Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology最新文献

Infectious Bursal Disease Virus (IBDV) remains a significant threat to global poultry health due to its immunosuppressive effects and high mutation rate, which challenge existing vaccine strategies. This study presents a comprehensive computational analysis of the VP2 protein from Malaysian IBDV isolate UPM1432/2019 to elucidate its structural stability and antigenic potential. Phylogenetic analysis revealed evolutionary divergence among VP2 sequences, while physicochemical profiling demonstrated the protein’s high thermostability (aliphatic index: 98.77) and cellular stability (instability index: 17.55). Molecular dynamics simulations at 20 °C, 40 °C, 60 °C, and 80 °C showed progressive destabilization at elevated temperatures, indicated by increased RMSD, reduced hydrogen bonding, and higher solvent accessibility. Epitope prediction identified twelve linear and seven conformational B-cell epitopes, with several conserved, surface-exposed regions demonstrating high antigenicity. The most immunodominant conformational epitope (L168–E181) achieved a high ElliPro score of 0.903, indicating strong immune recognition potential. These findings highlight structurally stable and immunoreactive domains within VP2, offering valuable insights for the development of next-generation, thermostable epitope-based vaccines for effective IBDV control.

MexCD-OprJ is one of the major efflux systems which confers significant drug resistance to Pseudomonas aeruginosa. This study aimed to investigate the effects of two herbal compounds, menthol and thymol, on the MexCD-OprJ efflux pump in P. aeruginosa isolates. Ethidium bromide (EtBr) agar cartwheel, disk diffusion, and antibiogram tests were carried out for the isolates, with and without exposure to sub-MIC values of menthol and thymol. The expression level of the oprJ gene was evaluated through reverse transcription quantitative PCR (RT-qPCR). In order to check the interactions between the OprJ protein and the herbal agents, molecular docking was conducted using Autodock v4.2.6. Cartwheel method demonstrated inhibition of pump activity in all isolates grown under sub-MIC of the bioactive compounds. The untreated bacteria (control group) were resistant to antibiotics; however, the antibiotic sensitivity of the isolates shifted toward sensitive or intermediate patterns in several cases after exposure to menthol and thymol, depending on the specific antibiotics employed. Additionally, thymol and menthol downregulated the expression of the oprJ (P < 0.05). According to the in silico analysis, the herbal compounds may potentially interact with the α-barrel and β-barrel channels considering the amino acids involved in the interactions, with menthol showing greater binding energy (ΔG = -5.81 kcal.mol⁻¹) with the OprJ protein compared to thymol (ΔG = -5.63 kcal.mol⁻¹). Our findings indicate that menthol and thymol may serve as potential inhibitors of the MexCD-OprJ efflux system of P. aeruginosa, offering a promising avenue for antibiotic treatment.

A Gram-stain-negative, rod-shaped, flagellated and motile bacterium, designated 10H^T was isolated from soil sample collected in Guangxi Province, China. This strain displays activities including catalase, urease, and activities related to Tween 20, 40, and 80. Optimal growth occurs at 33 °C, without NaCl and pH 7–8. The major quinone component is ubiquinone-8 (Q-8). The polar lipids mainly composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unknown amino lipid, and four unknown lipids. The major fatty acids were iso C_15:0, anteiso C_15:0 and Summed Feature 9 (iso C_17:1ω9c). The complete genome sequence was 3.56 Mbp in length with a G + C content of 71.27%. Strain 10H^T showed less than 98.73% 16S rRNA gene sequence similarity with type strains of the genus Pseudoxanthomonas. Phylogenetic analysis based on 16S rRNA gene, core genes, and genome-wide data indicated that the strain belongs to the genus Pseudoxanthomonas. Furthermore, the results showed that strain 10H^T established a unique and distinguishable lineage in conjunction with Pseudoxanthomonas kaohsiungensis J36^T. The average nucleotide identity (ANI) values between 10H^T and the closest Pseudoxanthomonas strains were 76.98%–85.95%, and the digital DNA‒DNA hybridization (dDDH) values were between 18.90% and 30.50%. Additionally, strain 10H^T demonstrated the ability to grow in a medium with sodium carboxymethyl cellulose as the sole carbon source, Whole-genome sequencing identified multiple genes associated with cellulose degradation, and experimental assays confirmed cellulase activity reaching up to 350 U/L. Based on these findings, we propose the novel species Pseudoxanthomonas fibrivorans sp. nov., with strain 10H^T (= CCTCC AB2024091^T = KCTC 8654 ^T) as the type strain, which demonstrates clear cellulose-degrading capabilities.

