MicrobiologyOpen[JOURNAL]
Sun
200 papers
Antibiotic Resistance, Biofilm Genes, and smeDEF Efflux Pump in Clinical Stenotrophomonas maltophilia Isolates From Iran.
Jasim HF, Majeed NS, Salam AA … +4 more , Hamad RH, Behrouzi Y, Rajabi E, Shahbazi R
Microbiologyopen · 2026 Feb · PMID 41588613 · Full text
Stenotrophomonas maltophilia is a nosocomial and opportunistic microorganism with increasing antibiotic resistance rates. This study aimed to assess its biofilm production capacity, antibiotic resistance distribution, an...
Stenotrophomonas maltophilia is a nosocomial and opportunistic microorganism with increasing antibiotic resistance rates. This study aimed to assess its biofilm production capacity, antibiotic resistance distribution, and the prevalence of biofilm- and resistance-related genes in clinical isolates. In this multiinstitutional study, 230 isolates were collected from hospitals across Iran between 2022 and 2024. Resistance trends were evaluated using disc diffusion and minimal inhibitory concentration E test methods, per Clinical and Laboratory Standards Institute guidelines. Crystal violet staining assessed biofilm production, while polymerase chain reaction (PCR) sequencing identified biofilm- and resistance-related genes. Real-time PCR was used to evaluate the relative expression of the smeD, smeE, and smeT genes, calibrated against TMP/SMX-sensitive control strains. Susceptibility rates to trimethoprim/sulfamethoxazole (TMP/SMX), levofloxacin, and minocycline were 97.39%, 93.47%, and 93.04%, respectively. TMP/SMX-resistant strains showed 19.8- and 16-fold higher expression of smeD and smeE, compared with sensitive isolates. The spgM gene was detected in all isolates, and 93.04% (n = 214) were biofilm producers, with most showing moderate-biofilm formation (n = 89, 38.70%). Additionally, the rpfF gene was closely associated with strong-biofilm formation (p ≤ 0.05). The L2, L1, smqnr, sul2, and sul1 resistance genes were identified in 214 (93.04%), 181 (78.69%), 135 (58.7%), 136 (59.1%), and 127 (55.2%) isolates, respectively. Our findings demonstrate that most isolates remain sensitive to TMP/SMX, while resistance to alternative antibiotics is rising. Moreover, biofilm production appears significantly associated with the rpfF gene.
Structural Insights Into the Nuclear Import of Gallid Alphaherpesvirus 1 Large Tegument Protein.
Nath BK, Swarbrick CMD, Blades R … +5 more , Ariawan D, Tietz O, Alvisi G, Forwood JK, Sarker S
Microbiologyopen · 2026 Feb · PMID 41569631 · Full text
Gallid alphaherpesvirus 1 (GaAHV-1), also referred to as infectious laryngotracheitis virus (ILTV), primarily targets the upper respiratory tract of chickens. This infection leads to significant economic setbacks worldwi...
Gallid alphaherpesvirus 1 (GaAHV-1), also referred to as infectious laryngotracheitis virus (ILTV), primarily targets the upper respiratory tract of chickens. This infection leads to significant economic setbacks worldwide in the poultry sector, driven by reductions in egg output, weight gain, and increased mortality rates. Even with the broad implementation of vaccination programs, ILTV outbreaks remain a challenge, as vaccine strains can revert to a virulent form under field conditions. This underscores the need to explore targeted therapeutic options, including a deeper understanding of GaAHV-1's nuclear trafficking mechanisms, critical for viral replication. The herpesvirus large tegument protein UL36 contains N-terminal nuclear localization signals (NLSs) that are essential for capsid routing to the nuclear pore complex (NPC). However, the mechanisms by which UL36 of GaAHV-1 mediates nuclear import remain poorly understood. In this study, we identified the NLS of GaAHV-1 UL36 and elucidated their binding mechanism with human nuclear import proteins. Using high-resolution crystal structures and quantitative assays, we mapped the specific residues and regions within UL36's N-terminal domain that facilitate binding to importin (IMP) α. Moreover, we revealed variations in binding affinities among different importin isoforms. Our biochemical and structural analyses demonstrate that the predicted N-terminal NLS of GaAHV-1 UL36 is critical for IMPα binding. These findings provide detailed molecular insights into the interaction between the GaAHV-1 large tegument protein and IMPs, paving the way for the development of targeted antiviral therapies.
Differentiating Damp-Heat and Cold-Damp Diarrhea in Rat Models via Gut Microbiota Dysbiosis and Short-Chain Fatty Acid Profiling.
Zhang H, Song X, Mi W … +3 more , Ji P, Wei Y, Hua Y
Microbiologyopen · 2026 Feb · PMID 41566926 · Full text
On the basis of gut microbiota and short-chain fatty acids (SCFAs), this study aims to identify diagnostic biomarkers for damp-heat diarrhea and cold-damp diarrhea. Rat models of damp-heat diarrhea and cold-damp diarrhea...
