learning models can enable rapid identification of bacterial antibiotic resistance while significantly reducing the associated time, cost, and workload.
The emergence of extreme and pan-drug-resistant strains of Acinetobacter baumannii has intensified the need for effective prevention strategies, including developing vaccines. This study evaluates the immunogenicity and protective efficacy of the outer membrane protein Omp34 and its engineered construct, rOmp34L3×5, as potential vaccine candidates against A. baumannii pulmonary infections. The recombinant proteins were expressed and purified using Ni-NTA columns. The clinical colistin-resistant strain of A. baumannii Ab/TU/ColR was used in the murine pneumonia challenge experiments. Mice were immunized intranasally with the recombinant proteins. IgG, IgA titers, and their reactivity were assessed. Bacterial challenges and survival analysis were performed. Post-challenge, bacterial burdens in organs and histopathology of the lungs were evaluated. The results demonstrated that both vaccine candidates elicited strong immune responses, particularly with significant IgA and IgG antibody production. However, immunization with rOmp34L3×5 showed relatively stable IgG levels over 22 weeks, whereas rOmp34 alone induced higher IgG titers. Lung, spleen, and liver cultures confirmed the effectiveness of the specific antibodies in clearing bacterial loads, with histological analysis revealing normal lung tissue in immunized mice, contrasting with severe inflammation in controls. These findings suggest that rOmp34 and rOmp34L3×5 have the potential to serve as effective immunogens in preventing A. baumannii infections. Nonetheless, the variability in immune response depending on the clinical strain underscores the need for further studies to optimize vaccine efficacy across diverse A. baumannii isolates.
The antibacterial potential of Aspergillus oryzae (A. oryzae) EO product (AOEP) extract against Klebsiella pneumoniae (K. pneumoniae) strains BAA-1706 and BAA-1705 was investigated through minimal inhibitory concentration (MIC), biofilm inhibition assays, electron microscopy, and gene expression analysis. AOEP extract exhibited inhibitory activity with MIC50 values ranging from 3.1% to 50% for both strains. Notably, AOEP suppressed biofilm formation at low concentrations (3.1%-12.5%), outperforming the positive control, kanamycin, at 6.25%. Morphological examination revealed significant alterations upon AOEP treatment, including reduced colony size and fragmented cells, distinct from kanamycin-induced changes. qRT-PCR demonstrated that AOEP significantly downregulated key virulence genes ompA, lppA, and mrkA in strain BAA-1706, and ompA and lppA in strain BAA-1705, while pal and wzi expression remained unaffected. LC-MS/MS profiling identified several lactone-related secondary metabolites, including acyl homoserine lactone (AHL) analogs and butyrolactone I analogs, suggesting possible quorum sensing interference as a mechanism of action. These findings highlight AOEP extract as a promising multifunctional antibacterial agent that disrupts K. pneumoniae growth, biofilm formation, and virulence, with potential applications in combating antibiotic-resistant infections.
Background Cisplatin, a widely used chemotherapeutic agent, is limited by dose-dependent multi-organ toxicity. Probiotic interventions have recently emerged as promising strategies to alleviate such adverse effects through antioxidative and cytoprotective mechanisms. Methods This preclinical study evaluated the protective effects of the spore-forming probiotic Bacillus subtilis against cisplatin-induced toxicity in female Wistar rats. Animals were assigned to control, cisplatin-only, probiotic-only, and cisplatin + probiotic groups. Biochemical indices, antioxidant enzyme activities, oxidative stress markers, and histopathological changes were systematically evaluated to determine the therapeutic efficacy of B. subtilis. Results Cisplatin disrupted hematological indices, altered carbohydrate and lipid metabolism, elevated oxidative stress markers (ROS, MDA), and increased DNA damage (8-OHdG) and apoptosis (caspase-3). B. subtilis supplementation restored antioxidant enzyme activities (CAT, SOD, GPx), reduced oxidative and apoptotic damage, and preserved tissue structure. These protective effects are consistent with modulation of the Nrf2/Keap1 and NF-κB pathways, suggesting enhancement of endogenous antioxidant defenses and suppression of pro-apoptotic signaling. Conclusions B. subtilis demonstrates potential as a safe, gut-resilient probiotic adjunct to chemotherapy, capable of mitigating systemic toxicity through redox regulation and cytoprotective mechanisms. These findings support further mechanistic and translational studies to validate probiotic-based microecological strategies in oncology care.