Lake Suigetsu, a deep meromictic lake connected to Wakasa Bay, receives freshwater inflow and exchange surface water with intruding seawater. To investigate bacterial community dynamics and substrate transport, we conducted seasonal 16S rRNA gene sequencing across three stratified layers (mixolimnion, chemocline, and monimolimnion) and two size fractions (0.2–0.8 µm for free-living; 0.8–3.0 µm for particle-attached). Community composition differed by depth, fraction, and season. Winter communities were dominated by Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia, forming a potential “seed” community. In the monimolimnion, Bacteroidia, Chlorobia, and Cloacimonadia prevalent in free-living fraction, while Desulfobacterales and Desulfatiglandales and Anaerolineae were in particle-attached fraction. In autumn, a community shift toward Pseudomonadales and Enterobacteriales corresponded with lowered salinity and temperature in the chemocline, suggesting episodic entrainment driven by mixing of freshwater and monimolimnetic water. These findings highlight seasonal and vertical microbial dynamics and suggest that hydrological mixing may facilitate microbial connectivity between surface and deep waters.

Leishmaniasis is one of the neglected tropical diseases that is endemic to over 90 countries, and its cases are being reported from non-endemic countries as well, like Austria. The cases of visceral leishmaniasis, caused by Leishmania donovani are concentrated on the Indian Subcontinent. There are several studies on the genetic heterogeneity, aneuploidy, and drug resistance emergence from Indian subcontinent as well as globally. However, no research has yet inspected the genomic data from the Indian subcontinent to conduct a comprehensive investigation at the nucleotide level of the genome. We have considered whole-genome sequence data from the publicly available database, i.e., European Nucleotide Archive. Genetic analysis has shown that there is tetraploidy in chromosome 31, trisomy in chromosomes 2 and 8, and trisomy was observed a in chromosomes 6 and 15 among some samples. This aneuploidy pattern is evolving over time as observed in the present study. The paromomycin drug has induced trisomy in chromosome 2. The pattern of aneuploidy variations in samples from the Indian subcontinent differs markedly from that in other continent's samples. Further, ATP-binding cassette family, Amastin-like surface proteins, A2 genes, amino acid permeases, heat shock 70-related protein 1, mitochondrial precursor, putative, partial and sodium stibogluconate resistance protein, putative proteins were those that exhibited the maximum number of mutations amid all the analyzed samples. The proteins showing higher number of mutations belong to membrane proteins that are involved in drug resistance mechanism. Most of these proteins are involved in the virulence and drug resistant mechanism (like transporter proteins). The present study provides the possible candidates which can be targeted to disarm the virulence of the protozoan and drug candidates for therapeutic interventions.

Introduced in the early 1990s, Nigeria’s most consumed potable water packaging material is dumped indiscriminately into various environments despite concerns about its harmful effects on these environments. The study was designed to isolate and characterise potential microbial degraders and their degradation potentials using various methods. Various environmental samples (soil, sediment, and marine water) were obtained using standard protocols. Microplastic from the sachet water (SW) plastic was generated mechanically using a sterile grater and used to enrich the various samples from which potential degraders were obtained. The isolates were further screened for their ability to degrade crude oil. Positive hydrocarbonoclastic isolates were used for the biodegradation experiments of the polyethylene sheets (3 × 3 cm) via weight loss, fourier transform infrared spectroscopy (FT-IR), and gas chromatography (GC–MS). A total of 38 experiments plus one control were set up. After incubation, a total of ten (10) very turbid flasks and their control were selected for FT-IR spectroscopy. Following FT-IR, the best (n = 1) experiment and its control were subjected to GC–MS. Selected isolates were confirmed using molecular characterisation to be Pseudomonas aeruginosa (PMB₄₅) and Rossellomorea aquimaris (HBSD₂₈). Plasmid profiling for the alkB gene was positive for isolate PMB₄₅ and negative for HBSD₂₈. Weight loss gave a biodegradation rate of 22.5% for SW sheets, respectively. Furthermore, FT-IR positive sheets had functional groups such as ketones, carbonyl, carboxylic, and amino groups, and this was consistent with the GC–MS report that showed a reduction in carbon atoms, signifying degradation in the broths containing the positive isolate. Our findings indicate that, R. aquimaris (HBSD₂₈) and P. aeruginosa (PMB₄₅) have potential to degrade SW plastic waste. Further studies aimed at optimising isolates, and revealing pathways and enzymes elaborated in polyethylene biodegradation should be prioritised.

Aim

Methicillin-resistant Staphylococcus aureus (MRSA) is a global public health concern owing to its resistance to conventional antibiotics. To overcome this challenge, innovative strategies such as nanotechnology and phage therapy have emerged as promising alternatives to conventional antimicrobial treatments.

Methods

This review explores the dual approach of using nanoparticles (NPs) and bacteriophages to treat MRSA. NPs, such as silver, gold, and zinc oxide, exhibit antimicrobial effects through mechanisms including membrane disruption, the generation of reactive oxygen species (ROS), and biofilm degradation. Phage therapy uses bacteriophages for the targeted lysis of MRSA. Additionally, CRISPR-Cas9 gene editing targeting the mecA gene and efflux pump inhibition strategies are discussed as adjunctive therapies for MRSA infections.