On the basis of gut microbiota and short-chain fatty acids (SCFAs), this study aims to identify diagnostic biomarkers for damp-heat diarrhea and cold-damp diarrhea. Rat models of damp-heat diarrhea and cold-damp diarrhea were established. Changes in body weight, body temperature, food intake, water consumption, and the diarrhea index were recorded. ELISA was employed to detect levels of IL-6, IL-1β, TNF-α, and IL-10. Histological evaluations were conducted using H&E staining and AB-PAS staining techniques. Transmission electron microscopy was utilized to observe ultrastructural changes in the colonic epithelium, while Western blot analysis was performed to assess the expression of Occludin, Claudin1, Claudin5, GPR41, GPR43, GPR109A, and NLRP3 in colon tissues. GC-MS analysis was carried out to determine the content of SCFAs in the cecal contents of rats; additionally, 16S rRNA sequencing was performed to analyze the composition of gut microbiota in these animals. Differential analysis methods were applied to evaluate similarities and differences in SCFAs profiles and gut microbiota between damp-heat diarrhea and cold-damp conditions. The body weight and food intake of rats with induced damp-heat diarrhea or cold-damp diarrhea significantly decreased over time as their diarrheal symptoms progressively worsened. However, following treatment with appropriate prescriptions tailored for each condition resulted in an improvement in diarrheal symptoms among the affected rats. In accordance with the "prescription-based syndrome differentiation" theory, the rat experimental animal models of damp-heat diarrhea and cold-dampness diarrhea were successfully established. The models exhibited characteristic diarrheal symptoms alongside increased levels of inflammatory factors indicative of severe histopathological damage; there was also a notable reduction in tight junction protein expression observed across all models studied. Furthermore, the Firmicutes/Bacteroidota ratio showed a significant decrease. Interestingly, differences between damp-heat diarrhea and cold-damp diarrhea manifested as follows: Both modeling groups showed an increase in the relative abundance of Lachnoclostridium and Marvinbryantia. In the damp-heat diarrhea group, the levels of Lachnoclostridium and Marvinbryantia were relatively low; however, these levels gradually increased after successful treatment. In contrast, in the cold-damp diarrhea group, the trends of Lachnoclostridium and Marvinbryantia were opposite. Mucosal color has the potential for clinical diagnosis of damp-heat diarrhea and cold-damp diarrhea. Moreover, Lachnoclostridium and Marvinbryantia are potential biomarkers for distinguishing between damp-heat diarrhea and cold-damp diarrhea. However, the diagnostic basis and accuracy of Lachnoclostridium and Marvinbryantia biomarkers still need to be further validated.
BvrR From Brucella abortus Induces Neuroinflammation Through IRE1-Mediated Activation of ATF2 and NF-κB.
Wang Z, Yu X, Liu B … +1 more , Ren D
Microbiologyopen · 2026 Feb · PMID 41566528 · Full text
Brucella-induced neuroinflammation represents a key mechanism in the development of neurobrucellosis. The objective of this investigation was to clarify the molecular pathways through which the BvrR contributes to neuroi...
Brucella-induced neuroinflammation represents a key mechanism in the development of neurobrucellosis. The objective of this investigation was to clarify the molecular pathways through which the BvrR contributes to neuroinflammation and cognitive dysfunction. Human microglial clone 3 (HMC3) cells were transfected with pcDNA3.1-BvrR-His to examine the effects of BvrR from Brucella abortus on endoplasmic reticulum (ER) function and the activation of activating transcription factor 2 (ATF2) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) p65. The role of phosphorylated inositol-requiring enzyme 1 (p-IRE1) in mediating BvrR-induced activation of ATF2 and NF-κB p65 was assessed by applying the IRE1 activator IXA4 and the IRE1 inhibitor GSK2850163, followed by evaluation with western blotting and RT-qPCR. Interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α) concentrations in cell culture supernatants were quantified using ELISA. For in vivo analysis, HBAAV2/9-IBA-1-BvrR-6*HIS-ZsGreen was stereotactically delivered into the right hippocampus of mice. Expression of BvrR in HMC3 cells induced phosphorylation of IRE1 and expansion of the ER. This activation enhanced ATF2 and NF-κB p65 phosphorylation, facilitated their nuclear translocation, and significantly increased IL-6 and TNF-α expression at both the protein and mRNA levels. Inhibition of IRE1 with GSK2850163 suppressed these responses, whereas IRE1 activation with IXA4 reproduced the effects of BvrR. Findings indicate that BvrR from B. abortus activates IRE1, which subsequently stimulates ATF2 and NF-κB p65, leading to increased expression of IL-6 and TNF-α and the induction of inflammatory responses in HMC3 cells.
Septic Shock Caused by Coinfection of Shewanella algae Bloodstream Infection and Epstein-Barr Virus: Clinical Characteristics and Genomic Analysis.
Chen J, Ling D, Wang F … +4 more , Liu L, Ren Y, Chen C, Su N
Microbiologyopen · 2026 Feb · PMID 41556085 · Full text
Shewanella algae, a marine-origin opportunistic pathogen, has shown a significant increase in non-coastal infections, yet its environmental adaptability and synergistic pathogenic mechanisms with Epstein-Barr virus (EBV)...
Shewanella algae, a marine-origin opportunistic pathogen, has shown a significant increase in non-coastal infections, yet its environmental adaptability and synergistic pathogenic mechanisms with Epstein-Barr virus (EBV) coinfection remain unclear. This study reports a clinical case of S. algae bloodstream infection complicated by EBV reactivation leading to septic shock in Sichuan Province, China, and elucidates the molecular mechanisms through genomic analysis. Pathogen identification was performed via blood culture, antibiotic susceptibility testing, and genomic annotation. The strain harbored resistance genes (acrB, tolC, tet(35), golS) and virulence factors (bplL/bplF, clpC/clpP, tonB). Phylogenetic analysis indicated the highest genetic affinity to freshwater-derived Shewanella chilikensis, while pan-genome analysis identified 1412 unique genes, including transmembrane transporters and carbohydrate-active enzyme genes, suggesting freshwater adaptive evolution. Metagenomic next-generation sequencing (mNGS) detected a high EBV load. The patient succumbed to multi-organ failure. This study reveals that S. algae may evolve freshwater adaptability to cause inland infections, and EBV coinfection accelerates septic shock through immunosuppression and inflammatory cascades. Genomic analysis provides critical insights for precision diagnosis and treatment of polymicrobial infections.
Staphylococcus aureus Extracellular Vesicles Enhance PslE-Mediated Pathogenesis in Pseudomonas aeruginosa.
Subsomwong P, Sukchawalit R, Watabe N … +2 more , Nakane A, Asano K
Microbiologyopen · 2026 Feb · PMID 41555505 · Full text
Coinfection of Pseudomonas aeruginosa (P. aeruginosa) and Staphylococcus aureus (S. aureus) is frequently observed. Our previous study demonstrated that S. aureus-derived extracellular vesicles (SaEVs) promote P. aerugin...
Coinfection of Pseudomonas aeruginosa (P. aeruginosa) and Staphylococcus aureus (S. aureus) is frequently observed. Our previous study demonstrated that S. aureus-derived extracellular vesicles (SaEVs) promote P. aeruginosa pathogenicity by increasing lipopolysaccharide (LPS) production, promoting biofilm formation and decreasing the uptake of P. aeruginosa by macrophages. Proteomic analysis revealed that SaEVs enhance the production of PslE, an exopolysaccharide biosynthetic protein in P. aeruginosa, but the role of Psl exopolysaccharide polymerization on SaEV-mediated P. aeruginosa pathogenicity is unclear. In this study, a pslE-deletion mutant of P. aeruginosa (PaΔpslE) was constructed, and the effect of SaEVs on the pathogenicity of this mutant was evaluated. Our results showed that SaEVs significantly increased the expression of pslA, E, J, K, and L genes in the psl cluster of P. aeruginosa wildtype (PaWT), and this effect was abolished in PaΔpslE. In addition, LPS production and biofilm formation were reduced in PaΔpslE compared to PaWT. SaEVs significantly enhanced LPS production and biofilm formation in PaWT. On the other hand, the effects of SaEVs on the production of lipid A and LPS core and biofilm formation in PaΔpslE were abolished. Invasion of PaWT and PaΔpslE into HaCaT human epithelial cells was not significantly different and the effect of SaEVs on these bacterial cell invasions was not found. However, the uptake of SaEV-treated PaWT by macrophages significantly reduced compared to nontreated PaWT, whereas SaEVs did not alter the uptake of PaΔpslE. These results suggest that PslE is required for SaEV-mediated P. aeruginosa pathogenicity. SaEVs upregulate pslE gene as well as other exopolysaccharide polymerization-related genes, increase LPS production and biofilm formation, and affect the uptake of P. aeruginosa by macrophages.
Bacterial Communities Associated With Crustose Coralline Algae Are Host-Specific.
Turnlund AC, O'Brien PA, Rix L … +8 more , Ferguson S, Boulotte N, Jeong SY, Webster NS, Diaz-Pulido G, Wahab MA, Lurgi M, Vanwonterghem I
Microbiologyopen · 2026 Feb · PMID 41536161 · Full text
Crustose coralline algae (CCA) comprise hundreds of different species and are critical to coral reef growth, structural stability and coral recruitment. Despite their integral role in reef functioning, little is known ab...
Crustose coralline algae (CCA) comprise hundreds of different species and are critical to coral reef growth, structural stability and coral recruitment. Despite their integral role in reef functioning, little is known about the diversity and structure of bacterial communities associated with CCA. We address this knowledge gap by characterising the surface microbial communities of 15 Indo-Pacific CCA species across eight different families from the Great Barrier Reef, using 16S rRNA amplicon sequencing. CCA microbial community composition was distinct and found to primarily differentiate by algal host species. When looking at the core bacterial communities, divergence across CCA microbiomes was additionally correlated to host phylogeny. CCA from similar light environments and depths also had more similar microbial communities, suggesting the potential role of environmental parameters in influencing microbial community organisation. The fundamental descriptions of CCA bacterial communities for a wide range of Indo-Pacific species presented here provide essential baseline information to further inform CCA microbial symbiosis research.
Climatic Variables and Virulence May Contribute to the Population Dynamics of Pyricularia oryzae at Local Scale.
Bosco S, Sillo F, Ruffa P … +6 more , Bergonzi L, Tenni D, Abbruscato P, Torello Marinoni D, Romani M, Spadaro D
Microbiologyopen · 2026 Feb · PMID 41536158 · Full text
Rice blast disease, caused by Pyricularia oryzae Cavara, is the most threatening rice pathogen in Italy. The development of resistant cultivars is a sustainable approach to mitigate yield losses. However, P. oryzae genom...