Results

Studies have shown that synergistic nanocomposites can enhance the efficacy of existing antibiotics against resistant strains. Engineered phages have demonstrated expanded host ranges, improved biofilm degradation, and resistance evasion to these mechanisms. ROS production by nanoparticles leads to oxidative stress and bacterial death. Blocking bacterial efflux pumps increases intracellular drug retention and improves therapeutic outcomes.

Discussion

The combination of nanotechnology and phage therapy offers a complementary approach, with nanotechnology providing broad-spectrum activity and phages providing specificity and adaptability to the host. Challenges such as nanoparticle toxicity, environmental impact, and potential phage resistance require interdisciplinary research efforts and improved regulatory frameworks.

Conclusion

Integrating advanced nanotechnology and phage therapy into healthcare systems could transform the MRSA treatment landscape. Future research guided by systems biology and personalized medicine principles will be crucial for mitigating antimicrobial resistance and ensuring equitable access to novel therapeutics.

Graphical Abstract:

Graphical representation of emerging combination therapies to combat methicillin-resistant Staphylococcus aureus (MRSA). Strategies include nanoparticle-induced ROS generation, phage-mediated lysis, CRISPR–Cas9 gene editing targeting mecA, and efflux pump inhibition, which offer targeted approaches to combat antibiotic resistance.

Vibrio cholerae is traditionally recognised as the causative agent of cholera in humans; however, increasing evidence indicates that non-O1/non-O139 strains are widely distributed in aquatic environments and can infect aquatic animals. In this study, we report the first isolation and characterisation of V. cholerae from diseased Pelophylax nigromaculatus tadpoles exhibiting severe intestinal symptoms during an outbreak in a freshwater farm in Huanggang, China. The isolates were identified through 16S rRNA and gyrB gene sequencing, and further confirmed by species-specific genes (lolB and dnaJ) and phenotypic traits, including sucrose fermentation and sodium-independent growth. Whole-genome analysis revealed multiple virulence-associated genes, such as AHA_3493 (haemolysin III), wbkC (LPS biosynthesis), ricA (intracellular survival), and lbtC (siderophore-mediated iron uptake), as well as antibiotic resistance genes including crp, qnrVC5, and two chromosomal copies of catB9. These findings highlight the pathogenic potential of non-O1/non-O139 V. cholerae in amphibians and its adaptation to freshwater environments. This study expands the known host range of V. cholerae and highlights the need for early surveillance in amphibian aquaculture.

A novel strain of the genus Sinomonas, designated G460-2 ^T, was isolated from rice paddy soil. The cells of strain G460-2 ^T were Gram-positive, aerobic, and non-motile rods. The optimal growth conditions for this strain were observed at 30 °C and a pH of 7.0. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain G460-2 ^T shared the highest sequence similarity (98.41%) with Sinomonas albida LC13^T. The genomic DNA of strain G460-2 ^T had a G + C content of 68.6 mol%. The genome size was determined to be 4.4 Mbp, and the average nucleotide identity (ANI) with the closest related reference strains was 86.39%, which is below the species delineation threshold of 95%. Digital DNA–DNA hybridization (dDDH) calculations yielded a relatedness value of 32.0% with the nearest neighbor. The predominant respiratory quinone identified in strain G460-2 ^T was MK-9(H2). The major fatty acids were C15:0 anteiso (44.8%), C17:0 anteiso (28.7%), C15:0 iso (11.6%), and C16:0 iso (10.1%).

Idiopathic male infertility remains a major challenge in reproductive medicine despite extensive diagnostic workups, prompting research into novel etiologies and interventions. Emerging evidence highlights the microbiome’s role in modulating male reproductive health. This study analyzes global research trends on idiopathic male infertility and associated microbial health over the past two decades using a structured bibliometric approach. Data extracted from Scopus were examined through Biblioshiny and VOSviewer. The analysis reveals a clear transition from traditional genetic and oxidative stress–based studies to microbiome-centered and multi-omics investigations. Increased Research output and citation rates in recent years, underscoring the growing relevance of microbiome studies. Key contributors like Agarwal A, Wang X, Zhang H, and Lundy SD advanced understanding from genetic and oxidative causes to gut-testis and semen microbiome interactions. Leading contributors and countries, particularly China and the USA dominate collaborative networks. Key themes link microbial dysbiosis, oxidative stress, inflammation, and hormonal imbalance with impaired spermatogenesis. Environmental and lifestyle factors, including diet, alcohol, antibiotics, endocrine disruptors, and microplastics, were increasingly recognized as influencing microbiome-mediated fertility. Mechanistic insights into the gut–testis axis, endotoxemia, immune modulation, and nutrient metabolism suggest avenues for diagnostics and microbiome-based interventions, including probiotics, nutritional modulation, and fecal microbiota transplantation.

Graphical abstract