Rice blast disease, caused by Pyricularia oryzae Cavara, is the most threatening rice pathogen in Italy. The development of resistant cultivars is a sustainable approach to mitigate yield losses. However, P. oryzae genomic plasticity often allows rapid adaptation to host resistance. Understanding the population structure of plant pathogens is crucial for assessing their genetic diversity and implementing durable management strategies. Despite first attempts from Piotti et al. (2005) to study the Italian P. oryzae population, a gap in current local P. oryzae genetic variability still needs to be addressed. Here, the population structure of a large set of P. oryzae isolates from diseased rice panicles, collected in five different Italian regions between 2011-2012 and 2020-2022, was characterized using SSR genotyping. Mating type was determined to investigate the occurrence of sexual reproduction in Italy. The integration of different cluster analyses of 200 unique multilocus genotypes allowed to identify five distinct genetic clusters. Analysis of molecular variance and of genetic divergence revealed a limited influence of geographic origin and time on population structure. A strong positive correlation was detected between climatic variables and allelic diversity in Piedmont, the most evenly sampled region in this study. The gradual disappearance over time of a genetic cluster could be linked to lower virulence on a susceptible rice cultivar. This study provides new insights into the genetic dynamics of Italian P. oryzae population, supporting the strategic deployment of resistance genes in rice breeding programs.
Efficacy, Safety and Biological Characteristics of Formulation Based on Essential Oil Against Co-Infections of Herpes Simplex Virus-1 and Candida albicans.
Di Vito M, Coggiatti D, La Sorda M … +9 more , Garzoli S, Lombardini G, Talamonti D, Pizzarelli S, Zhiri A, Cacaci M, Torelli R, Sanguinetti M, Bugli F
Microbiologyopen · 2026 Feb · PMID 41531279 · Full text
Oral coinfections involving herpes simplex virus (HSV) and Candida albicans can potentially interact and exacerbate each other. Starting from bibliographical investigation, this study aimed to examine the effectiveness o...
Oral coinfections involving herpes simplex virus (HSV) and Candida albicans can potentially interact and exacerbate each other. Starting from bibliographical investigation, this study aimed to examine the effectiveness of some essential oils (EOs), and their commercial formulations, both against C. albicans and HSV-1, identifying their antimicrobial, anti-inflammatory and allergenic potential. A preliminary review examined essential oils' efficacy against HSV-1. Broth microdilution tested 14 EOs, a commercial formulation (LA), and a homemade one (MIX) against three fungal strains. The quality of LA, MIX and single EOs was assessed by Solid Phase Microextraction (SPME) sampling coupled with gas chromatography-mass spectrometry (GC-MS) analysis. To assess the allergenic activity of MIX, LA, and single EOs a Basophil Activation Test (BAT) was standardized. ELISA tests were done to evaluate the anti-inflammatory activity. The bibliographic search highlighted seven EOs active against HSV-1. Four EOs showing strong antifungal activity were blended, following IFRA lip-application limits, to create a formulation (MIX) for comparison with a commercial herpes treatment (LA). Formulations were active against HSV-1, able to modulate the expression of pro (TNF-α = -29.7% and TNF-α = -33.6%) and anti-inflammatory (IL-1β = -50.0% and IL-1β = -25.0%) cytokines and no allergenic. MIX reinforces target cells and blocks viral entry, while LA also limits intracellular replication. EO-based formulations show promise for managing HSV-1 and Candida co-infections, offering antiviral, antifungal, and anti-inflammatory effects. BAT results indicate no basophil activation at tested concentrations, supporting their safety.
Patulin Biodegradation by Rhodosporidiobolus ruineniae and Meyerozyma guilliermondii Isolated From Fruits.
Ji Y, Hong SY, Qu J … +3 more , Chu Q, Ma S, Om AS
Microbiologyopen · 2026 Feb · PMID 41492961 · Full text
Patulin (PAT) is a toxic secondary metabolite produced by certain species of Penicillium and Aspergillus on pome fruits. In this study, we isolated Rhodosporidiobolus ruineniae (R. ruineniae) and Meyerozyma guilliermondi...
Patulin (PAT) is a toxic secondary metabolite produced by certain species of Penicillium and Aspergillus on pome fruits. In this study, we isolated Rhodosporidiobolus ruineniae (R. ruineniae) and Meyerozyma guilliermondii (M. guilliermondii) from a peach and an apple as candidates for PAT degradation, respectively, and investigated the effects of three key parameters (incubation time and temperature, and initial PAT concentration) on PAT removal rates, and the mechanism involved in PAT degradation by the yeast strains. The PAT degradation rate by the yeast strains was dependent on the three key parameters. Both yeast strains were able to degrade 1 μg mL of PAT to below the regulatory limit (50 µg L) at 60 h when they were incubated at 35°C. The PAT removal by the yeast strains was not due to either binding onto yeast cell walls or degradation by extracellular fractions of the yeast culture among three yeast cell fractions (cell walls, extracellular, or intracellular fractions). The use of spheroplast or intracellular enzymes confirmed that PAT degradation occurred inside the yeast cells. Moreover, the PAT degradation ability was inducible in M. guilliermondii. LC/MS/MS analysis showed that (E)-ascladiol is the sole PAT biodegradation product from both yeast strains. Our data demonstrated that both yeast strains were able to degrade PAT and produce (E)-ascladiol, a less toxic product. These results could be exploited for practical applications to efficiently control PAT on fruits such as apples and peaches.
Hidden Partners in Diversity: Acidobacteriota and Their Distribution in the Cape Floristic Region.
Pieters J, Jacobs K, Conradie TA
Microbiologyopen · 2026 Feb · PMID 41486474 · Full text
The Cape Floristic Region, a biodiversity hotspot in South Africa, is characterised by acidic, nutrient-poor soils and distinctive fynbos vegetation. Despite the ecological importance and metabolic versatility of Acidoba...
The Cape Floristic Region, a biodiversity hotspot in South Africa, is characterised by acidic, nutrient-poor soils and distinctive fynbos vegetation. Despite the ecological importance and metabolic versatility of Acidobacteriota, their diversity and functional roles in fynbos soils remain poorly understood. This study investigated the diversity and abundance of Acidobacteriota in two nature reserves, Jonkershoek and Kogelberg, and the influence of soil abiotic factors and enzyme activities on their distribution and composition at the subdivision (SD) level. A total of 26 bulk soil samples were collected, and the V1-V9 regions of the 16S rRNA gene were sequenced using the Oxford Nanopore platform. The mean relative abundance of Acidobacteriota ranged from 1.5% to 36.25%. Subdivision 1 was the most dominant, with relative abundances of 66.96 ± 8.96% in Kogelberg Nature Reserve and 30.35 ± 0.15% in Jonkershoek Nature Reserve (p = 0.001). Other prevalent SDs included SDs 2, 3, and 5, with this study being the first to report the presence of SDs 22 and 17 in fynbos soils. Beta-diversity analysis revealed distinct community compositions between the two reserves, driven by soil pH, moisture content, available phosphate, electrical conductivity, and enzyme activities (p = 0.001). Several positive and negative correlations between Acidobacteriota SDs and soil properties were also identified. Overall, this study highlights the high diversity of Acidobacteriota in fynbos soils and their close associations with soil abiotic properties, underscoring the need for cultivation-based research to elucidate their ecological roles in these oligotrophic environments.
Semi-Quantitative Detection of Respiratory Pathogens: A Systematic Review and Meta-Analysis of Results From the BIOFIRE FILMARRAY Pneumonia Panel and Culture.
Hommel B, Hurtado O, Noble B … +6 more , Jones J, Allantaz F, Timbrook TT, De Pascale G, Posteraro B, Sanguinetti M
Microbiologyopen · 2026 Feb · PMID 41466028 · Full text
This systematic review and meta-analysis compared bacterial semi-quantification of respiratory samples from the BIOFIRE FILMARRAY Pneumonia (PN) Panels with quantitative and semi-quantitative culture methods (qCMs). Four...
This systematic review and meta-analysis compared bacterial semi-quantification of respiratory samples from the BIOFIRE FILMARRAY Pneumonia (PN) Panels with quantitative and semi-quantitative culture methods (qCMs). Fourteen studies comprising 1,654 samples were included. Across both bronchoalveolar lavage-like and endotracheal aspirate-like specimens, the BIOFIRE PN Panel reported consistently higher bacterial loads than qCMs, with pooled mean differences of 1.17 and 0.95 log, respectively. Discrepancies decreased as culture-reported bacterial burden increased. The concordance rate in identifying the predominant pathogen was 94%, supporting the panel's clinical relevance. However, differential reporting at lower bacterial loads suggests that existing culture-based thresholds may not translate directly to molecular diagnostics. These findings highlight the need for pathogen- and method-specific interpretive thresholds to optimize the diagnostic utility of semi-quantitative molecular results and inform antimicrobial stewardship decisions.
An Eco-Friendly Synthesis and Characterization of Antibacterial, Antifungal, and Antioxidant Silver Nanoparticles From Bioactive Streptomyces sp. Strain WSN-2.
Anjum MS, Khaliq S, Ashraf N … +2 more , Anwar MA, Akhtar K
Microbiologyopen · 2026 Feb · PMID 41457186 · Full text
The present study reports the isolation and molecular identification of Streptomyces sp. strain WSN-2 using 16S rRNA gene sequencing and BLASTn analysis (GenBank Accession No. MN128377), followed by its application in th...
The present study reports the isolation and molecular identification of Streptomyces sp. strain WSN-2 using 16S rRNA gene sequencing and BLASTn analysis (GenBank Accession No. MN128377), followed by its application in the green synthesis of silver nanoparticles (AgNPs). Biomass filtrate of Streptomyces sp. WSN-2 efficiently reduced silver ions to form stable AgNPs, confirmed by a characteristic UV-Vis surface plasmon resonance (SPR) peak at 423 nm. Structural and morphological characterization using FTIR, SEM, TEM, and EDX revealed spherical nanoparticles with a smooth texture and well-dispersed arrangement. TEM analysis indicated particle size predominantly between 50 and 60 nm (overall range 0.83-100 nm), while the zeta potential of -22.9 mV confirmed moderate colloidal stability. EDX spectra displayed strong elemental silver absorption peaks at 3-4 keV, indicating crystalline Ag formation. The biosynthesized AgNPs exhibited strong antimicrobial activity against wide range of pathogenic microbes. Maximum antibacterial growth inhibition zones were observed against S. typhi (24 ± 1.53 mm), followed by E. coli (23 ± 1.25 mm), B. subtilis (23 ± 1.73 mm), and P. aeruginosa (22 ± 1.53 mm). Antifungal assays revealed highest antifungal activity against A. flavus (16 ± 1.15 mm), and notable inhibition of A. niger (16 ± 1.25 mm), A. fumigatus (15 ± 1.70 mm), and F. oxysporum (14 ± 1.53 mm). MIC values ranged from 8.00 ± 0.05 µg/mL for P. aeruginosa to 18.000.07 µg/mL for A. fumigatus. The AgNPs also demonstrated remarkable antioxidant potential, achieving 65.2% H₂O₂ scavenging activity at 50 µg/mL, surpassing L-ascorbic acid (45.1%). These findings highlight Streptomyces sp. WSN-2 as a promising biogenic source for the synthesis of stable AgNPs with significant antibacterial, antifungal, and antioxidant potential.
Nanomedicine Strategies Against Biofilm-Associated Infections: Advances, Challenges, and Translational Barriers.
Farah H, Kadhim-Abosaoda M, Mohaisen-Mousa H … +6 more , Renuka Jyothi S, Priyadarshini-Nayak P, Bethanney Janney J, Singh G, Singh-Chauhan A, Kumar-Mishra M
Microbiologyopen · 2026 Feb · PMID 41457060 · Full text
Antimicrobial resistance continues to rise globally, with biofilm-associated infections intensifying the clinical burden through persistent tolerance to antibiotics and evasion of immune responses. Biofilms, structured m...
Antimicrobial resistance continues to rise globally, with biofilm-associated infections intensifying the clinical burden through persistent tolerance to antibiotics and evasion of immune responses. Biofilms, structured microbial communities embedded in a protective extracellular matrix, underlie many chronic and recurrent infections, including endocarditis, urinary tract infections, cystic fibrosis lung disease, and device-related infections. Conventional antibiotics often fail in these contexts, and the discovery pipeline for novel agents remains limited. Nanotechnology has therefore emerged as a promising alternative, offering unique physicochemical features that enable enhanced penetration into biofilm matrices, improved drug stability, and targeted delivery of therapeutic agents. Diverse nanosystems, including metallic, polymeric, lipid-based, and ligand-functionalized platforms, have shown encouraging results in vitro and in vivo, demonstrating superior biofilm disruption and bacterial eradication compared with conventional therapies. Nevertheless, translating these advances into clinical practice remains challenging. Key barriers include complex and costly synthesis, scalability under good manufacturing practices, limited drug loading efficiencies, variability of preclinical biofilm models, regulatory uncertainties, and the risks of nanoparticle (NP)-induced toxicity, unpredictable biodistribution, and potential resistance development. Moreover, the dynamic interactions between NPs, host fluids, and biofilm extracellular matrices complicate pharmacokinetic and pharmacodynamic predictability. Addressing these obstacles requires coordinated efforts to refine manufacturing processes, standardize biofilm models, and implement nanospecific regulatory frameworks. With careful optimization, nanomedicine holds the potential to redefine the therapeutic landscape for biofilm-related infections.
Omics Analysis of Lignin Degradation by the Gut Microbiomes of Wood-Eating Hypomeces squamosus Fabricius.
Mao C, Zhang Q, Zhang J … +1 more , Li X
Microbiologyopen · 2025 Dec · PMID 41456898 · Full text
Microbial degradation of lignin is important to carbon cycling. The gut microbiome of wood-feeding Hypomeces squamosus Fabricius has been shown to degrade lignin efficiently. However, the specific degradation mechanisms...
Microbial degradation of lignin is important to carbon cycling. The gut microbiome of wood-feeding Hypomeces squamosus Fabricius has been shown to degrade lignin efficiently. However, the specific degradation mechanisms remain incompletely understood. In this study, we investigated the mechanism of lignin degradation using omics comparative analysis, focusing on differentially expressed genes and metabolic pathways in the gut microbiome of insects fed with a lignin-rich diet. The dominant genus taxon was Pantoea (29.82%), which was predominant in insects fed with high lignin-containing Iris ensata Thunberg, whereas Wolbachia and Enterobacter were predominant in insects fed with cabbage leaves (MHS_K group). Furthermore, expression levels of carbohydrate-active enzymes from the auxiliary activities (AAs) families in the MHS_I group were 1.18 times higher than those in the MHS_K group. These mainly included lignin peroxidase and manganese peroxidase of the AA2 family, vanillyl-alcohol oxygenase of the AA4 family, and 1,4-benzoquinone reductase of the AA6 family. Expression levels of multiple genes encoding aromatic compound-degrading genes (2303 accounted for 75.76% of the total upregulated genes) were found, including about 0.03% was related to lignin degradation. Genes MHS-HN_11398_2 (protocatechuate 2,3-dioxygenase) and MHS-HN_4821_1 (muconolactone d-isomerase) were enriched in the MHS_I group. Three lignin-degrading pathways were found: ortho-cleavage and meta-cleavage of catechol, as well as ring-opening of protocatechuate. This study provides a comprehensive and theoretical evidence of the gut microbiome roles of H. squamosus Fabricius in lignin degradation.
Phylogenetic Footprints of Coagulase-Negative Staphylococci and Mammaliicoccus Isolated From Raw Caprine Milk.
Omer AB, Eltom KH, Tawor AB … +1 more , Erganiş O
Microbiologyopen · 2025 Dec · PMID 41431405 · Full text
Coagulase-negative staphylococci (CNS) and Mammaliicoccus species recently reclassified from the Staphylococcus sciuri group, are increasingly recognized as opportunistic pathogens in dairy animals and humans. This study...
Coagulase-negative staphylococci (CNS) and Mammaliicoccus species recently reclassified from the Staphylococcus sciuri group, are increasingly recognized as opportunistic pathogens in dairy animals and humans. This study investigated phylogenetic diversity and antimicrobial resistance in raw caprine milk from Sudan by integrating conventional bacteriological methods, molecular sequencing, and antimicrobial susceptibility testing. Raw goat milk samples were cultured, and presumptive CNS isolates were identified using phenotypic tests (novobiocin, oxidase, urease, and carbohydrate fermentation) following the standard Staphylococcus identification flow chart. PCR amplification of the elongation factor Tu (tuf) gene and the methicillin-resistance gene (mecA) enabled molecular confirmation and assessment of antimicrobial resistance. Sequenced tuf amplicons (~370 bp) were analyzed by BLAST and aligned in MEGA 12 for maximum-likelihood phylogenetic reconstruction. Staphylococcus simulans and Mammaliicoccus lentus were isolated in this study; antimicrobial susceptibility testing revealed that S. simulans, but not M. lentus, was methicillin-resistant and carried the mecA gene. Partial tuf gene sequencing confirmed 99.6%-99.7% identity with reference strains of the respective species. Phylogenetic analysis revealed that the isolated S. simulans formed a distinct branch within the global clusters. Meanwhile, M. lentus was found to be closely related to the global strains, showing only minor divergence. This study reports the presence of S. simulans and M. lentus in caprine milk from Sudan using both phenotypic and genotypic identification methods. This underscores the importance of integrating traditional laboratory methods with molecular techniques for precise species identification. The identification of methicillin-resistant S. simulans highlights the need for ongoing monitoring of CNS in raw milk.
Probing the Role of Meso-DAP and Lysine for Growth and Pathogenicity of Pseudomonas aeruginosa.
Hawkins DA, Impey RE, Hind CK … +2 more , Sutton JM, Soares da Costa TP
Microbiologyopen · 2025 Dec · PMID 41431381 · Full text
Antibiotic-resistant bacteria represent a major global challenge as increasing infections become recalcitrant to standard treatments. A lack of novel therapeutics entering the market in the past 30 years further exacerba...
Antibiotic-resistant bacteria represent a major global challenge as increasing infections become recalcitrant to standard treatments. A lack of novel therapeutics entering the market in the past 30 years further exacerbates this issue and highlights the importance of identifying and validating novel antibiotic targets. In this study, we explored prospective therapeutic targets by examining two metabolites in the lysine biosynthesis pathway, meso-diaminopimelate (DAP) and lysine, within the critically listed pathogen Pseudomonas aeruginosa. These metabolites are involved in bacterial cell wall and protein synthesis; therefore, enzymes present in this pathway represent potential targets for novel therapeutics. To elucidate the validity of these targets, we generated for the first time, gene deletion mutants of the P. aeruginosa DHDPR- and DAPDC-encoding genes using a two-step allelic exchange method. Both the mutants resulted in a lethal phenotype that could be rescued by supplementation with meso-DAP and/or lysine. We subsequently characterized the mutants' pathogenicity in a Galleria mellonella infection model. The DHDPR mutant was unable to provide a lethal infection in this model. Given the importance of these metabolites to membrane and cell wall synthesis, we investigated membrane permeability utilizing a fluorescent probe assay and transmission electron microscopy. Due to their increased membrane permeability, these mutants exhibited greater sensitivity to antibiotics commonly used against Pseudomonas infections. Overall, this study highlights that targeting the lysine biosynthesis pathway could enhance bacterial susceptibility to existing antibiotics, supporting its development as an adjuvant strategy to potentiate current treatments and extend their clinical utility.
Bioimaging With Fluorescent Nucleic-Acid Aptamers for the Specific Detection and Quantification of Pseudomonas aeruginosa Alone and in Heterogeneous Bacterial Populations.
Mezouarhi C, Vauchelles R, Abdallah B … +6 more , Janel R, Ouadghiri M, Benhassou HA, Pelet S, Fechter P, Choulier L
Microbiologyopen · 2025 Dec · PMID 41431270 · Full text
Aptamers, short nucleic acid sequences with high specificity and affinity for their targets, are promising candidates for diagnostic applications due to their ability to detect a wide range of pathogens. We present a flu...
Aptamers, short nucleic acid sequences with high specificity and affinity for their targets, are promising candidates for diagnostic applications due to their ability to detect a wide range of pathogens. We present a fluorescent bioimaging approach for detecting Pseudomonas aeruginosa, based on aptamer F23. Conjugated with fluorescent dye, its detection efficacy was evaluated on 15 Gram-negative and -positive bacteria, including fixed and live cells, as homogeneous and heterogeneous populations. We developed an automated, open-access software for quantifying microscopy images. Its high sensitivity enables accurate quantification of bacteria labeled with aptamers. For example, it successfully detected 1122 P. aeruginosa cells labeled with aptamer F23 out of a total of 1123 P. aeruginosa cells in a single image. With 200,000 analyzed bacteria, we demonstrated that the aptamer effectively detects various reference and clinical strains of P. aeruginosa, while failing to detect Gram-positive Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus epidermidis, and Corynebacterium striatum, as well as Gram-negative Klebsiella pneumoniae, Acinetobacter baumannii, and Escherichia coli. This aptamer is therefore a promising tool to distinguish P. aeruginosa from different strains of the skin microbiota. However, our quantitative method also revealed partial labeling to other bacterial cells, highlighting the issue of refining aptamer selection to improve selectivity.
Uncovering Insights Into the Biology of Mycobacterium tuberculosis Using Genetic Tools.
Stamilla A, Recchia D, Stelitano G … +6 more , Maci L, Marturano MC, De Rossi E, Chiarelli LR, Pasca MR, Degiacomi G
Microbiologyopen · 2025 Dec · PMID 41423823 · Full text
Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, is one of the most challenging pathogens due to its complex physiology, diverse clinical manifestations, and growing multidrug resistance. The glob...
Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, is one of the most challenging pathogens due to its complex physiology, diverse clinical manifestations, and growing multidrug resistance. The global rise of drug-resistant Mtb strains has prompted the search for innovative genetic and molecular strategies to accelerate drug discovery and vaccine development. Progress in Mtb research has long been hindered by its slow replication rate and impermeable cell envelope, which limit the efficacy of genetic manipulation. This review outlines methodological advances that have transformed the study of Mtb pathogenesis and drug resistance mechanisms. Traditional homologous recombination-based approaches, including allelic exchange and specialized transduction, laid the groundwork for targeted mutagenesis but were limited by low efficiency. The advent of phage-derived recombineering systems, such as the Che9c RecET, has substantially improved the precision and throughput of genetic modification. Hybrid systems such as ORBIT, which combines oligonucleotide-mediated recombineering with Bxb1 integrase, have further enabled rapid and versatile genome engineering across mycobacterial species. Parallel developments in conditional gene expression systems (e.g., the use of TetR/Pip-based promoters) have facilitated the functional analysis of essential genes and the validation of novel drug targets. The advent of CRISPR-Cas technologies has represented a paradigm shift, by enabling programmable, high-fidelity gene regulation and functional genomics even in slow-growing mycobacteria. Together, these genetic innovations are transforming Mtb research by accelerating drug discovery and vaccine design, and shedding light on host-pathogen interactions.
NanoMLST: A High-Throughput Bacterial Multi-Locus Sequence Typing Workflow Using Oxford Nanopore Next-Generation Sequencing for ESKAPE + E Pathogens.
García-Pérez I, Lázaro-Perona F, Reyes-Zuñagua DS … +8 more , Sotelo J, Rodríguez-Tejedor M, Cañada-García JE, Bloise I, Portugués-Rodríguez SM, Mingorance J, Oteo-Iglesias J, Dahdouh E
Microbiologyopen · 2025 Dec · PMID 41413952 · Full text
Multi-Locus Sequence Typing (MLST) is a key method for allocation of Sequence Types (STs) for bacterial isolates. Traditionally, this is performed by the Sanger sequencing method, which can be highly time-consuming and l...
Multi-Locus Sequence Typing (MLST) is a key method for allocation of Sequence Types (STs) for bacterial isolates. Traditionally, this is performed by the Sanger sequencing method, which can be highly time-consuming and laborious. In this study, we present NanoMLST, a high-throughput MLST workflow using multiplex PCR, Oxford Nanopore Technologies Next-Generation Sequencing, and the Krocus program for typing ESKAPE + E pathogens (Enterococcus faecium [E. faecium], Staphylococcus aureus, Klebsiella pneumoniae [K. pneumoniae], Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli). Bacterial isolates were obtained from the Hospital Universitario La Paz's Microbiology Department and the Centro Nacional de Microbiología. Primers that can be multiplexed in a single PCR reaction were designed for the seven housekeeping genes for each species. DNA was extracted from single colonies by heating at 95°C for 10 min, mechanical lysis at 4.20 m/s for 2 min, and then by the MagCore extraction system. Multiplex PCRs were then performed with the respective primer mixes for each species, and libraries were prepared for sequencing by ONT Flongle cells. The Krocus program was then used to determine the STs from the raw FastQ reads. STs for 221 isolates were obtained through this workflow with an average time of 12 h per 24 isolates. In line with local data, the K. pneumoniae and E. faecium isolates were relatively oligoclonal, while the rest were polyclonal. STs from representative isolates showed 100% concordance between Sanger sequencing and the proposed workflow. NanoMLST offers a fast, cheaper, and less labor-intensive alternative for large-scale MLST applications targeting clinically important pathogens.
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